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This page was generated on 2022-07-07 11:11:25 -0400 (Thu, 07 Jul 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4343
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4148
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4160
kjohnsonmacOS 12.4 Montereyarm644.2.0 Patched (2022-06-09 r82473) -- "Vigorous Calisthenics" 3115
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

BUILD results for maftools on kjohnson


To the developers/maintainers of the maftools package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maftools.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 1053/2124HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maftools 2.13.0  (landing page)
Anand Mayakonda
Snapshot Date: 2022-07-06 14:00:06 -0400 (Wed, 06 Jul 2022)
git_url: https://git.bioconductor.org/packages/maftools
git_branch: master
git_last_commit: 07aa856
git_last_commit_date: 2022-04-26 11:33:50 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnsonmacOS 12.4 Monterey / arm64  ERROR    ERROR  skippedskipped

Summary

Package: maftools
Version: 2.13.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data maftools
StartedAt: 2022-07-06 23:36:39 -0400 (Wed, 06 Jul 2022)
EndedAt: 2022-07-06 23:37:31 -0400 (Wed, 06 Jul 2022)
EllapsedTime: 52.5 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data maftools
###
##############################################################################
##############################################################################


* checking for file ‘maftools/DESCRIPTION’ ... OK
* preparing ‘maftools’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘cancer_hotspots.Rmd’ using rmarkdown
--- finished re-building ‘cancer_hotspots.Rmd’

--- re-building ‘cnv_analysis.Rmd’ using rmarkdown
--- finished re-building ‘cnv_analysis.Rmd’

--- re-building ‘maftools.Rmd’ using rmarkdown
Capture size [TCGA]:  35.8
Capture size [Input]: 50
Performing pairwise t-test for differences in mutation burden (per MB)..
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "axes" is not a graphical parameter
Estimating background scores from synonymous variants..
Not enough genes to build background. Using predefined values. (Mean = 0.279; SD = 0.13)
Estimating cluster scores from non-syn variants..
Comapring with background model and estimating p-values..
Done !
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "axes" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "axes" is not a graphical parameter
Gene: PML
9 transcripts available. Use arguments refSeqID or proteinID to manually specify tx name.
Using longer transcript NM_033238 for now.
9 transcripts available. Use arguments refSeqID or proteinID to manually specify tx name.
Using longer transcript NM_033238 for now.
Quitting from lines 482-485 (maftools.Rmd) 
Error: processing vignette 'maftools.Rmd' failed with diagnostics:
there is no package called 'BSgenome.Hsapiens.UCSC.hg19'
--- failed re-building ‘maftools.Rmd’

--- re-building ‘oncoplots.Rmd’ using rmarkdown
--- finished re-building ‘oncoplots.Rmd’

SUMMARY: processing the following file failed:
  ‘maftools.Rmd’

Error: Vignette re-building failed.
Execution halted