The dot-dot notation (`..count..`) was deprecated in ggplot2 3.4.0.

Dear authors,

I encountered the following error message upon executing the 2nd step of the pipeline:

> CAMDAC:::format_output(patient_id="P1", sample_id= sample_id, sex=sex, is_normal=FALSE, 
+               path=path, path_to_CAMDAC=pipelines, build="hg38")

  Msp1 fragments information obtained for patient
  Warning message:
  The dot-dot notation (`..count..`) was deprecated in ggplot2 3.4.0.
  ℹ Please use `after_stat(count)` instead.
  ℹ The deprecated feature was likely used in the CAMDAC package.
    Please report the issue to the authors.
  This warning is displayed once every 8 hours.
  Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.

> lifecycle::last_lifecycle_warnings()
---
Backtrace:
     ▆
  1. └─CAMDAC:::format_output(...)
  2.   └─CAMDAC:::get_msp1_fragments(...)
  3.     └─ggplot2::ggsave(...)
  4.       ├─grid::grid.draw(plot)
  5.       └─ggplot2:::grid.draw.ggplot(plot)
  6.         ├─base::print(x)
  7.         └─ggplot2:::print.ggplot(x)
  8.           ├─ggplot2::ggplot_build(x)
  9.           └─ggplot2:::ggplot_build.ggplot(x)
 10.             └─ggplot2:::by_layer(...)
 11.               ├─rlang::try_fetch(...)
 12.               │ ├─base::tryCatch(...)
 13.               │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 14.               │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15.               │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 16.               │ └─base::withCallingHandlers(...)
 17.               └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
 18.                 └─l$compute_aesthetics(d, plot)
 19.                   └─ggplot2 (local) compute_aesthetics(..., self = self)
 20.                     └─ggplot2:::is_calculated_aes(aesthetics, warn = TRUE)
 21.                       └─base::vapply(...)
 22.                         └─ggplot2 (local) FUN(X[[i]], ...)
 23.                           └─ggplot2:::is_calculated(quo_get_expr(x), warn = warn)
 24.                             └─ggplot2:::deprecate_warn0("3.4.0", what, with, id = "ggplot-warn-aes-dot-dot")

The step is fully executed despite of the error.

VanLoo-lab / CAMDAC

The dot-dot notation (`..count..`) was deprecated in ggplot2 3.4.0. #13