[Rd] Compatibility issues caused by new simplify argument in apply function

[Lukas Lehnert]

I am sorry for being not specific enough. Both of you were right with your 
guess how the initial problem looked like.

I followed the suggestion of Henrik and at least on my computer it seems to 
work (sometimes solutions are much easier than you think). Let's see what CRAN 
tells me...

Thank you for your time and thinking about the problem!

Best

Lukas

Am Freitag, 22. Mai 2020, 17:47:00 CEST schrieb Henrik Bengtsson:
> Interesting problem.  I'm very rusty on S4 but would one solution be
> to, already now, add 'simplify = TRUE' to the S4 method and document
> it;
> 
> setMethod("apply", signature(X = "Speclib"),
>           function(X,
>                    FUN,
>                    bySI = NULL,
>                    ...,
>                    simplify = TRUE) {
> 
> ?
> 
> Henrik
> 
> On Fri, May 22, 2020 at 6:26 AM Duncan Murdoch <murdoch.duncan using gmail.com> 
wrote:
> > You didn't explained what the error is.  This is what it looks like to
> > me, but I'm probably wrong in some details:
> > 
> > 1. R-devel added an argument to the apply() function, so the header has
> > changed from
> > 
> >    function (X, MARGIN, FUN, ...)
> > 
> > to
> > 
> >    function(X, MARGIN, FUN, ..., simplify = TRUE)
> > 
> > 2. Your package converted the function apply() to an S4 generic.
> > 
> > 3. Now the signatures of your methods for this generic need to have the
> > simplify argument, but if you do that, they won't work in previous
> > versions of R.
> > 
> > You'd like to have conditional code and documentation to depend on the
> > version of R.
> > 
> > Is that all correct?
> > 
> > I don't think it's possible, for the reasons you found.  Certainly you
> > can have conditional code, but the docs are going to fail.
> > 
> > One thing that might work is in versions of R before this change, export
> > your own version of apply, with the change in place, i.e.
> > 
> > if(!("simplify" %in% names(formals(base::apply))))
> > 
> >    apply <- function(X, MARGIN, FUN, ..., simplify = TRUE) {
> >    
> >      base::apply(X, MARGIN, FUN, ...)
> >    
> >    }
> > 
> > and then conditionally export "apply" in these old versions.  Then your
> > docs could match the new version everywhere.
> > 
> > Another thing is to maintain two versions of your package, one for R
> > versions before the change, another for versions after the change.  Add
> > appropriate entries in the DESCRIPTION file, e.g.
> > 
> > Depends:  R (> 4.0)
> > 
> > Another is to argue with R Core that this change to a really old
> > function is too hard to accommodate, and they should back it out, maybe
> > by making a new function with the new signature.
> > 
> > Or you could make a new function with the old signature, and use that
> > instead of apply().
> > 
> > Duncan Murdoch
> > 
> > On 22/05/2020 6:26 a.m., Lukas Lehnert via R-devel wrote:
> > > Dear R Developers,
> > > 
> > > the new  simplify argument in apply causes that my package (hsdar) does
> > > not
> > > pass the
> > > checks in R-devel.
> > > 
> > > The workaround, Kurt Hornik send me, is working for the R-code:
> > > if("simplify" %in% names(formals(base::apply)))
> > > 
> > >   do something
> > > 
> > > else
> > > 
> > >   do something else
> > > 
> > > Unfortunately, I cannot conditionalize the man pages of the functions. I
> > > get the message
> > > that "applySpeclib.Rd:12-14: Section \Sexpr is unrecognized and will be
> > > dropped" if I try to
> > > dynamically define the entire usage section. If I try to use \Sexpr
> > > inside the \usage section,
> > > I get the following warning: "applySpeclib.Rd:13-15: Tag \Sexpr is
> > > invalid in a \usage block"
> > > 
> > > Does anybody have an idea how to proceed. The full code is available
> > > below.
> > > 
> > > Thanks
> > > 
> > > Lukas
> > > 
> > > 
> > > *1. Code for full usage section:*
> > > ..
> > > \description{
> > > Apply function over all spectra or a subset of spectra in a
> > > \code{Speclib}.
> > > }
> > > 
> > > \Sexpr[echo=TRUE,results=rd,stage=install]{
> > > 
> > >    hsdar:::.applyInHelp1("Speclib", usage = TRUE)
> > > 
> > > }
> > > 
> > > \arguments{
> > > ..
> > > 
> > > *Function .applyInHelp1*
> > > .applyInHelp1 <- function(fun_name, usage)
> > > {
> > > 
> > >    if (usage)
> > >    {
> > >    
> > >      if ("simplify" %in% names(formals(base::apply)))
> > >      {
> > >      
> > >        return(paste0("\\usage{\n",
> > >        
> > >                      "\\S4method{apply}{", fun_name, "}(X, MARGIN, FUN,
> > >                      ...,
> > > 
> > > simplify = TRUE)\n",
> > > 
> > >                      "}"))
> > >      
> > >      } else {
> > >      
> > >        return(paste0("\\usage{\n",
> > >        
> > >                      "\\S4method{apply}{", fun_name, "}(X, MARGIN, FUN,
> > >                      ...)
> > > 
> > > \n",
> > > 
> > >                      "}"))
> > >      
> > >      }
> > >    
> > >    } else {
> > >    
> > >      if ("simplify" %in% names(formals(base::apply)))
> > >      {
> > >      
> > >        return("}\n\\item{simplify}{Currently ignored")
> > >      
> > >      } else {
> > >      
> > >        return("")
> > >      
> > >      }
> > >    
> > >    }
> > > 
> > > }
> > > 
> > > 
> > > *2. Using \Sexpr inside the \usage block*
> > > \usage{
> > > \S4method{apply}{Speclib}(X, FUN, bySI = NULL, ...
> > > \Sexpr[echo=TRUE,results=rd,stage=install]{
> > > 
> > >    hsdar:::.applyInHelp2(usage = TRUE)
> > > 
> > > }
> > > )
> > > }
> > > 
> > > 
> > > *Function .applyInHelp2*
> > > .applyInHelp2 <- function(usage)
> > > {
> > > 
> > >    if (usage)
> > >    {
> > >    
> > >      if ("simplify" %in% names(formals(base::apply)))
> > >      {
> > >      
> > >        return(", simplify = TRUE)")
> > >      
> > >      }
> > >    
> > >    } else {
> > >    
> > >      if ("simplify" %in% names(formals(base::apply)))
> > >      {
> > >      
> > >        return("}\n\\item{simplify}{Currently ignored")
> > >      
> > >      } else {
> > >      
> > >        return("")
> > >      
> > >      }
> > >    
> > >    }
> > > 
> > > }
> > > 
> > > ______________________________________________
> > > R-devel using r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-devel
> > 
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