[R-pkg-devel] Visible bindings and reference classes

You can avoid the temporary file by replacing
 dput(def, file= (tf <- tempfile()))
 compiler::cmpfile(tf)
with
 cdef <- compiler::compile(def)
 #Note: no visible binding for '<<-' assignment to 'ConfigString'
The compiled code appears to work.
 eval(cdef)
 c1 <- Config$new()
 c1
 #Reference class object of class "Config"
 #Field "ConfigString":
 #[1] "Hello, World!"

 > objects(all=TRUE)

 #[1] ".__C__Config"           ".__global__"
 #[3] ".requireCachedGenerics" "c1"
 #[5] "cdef"                   "Config"
 #[7] "def"

a$getX

codetools::checkUsage(a$getX)

v <- d1$new()
v$getX

codetools::checkUsage(v$getX)

Bill Dunlap
TIBCO Software
wdunlap tibco.com

On Tue, Aug 11, 2015 at 8:47 AM, William Dunlap <wdunlap at tibco.com> wrote:

This is a problem in the compiler package.  Here is a way to reproduce it:

def <- quote(Config <- setRefClass("Config",
    fields = list(
        ConfigString = "character"),
    methods = list(
        # Constructor
        initialize = function() {
            ConfigString <<- "Hello, World!"
        })
))
dput(def, file= (tf <- tempfile()))
compiler::cmpfile(tf)
#Note: no visible binding for '<<-' assignment to 'ConfigString'
saving to file
#"C:\Users\wdunlap\AppData\Local\Temp\Rtmpk91qvT\file26d447c45b81.Rc" ...
done




Bill Dunlap
TIBCO Software
wdunlap tibco.com

On Tue, Aug 11, 2015 at 4:24 AM, Martin Maechler <
maechler at stat.math.ethz.ch> wrote:

Colin Gillespie <csgillespie at gmail.com>
    on Mon, 10 Aug 2015 20:33:32 +0000 writes:

Dear All,

I have a package that uses reference classes. When I build the package I
get numerous notes of the sort

Note: no visible binding for '<<-' assignment to 'pars'

I've tried using GlobalVariables, but that didn't solve the issue.

[ You mean globalVariables(): and it's a bad idea anyway IMO,
  even if it is recommended : If you declare a variable in
  there, it is "global" in all places in your package and the
  codetools won't report it anywhere anymore.
  Much better in my view is to use something like

  var7 <- NULL # ~= globalVariables("var7")

]

To your question:

Reference classes are used in *many* places,  and the use of  ' <<- '
is really "standard" there.
e.g., package 'lme4', or 'pcalg' are two packages I'm involved with,
which use ref.classes and ' <<- '  but are "fine" with that.

So there must be something peculiar in your package leading to
the  <<-  warnings.

Maybe you should look into the source code of such other CRAN
packages to see how "they" do it differently than you.

Best regards,
Martin

Martin Maechler, ETH Zurich

After some googling, I came across the page
http://stackoverflow.com/q/23475309/203420 which suggests

suppressBindingNotes <- function(variablesMentionedInNotes) {
  for(variable in variablesMentionedInNotes) {
    assign(variable,NULL, envir = .GlobalEnv)
  }
}
suppressBindingNotes(c("dat", "internal", "xmin", "pars", "no_pars"))

But checking the package with --as-cran raises the note

* checking R code for possible problems ... NOTE
Found the following assignments to the global environment:
  File ?poweRlaw/R/aaa_all_classes.R?:
  assign(variable, NULL, envir = .GlobalEnv)

What is the correct way of removing the "visible bindings" notes?

Thanks

Colin

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