On Feb 11, 2010, at 12:24 PM, Romain Francois wrote:
> Thanks.
>
> On 02/11/2010 05:55 PM, Simon Urbanek wrote:
>> Romain,
>>
>> I think your'e confusing two entirely different concepts here:
>
> Yes. The name "LinkingTo" probably helped my confusion.
>
Admittedly, it's probably not the best name ;).
>> 1) LinkingTo: allows a package to provide C-level functions to other
>> packages (see R-ext 5.4). Let's say package A provides a function foo by
>> calling R_RegisterCCallable for that function. If a package B wants to use
>> that function, it uses LinkingTo: and calls R_GetCCallable to obtain the
>> function pointer. It does not actually link to package A because that is in
>> general not possible - it simply obtains the pointers through R. In
>> addition, LinkingTo: makes sure that you have access to the header files of
>> package A which help you to cast the functions and define any data
>> structures you may need. Since C++ is a superset of C you can use this
>> facility with C++ as long as you don't depend on anything outside of the
>> header files.
>>
>> 2) linking directly to another package's shared object is in general not
>> possible, because packages are not guaranteed to be dynamic libraries. They
>> are usually shared objects which may or may not be compatible with a dynamic
>> library on a given platform. Therefore the R-ext describes other way in
>> which you may provide some library independently of the package shared
>> object to other packages (see R-ext 5.8). The issue is that you have to
>> create a separate library (PKG/libs[/arch]/PKG.so won't work in general!)
>> and provide this to other packages. As 5.8 says, this is in general not
>> trivial because it is very platform dependent and the most portable way is
>> to offer a static library.
>>
>> To come back to your example, LinkingTo: A and B will work if you remove
>> Makevars from B (you don't want to link)and put your hello method into the
>> A.h header:
>
> Sure. but in real life I can't realistically put everything in the header
> files.
>
It was just an example based on your example ;) - which was not very realistic,
either. It practice it is reasonable, because it is sufficient to declare in
the headers whatever you're providing so the only homework is to cast function
pointers you have obtained via R_GetCCallable to the declarations from the
header file.
I suspect what you meant is not as much related to LinkingTo: (since the mess
C++ creates at the binary level is rather hard to pass through dl pointers -
but if someone has a working solution it may be worth to create a package), but
rather to provide a library. That is not covered by R at this point so you're
in realm of R-ext 5.8. Given how non-trivial task this is (to get it right) it
may be worthwhile thinking about a portable solution and add it to R, but I
don't think anyone has done that yet (mainly due to the low benefit/cost ratio
I suspect). For all cases so far it was sufficient to create C or R level API
for other package to use.
Cheers,
Simon
>
>
>>> library (B)
>> Loading required package: A
>>> .Call("say_hello", PACKAGE = "B")
>> [1] "hello"
>>
>> However, your'e not really using the LinkingTo: facilities for the functions
>> so it's essentially just helping you to find the header file.
>>
>> Cheers,
>> Simon
>>
>>
>>
>> On Feb 11, 2010, at 4:08 AM, Romain Francois wrote:
>>
>>> Hello,
>>>
>>> I've been trying to make LinkingTo work when the package linked to has c++
>>> code.
>>>
>>> I've put dumb packages to illustrate this emails here ;
>>> http://addictedtor.free.fr/misc/linkingto
>>>
>>> Package A defines this C++ class:
>>>
>>> class A {
>>> public:
>>> A() ;
>>> ~A() ;
>>> SEXP hello() ;
>>> } ;
>>>
>>> Package B has this function :
>>>
>>> SEXP say_hello(){
>>> A a ;
>>> return a.hello() ;
>>> }
>>>
>>> headers of package A are copied into inst/include so that package B can
>>> have.
>>>
>>> LinkingTo: A
>>>
>>> in its DESCRIPTION file.
>>>
>>> Also, package B has the R function ;
>>>
>>> g<- function(){
>>> .Call("say_hello", PACKAGE = "B")
>>> }
>>>
>>> With this I can compile A and B, but then I get :
>>>
>>> $ Rscript -e "B::g()"
>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>> unable to load shared library '/usr/local/lib/R/library/B/libs/B.so':
>>> /usr/local/lib/R/library/B/libs/B.so: undefined symbol: _ZN1AD1Ev
>>> Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
>>>
>>> If I then add a Makevars in B with this :
>>>
>>>
>>> # find the root directory where A is installed
>>> ADIR=$(shell $(R_HOME)/bin/Rscript -e "cat(system.file(package='A'))" )
>>>
>>> PKG_LIBS= $(ADIR)/libs/A$(DYLIB_EXT)
>>>
>>>
>>> Then it works:
>>>
>>> $ Rscript -e "B::g()"
>>> [1] "hello"
>>>
>>> So it appears that adding the -I flag, which is what LinkingTo does is not
>>> enough when the package "linking from" (B) actually has to link to the
>>> "linked to" package (A).
>>>
>>> I've been looking at
>>> http://cran.r-project.org/doc/manuals/R-exts.html#Registering-native-routines
>>> but it seems only applicable to c(++) functions and not classes ...
>>>
>>> What am I missing ? Should/can linkingto be extended in a way that
>>> accomodates c++
>>>
>>> Romain
>
>
>
> --
> Romain Francois
> Professional R Enthusiast
> +33(0) 6 28 91 30 30
> http://romainfrancois.blog.free.fr
> |- http://tr.im/NrTG : Rcpp 0.7.5
> |- http://tr.im/MPYc : RProtoBuf: protocol buffers for R
> `- http://tr.im/KfKn : Rcpp 0.7.2
>
>
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