Yikun / BBS

The Bioconductor Build System
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maftools.build #42

Closed Yikun closed 11 months ago

Yikun commented 1 year ago
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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data maftools
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* 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
Could not fetch https://user-images.githubusercontent.com/8164062/160853684-85021668-a515-4e3d-8ccb-dddf992098d9.png
HttpExceptionRequest Request {
  host                 = "user-images.githubusercontent.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/8164062/160853684-85021668-a515-4e3d-8ccb-dddf992098d9.png"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 ResponseTimeout
Error: processing vignette 'cnv_analysis.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘cnv_analysis.Rmd’

--- re-building ‘maftools.Rmd’ using rmarkdown
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
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "axes" is not a graphical parameter
--- finished re-building ‘maftools.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
martin-g commented 11 months ago

https://bioconductor.org/checkResults/3.18/bioc-LATEST/maftools/ build fine! There are warnings in check