On 04/06/2018 7:34 AM, David Hugh-Jones wrote:
Hi all,
Latest release of my package has an error when checked on r-patched-linux
and r-devel-linux. Relevant output is shown below (from
https://cran.r-project.org/web/checks/check_results_huxtable.html). It
suggests that there's no method for `align<-` and `bold` for huxtable
objects. In fact the package defines and exports such methods. Selected
lines from the NAMESPACE file:
S3method("align<-",huxtable)
S3method(bold,huxtable)
export("align<-")
export("align<-.huxtable")
export(bold)
export(bold.huxtable)
I'd worry a little bit about your "make_getter_setters" function: it
saves the result using
lapply(names(funs), function (x) {
assign(x, funs[[x]], envir = parent.frame(3)) # 3: 1 for
function(x), 2 for lapply, 3 for the caller!
})
That count of 3 looks like an implementation detail that could
conceivably vary, for instance if the compiler decided to optimize out a
call or two, or lapply's implementation changed. (I suspect this isn't
the cause of the error you saw, or you would have seen it a lot more:
but I'd still fix it.)
I think a safer way to find the huxtable namespace is something like
huxtableNamespace <- .getNamespace("huxtable")
though this is advised against; a documented but less obvious way to do
it would be
huxtableNamespace <- environment(huxtable)
The "huxtable" on the right is the function; most other functions in
your package would also be fine, as long as you haven't done anything
tricky to change their environments.
With one of those definitions, you could change your lapply() to
lapply(names(funs), function (x) {
assign(x, funs[[x]], envir = huxtableNamespace)
})
> Checks are passing fine on other platforms. Is this just a weirdness
to do
> with the changes in R 3.5.0 on Linux? Or does it indicate a real problem?
A possibility is memory corruption at the C level. Since you don't have
any C code in huxtable that couldn't be caused by what you did, but you
might still be a victim of it.
Duncan Murdoch
Cheers,
David
> ### ** Examples
>
>
> ht <- huxtable(a = 1:3, b = 1:3)
> align(ht) <- 'right'
Error in UseMethod("align<-") :
no applicable method for 'align<-' applied to an object of class
"c('huxtable', 'data.frame')"
Calls: align<-
Execution halted
Flavor: r-patched-linux-x86_64
<https://www.r-project.org/nosvn/R.check/r-patched-linux-x86_64/huxtable-00check.html>
Version: 4.0.0
Check: re-building of vignette outputs
Result: WARN
Error in re-building vignettes:
...
Quitting from lines 52-104 (design-principles.Rmd)
Error: processing vignette ‘design-principles.Rmd’ failed with
diagnostics:
no applicable method for ‘bold’ applied to an object of class
"c('huxtable', 'data.frame')"
Execution halted
Flavor: r-patched-linux-x86_64
<https://www.r-project.org/nosvn/R.check/r-patched-linux-x86_64/huxtable-00check.html>
David
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