Re: [Rd] FW: [Rcpp-devel] Question on 5.6 Interfacing C++ code

From: Sean Robert McGuffee <sean.mcguffee_at_gmail.com>
Date: Thu, 21 Apr 2011 11:16:39 -0400

So, how is the package turning it's name into those commands? Does the installation automatically list the src directory and iteratively run a loop over each file and call 'R CMD SHLIB objectOfIterator' ? The reason this is so important is because itıs easy to get things to work via a terminal command 'R CMD SHLIB someSourceFile.cppı, so I want to be able to take things that work that way and put them inside a package. It seems peculiar to me that R needs to access functions through a C wrapper too. Iım not sure why it canıt access C++ functions directly. What R is doing is over my head because it is calling functions that were not compiled into it. I mean, if I want to call a C or C++ function from C++ code, I have to convince my compiler that I have a header and all definitions behind the declarations in my source files to compile my own programs. I donıt know how R works when the program is compiled way in advance and is then somehow calling on declarations made later in another place. I think objective C/C++ allows for this type of thing where you can write code to call something that is declared but not yet defined. However, Iım not sure what R is doing? Is R doing the same thing a compiler would do and creating itıs own binary instructions for the launch of a function, or is it creating a new executable and launching that as itıs own application and then somehow communicating with it?
Sean

On 4/21/11 7:52 AM, "Dirk Eddelbuettel" <edd_at_debian.org> wrote:

>
> On 21 April 2011 at 07:16, Duncan Murdoch wrote:
> | On 11-04-20 11:33 AM, Sean Robert McGuffee wrote:
> | > Hi, apparently I sent my question about using R and C++ to the wrong list,
> | > ironically seeing as that list was called Rcpp. Anyway, I was directed to
> | > post my question here. To summarize my current question, I have found two
> | > commands that I want to be able to put into a package. The commands are 'R
> | > CMD SHLIB X.cc X_main.cc' and
> | > 'dyn.load(paste("X",.Platform$dynlib.ext,sep="")),' which I would like to
> | > run when my package is installed and maybe have the second command run
> again
> | > when my package is to be used. I've been trying to figure out the
> | > documentation and learn through examples, but I'm just not getting it and
> | > have been trying for weeks.
> | > Does anyone on this site have any suggestions for me?

> |
> | Assuming those lines work on their own, just do the following:
> |
> | 1. Put those *.cc files into the src directory of your package. (You
> | may need to create it.)
> |
> | 2. Put useDynLib(foo) into the NAMESPACE file of your foo package.
> |
> | 3. Call those functions using .C("X", args, PACKAGE="foo").
> |
> | That's it.
>
> We told Sean this twice or three times already over in this thread
>
> http://thread.gmane.org/gmane.comp.lang.r.rcpp/1808
>
> but the message does not seem to sink in. He keeps asking where to put 'R
> CMD SHLIB' and doesn't seem to hear when we say there is none in a package...
>
> Dirk
>
> | Duncan Murdoch
> |
> | > Thanks, Sean
> | >
> | > |On 20 April 2011 at 10:20, Sean Robert McGuffee wrote:
> | > |
> | > |
> | > | Hi, thanks!
> | > |
> | > |>On 4/20/11 10:03 AM, "Steve Lianoglou"<mailinglist.honeypot_at_gmail.com>
> | > wrote:
> | > |> Hi,
> | > |>
> | > |> On Wed, Apr 20, 2011 at 9:49 AM, Sean Robert McGuffee
> | > |> <sean.mcguffee_at_gmail.com> wrote:
> | > |>> Hi, I have a quick couple of questions about some of the
> documentation
> | > on
> | > |>> the web page:
> | > |>>
> | >
> http://cran.r-project.org/doc/manuals/R-exts.html#Linking-GUIs-and-other-fro
> | > n
> | > |>> t_002dends-to-R
> | > |>> under the heading:
> | > |>> 5.6 Interfacing C++ code
> | > |>>
> | > |>> Question 1:
> | > |>> If Iım at a terminal, I can type the instructions they suggest:
> | > |>> R CMD SHLIB X.cc X_main.cc
> | > |>> If I wanted a package to do this, how would I tell the package to do
> | > that
> | > |>> same thing?
> | > |>
> | > |> Just to make sure we're all on the same page, you want an R package to
> | > |> compile some source code into a shared library/dll from inside R?
> | > |>
> | > |> Not sure if there's a "baked in" way for that to happen, but maybe you
> | > |> can invoke `R CMD WHATEVER` from inside R using the `system` function:
> | > |>
> | > |> R> ?system
> | > |>
> | > |
> | > | ok, so where in the package would I put the system call in the package
> to
> | > | have it run when installing the package?
> | >
> | >> You don't. As I said, 'R CMD INSTALL' et all do that.
> | >> Download an existing package with source, install it. Study its sources,
> | >> study the 'Writing R Extensions' manual. Ask on r-devel.
> | >> Basic R questions are off-topic here.
> | >
> | > |>> Would I use the same command and just include it in a file somewhere
> in
> | > the
> | > |>> package?
> | > |>> If so, which file?
> | > |>
> | > |> Hmm ... I'm curious what you're trying to do, exactly?
> | > |
> | > | I'm trying to figure out how take commands such as " R CMD SHLIB X.cc
> | > | X_main.cc" followed by "dyn.load(paste("X", .Platform$dynlib.ext, sep =
> | > | ""))," which are commands I can get to work for myself as a human
> | > | interactively, and put the commands into a package to be automatically
> run
> | > | when installing the package. I mean, it's great if I can compile a c++
> | > file
> | > | and then use it inside R, but I'm only doing that so I can let other
> | > people
> | > | do that via a package. As much as I read this documentation, I keep
> | > missing
> | >

> | >> Again, I like working from an existing, working package. As I said, there
> are
> | >> almost 1000 to pick from.
> | >> Please direct follow-ups that have no bearing on Rcpp to r-devel.
> | >> Dirk
> | >
> | > I've tried to figure this out for weeks by looking at other packages and
> | > reading the confusing and nonintegrated documentation, but it hasn't
> taught
> | > me how to put the two commands into a package so that they are run when
> the
> | > package is installed. I'm simply trying to find out where in my package I
> | > should put the commands 'R CMD SHLIB X.cc X_main.cc' and
> | > 'dyn.load(paste("X",.Platform$dynlib.ext,sep="")),'
> | > in order to have them run when my package is installed.
> | >
> | >
> | > | the connections between the different sections. This is a section I am
> | > | loving because it works very well. Thus, I want to figure out how to
> take
> | > | the baby steps I'm doing and combine them into a package. Specifically,
> I
> | > | want to take these two commands and insert them into a package so that
> | > these
> | > | commands will compile my code and make a dynamic ".so" file where R can
> | > | access its functions when others install my package.
> | > |
> | > |>
> | > |>> Question 2:
> | > |>> dyn.load(paste("X", .Platform$dynlib.ext, sep = ""))
> | > |>>
> | > |>> Where does .Platform$dynlib.ext come from?
> | > |>> What does it mean?
> | > |>> What do itıs components .Platform and $dynlib and .ext mean?
> | > |>
> | > |> .Platform is lust a normal list -- it is defined internally (I guess).
> | > |> You can access "named" elements of a list with `$`.
> | > |>
> | > |> .Platform$dynlyb (or .Platform[['dynlib']]) tells you the extension
> | > |> your particular system uses for shared libraries:
> | > |>
> | > |> R> .Platform
> | > |> $OS.type
> | > |> [1] "unix"
> | > |>
> | > |> $file.sep
> | > |> [1] "/"
> | > |>
> | > |> $dynlib.ext
> | > |> [1] ".so"
> | > |>
> | > |> $GUI
> | > |> [1] "X11"
> | > |>
> | > |> $endian
> | > |> [1] "little"
> | > |>
> | > |> $pkgType
> | > |> [1] "mac.binary.leopard"
> | > |>
> | > |> $path.sep
> | > |> [1] ":"
> | > |>
> | > |> $r_arch
> | > |> [1] "x86_64"
> | > |>
> | > |> See ?.Platform for more help.
> | > |
> | > | Ah, thanks, that clarifies exactly what .Platform$dynlib.ext is, it's
> | > ".so"
> | > | on my system.
> | > |
> | > | This, the dyn.load(paste("X", .Platform$dynlib.ext, sep = "")) is
> | > equivalent
> | > | to the command dyn.load("X.so) which now makes sense in that context!
> | > |
> | > |

> | > | _______________________________________________
> | > | Rcpp-devel mailing list
> | > | Rcpp-devel_at_lists.r-forge.r-project.org
> | > | https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
> | >
> |
> | ______________________________________________
> | R-devel_at_r-project.org mailing list
> | https://stat.ethz.ch/mailman/listinfo/r-devel

        [[alternative HTML version deleted]]



R-devel_at_r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel Received on Thu 21 Apr 2011 - 15:20:49 GMT

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Thu 21 Apr 2011 - 15:50:52 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-devel. Please read the posting guide before posting to the list.

list of date sections of archive