[R] Error generated by nlme::gnls

[Martin Maechler]

>>>>> Bill Dunlap 
>>>>>     on Sun, 24 Jul 2022 08:51:09 -0700 writes:

    > I think the intent of this code was to see if the formula
    > had solely a literal 1 on the right hand side.  Then
    > !identical(pp[[3]], 1) would do it, avoiding the overhead
    > of calling deparse.  Note that the 1 might be an integer,
    > which the current code would (erroneously) not catch, so
    > !identical(pp[[3]], 1) && !identical(pp[[3]], 1L) or
    > something equivalent would be better.

    > -Bill

Thanks a lot, Bill, Ivan, Ben  et al. !

This is indeed a very old coding bug triggered by the more
strict checks in  R 4.2.x.

I will indeed try Bill's proposal rather than remaining with
deparse by using deparse1().

"Of course", this should hopefully be fixed in the next release
of nlme.

Martin Maechler
ETH Zurich   and  R Core team


    > On Sun, Jul 24, 2022 at 5:58 AM Ivan Krylov
    > <krylov.r00t using gmail.com> wrote:

    >> Sorry for being too terse in my previous e-mail!
    >> 
    >> On Sun, 24 Jul 2022 23:03:02 +1200 Rolf Turner
    >> <r.turner using auckland.ac.nz> wrote:
    >> 
    >> > The maintainer of the nlme package (who is, according
    >> to maintainer(), > "R-core") could change the code so
    >> that it uses invokes deparse1() > rather than deparse,
    >> but the user cannot do so, not without in effect >
    >> re-creating the package.
    >> 
    >> You're right. I think there's a buglet in nlme::gnls that
    >> nobody noticed until R 4.2.0 was released *and* Aaron
    >> Crowley used the function with a sufficiently long
    >> formula.
    >> 
    >> > Also, the question remains: why did Aaron Crowley's
    >> code work in the > past, whereas now it throws an error?
    >> What changed?
    >> 
    >> gnls() may have been performing the `if (deparse(...) !=
    >> '1')` test for a long time, but never crashed before
    >> because it wasn't a fatal error until R
    >> 4.2.0. Previously, if() would issue a warning and use the
    >> first element of the boolean vector.
    >> 
    >> R 4.2.0 was released this April, which was less than 6
    >> months ago. I think it all fits.
    >> 
    >> A temporary solution would be to make use of the fact
    >> that R is a very dynamic language and perform surgery on
    >> a live function inside a loaded package:
    >> 
    >> library(codetools)
    >> 
    >> nlme <- loadNamespace('nlme') unlockBinding('gnls', nlme)
    >> nlme$gnls <- `body<-`(fun = nlme$gnls, value = walkCode(
    >> body(nlme$gnls), makeCodeWalker( call = function(e, w)
    >> as.call(lapply(as.list(e), function(ee) if (!missing(ee))
    >> walkCode(ee, w) )), leaf = function(e, w) if
    >> (is.symbol(e) && e == 'deparse') { as.name('deparse1') }
    >> else e ) )) lockBinding('gnls', nlme) rm(nlme)
    >> 
    >> grep('deparse', deparse(nlme::gnls), value = TRUE) # [1]
    >> " deparse1(pp[[3]]), sep = \"~\"), collapse = \",\"), " #
    >> [2] " if (deparse1(params[[nm]][[3]]) != \"1\") {" # [3]
    >> " list(row.names(dataModShrunk), deparse1(form[[2]]))), "
    >> 
    >> Aaron's example seems to work after this, modulo needing
    >> 12 starting values instead of 13.
    >> 
    >> --
    >> Best regards, Ivan
    >> 
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    > 	[[alternative HTML version deleted]]

    > ______________________________________________
    > R-help using r-project.org mailing list -- To UNSUBSCRIBE and
    > more, see https://stat.ethz.ch/mailman/listinfo/r-help
    > PLEASE do read the posting guide
    > http://www.R-project.org/posting-guide.html and provide
    > commented, minimal, self-contained, reproducible code.