On 02/11/2014 09:06 AM, Winston Chang wrote:
To state the issue that Kirill raised in a different way... A package
with S4 or reference classes and Depends:methods can throw an error
when you do something as simple as this:
Rscript -e "mypackage::foo()"
But this will work:
Rscript -e "library(mypackage); foo()"
This is because when mypackage has Depends:methods, calling
mypackage::foo() merely loads mypackage, and doesn't attach it -- and
when this happens, the methods package is also loaded and not
attached. In this situation, you can get errors of the type that Dirk
noted.
In contrast, library(mypackage) causes methods to be attached, and so
you won't get those errors. This seems like a problem with the
behavior of the :: operator. Why should it be that when a package is
loaded, the packages listed in Depends are not attached? Presumably,
when someone lists a package in Depends instead of Imports, it's for a
good reason, as is the case here with the methods package.
To me it's worth distinguishing between the particular problem associated with
the methods package, and the more general problem encountered when PkgA fails to
import symbols used in PkgB, and instead relies on PkgB symbols to be found on
the search path. In the latter it seems better practice to import(PkgB) (or
importFrom) in the NAMESPACE and probably Import: PkgB in DESCRIPTION.
In the following thread, it's stated that the defensive approach is to
use Depends:methods -- but that's still not enough for running the
code listed above.
http://r.789695.n4.nabble.com/advise-on-Depends-td4678930.html
A more defensive defensive approach might be to add
.onLoad <- function(...) require(methods)
but this leads to either
* checking dependencies in R code ... WARNING
'library' or 'require' call not declared from: ‘methods’
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
...
* checking R code for possible problems ... NOTE
File ‘PkgA/R/binding.R’:
.onLoad calls:
require(methods)
Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.
with Imports: methods, or
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘methods’ which was already attached by
Depends.
Please remove these calls from your code.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
...
* checking R code for possible problems ... NOTE
File ‘PkgA/R/binding.R’:
.onLoad calls:
require(methods)
Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.
with Depends: methods
So is there really any WARNING / NOTE-free way of using the methods package?
Martin
-Winston
On Mon, Feb 10, 2014 at 8:31 PM, Dirk Eddelbuettel <e...@debian.org> wrote:
On 11 February 2014 at 02:53, Kirill Müller wrote:
| Why does it seem to be necessary to load the methods package here?
"Just use littler (TM pending)".
It (auto-)load methods automagically, thanks to Jeff Horner. See below.
edd@max:~$ chmod 0755 /tmp/kirill.r
edd@max:~$ /tmp/kirill.r
[1] "refObjectGenerator"
attr(,"package")
[1] "methods"
edd@max:~$ cat /tmp/kirill.r
#!/usr/bin/r
newTest <- function() {
cl <- get("someClass")
cl$new
}
someClass <- setRefClass("someClass")
print(class(someClass))
edd@max:~$
For Rscript, you still need to load it explicitly like any other packages you
want to use.
Dirk
PS New littler release pending in a few days or weeks. The Github repo is
current and working.
--
Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com
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