How to patch an S4 method in an R package?

Question

If you find a bug in a package, it's usually possible to patch the problem with fixInNamespace, e.g. fixInNamespace("mean.default", "base").

For S4 methods, I'm not sure how to do it though. The method I'm looking at is in the gWidgetstcltk package. You can see the source code with

getMethod(".svalue", c("gTabletcltk", "guiWidgetsToolkittcltk"))

I can't find the methods with fixInNamespace.

fixInNamespace(".svalue", "gWidgetstcltk")

Error in get(subx, envir = ns, inherits = FALSE) : 
  object '.svalue' not found

I thought setMethod might do the trick, but

setMethod(".svalue", c("gTabletcltk", "guiWidgetsToolkittcltk"),
  definition = function (obj, toolkit, index = NULL, drop = NULL, ...) 
  {
      widget = getWidget(obj)
      sel <- unlist(strsplit(tclvalue(tcl(widget, "selection")), 
          " "))
      if (length(sel) == 0) {
          return(NA)
      }
      theChildren <- .allChildren(widget)
      indices <- sapply(sel, function(i) match(i, theChildren))
      inds <- which(visible(obj))[indices]
      if (!is.null(index) && index == TRUE) {
          return(inds)
      }
      if (missing(drop) || is.null(drop)) 
          drop = TRUE
      chosencol <- tag(obj, "chosencol")
      if (drop) 
          return(obj[inds, chosencol, drop = drop])
      else return(obj[inds, ])
  },
  where = "package:gWidgetstcltk"  
)

Error in setMethod(".svalue", c("gTabletcltk", "guiWidgetsToolkittcltk"),  : 
  the environment "gWidgetstcltk" is locked; cannot assign methods for function ".svalue"

Any ideas?

I would suggest submitting the patch to the package authors. — Shane, May 14 '10 at 15:37
@Shane: I have done, but I'm impatient and wanted to see the changed version immediately. — Richie Cotton, May 16 '10 at 09:12

score 1 · Accepted Answer · answered May 14 '10 at 15:34

1

How about the old-school way of getting the source, applying the change and rebuilding?

answered May 14 '10 at 15:34

Dirk Eddelbuettel

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I had a feeling this might be the only answer. Seems a lot of effort though. – Richie Cotton May 16 '10 at 09:14

score 0 · Answer 2 · answered Nov 24 '21 at 05:49

you can first get the generic out, and then fix the generic by setMethod in your global environment, and then assign it back to that namespace

.svalue <- gWidgetstcltk:::.svalue
setMethod(".svalue", c("gTabletcltk", "guiWidgetsToolkittcltk"),
  definition = function (obj, toolkit, index = NULL, drop = NULL, ...) 
  {
      widget = getWidget(obj)
      sel <- unlist(strsplit(tclvalue(tcl(widget, "selection")), 
          " "))
      if (length(sel) == 0) {
          return(NA)
      }
      theChildren <- .allChildren(widget)
      indices <- sapply(sel, function(i) match(i, theChildren))
      inds <- which(visible(obj))[indices]
      if (!is.null(index) && index == TRUE) {
          return(inds)
      }
      if (missing(drop) || is.null(drop)) 
          drop = TRUE
      chosencol <- tag(obj, "chosencol")
      if (drop) 
          return(obj[inds, chosencol, drop = drop])
      else return(obj[inds, ])
  }#,
  #where = "package:gWidgetstcltk"  
)
assignInNamespace(".svalue", .svalue, ns = "gWidgetstcltk")

How to patch an S4 method in an R package?

2 Answers2