ucl-cssb/cneta

Error with ggplot2 3.4.0

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teacakedeadlift commented

Hi

Great tool. Thanks.

FYI trying to run this on a mac locally I had some issues. It failed with the following error:

Start running cnetml 51.79 real 51.36 user 0.17 sys Finish running cnetml Warning message: The sizeargument ofelement_rect()is deprecated as of ggplot2 3.4.0. ℹ Please use thelinewidth` argument instead.
plot title

Plotting the tree in inputdir//MaxL-m3-o1-s2-cons0-estmu0-combined.txt
Error in geom_segment2():
! Problem while converting geom to grob.
ℹ Error occurred in the 3rd layer.
Caused by error in check.length():
! 'gpar' element 'lwd' must not be length 0
Backtrace:
▆

  1. ├─ggplot2::ggsave(out_file, p, width = 8, height = height)
  2. │ ├─grid::grid.draw(plot)
  3. │ └─ggplot2:::grid.draw.ggplot(plot)
  4. │ ├─base::print(x)
  5. │ └─ggplot2:::print.ggplot(x)
  6. │ ├─ggplot2::ggplot_gtable(data)
  7. │ └─ggplot2:::ggplot_gtable.ggplot_built(data)
  8. │ └─ggplot2:::by_layer(...)
  9. │ ├─rlang::try_fetch(...)
  10. │ │ ├─base::tryCatch(...)
  11. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  12. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  13. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
  14. │ │ └─base::withCallingHandlers(...)
  15. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
  16. │ └─l$draw_geom(d, layout)
  17. │ └─ggplot2 (local) draw_geom(..., self = self)
  18. │ └─self$geom$draw_layer(...)
  19. │ └─ggplot2 (local) draw_layer(..., self = self)
  20. │ └─base::lapply(...)
  21. │ └─ggplot2 (local) FUN(X[[i]], ...)
  22. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
  23. │ └─self$draw_panel(...)
  24. │ └─ggtree (local) draw_panel(...)
  25. │ ├─grid::segmentsGrob(...)
  26. │ │ └─grid::grob(...)
  27. │ └─grid::gpar(...)
  28. │ └─grid:::validGP(list(...))
  29. │ └─grid (local) numnotnull("lwd")
  30. │ └─grid (local) check.length(gparname)
  31. │ └─base::stop(...)
  32. └─base::.handleSimpleError(...)
  33. └─rlang (local) h(simpleError(msg, call))
  34. └─handlers[[1L]](cnd)

  35.   └─cli::cli_abort(...)

  36.     └─rlang::abort(...)

Execution halted
`

I had to install a mamba virtual environment with ggplot2 3.3.0 to get it to work. Assume it's due to lwd in gpar?

Thanks

Phil