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

From: Joshua Ulrich <josh.m.ulrich_at_gmail.com>
Date: Thu, 21 Apr 2011 10:21:15 -0500

Please, please, please read the documentation before sending more questions to the list. You also have the source code, so you can look at what "R CMD build" and "R CMD INSTALL" are doing.

--
Joshua Ulrich  |  FOSS Trading: www.fosstrading.com



On Thu, Apr 21, 2011 at 10:16 AM, Sean Robert McGuffee
<sean.mcguffee_at_gmail.com> wrote:

>
> 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 itšs easy to get things to work
> via a terminal command 'R CMD SHLIB someSourceFile.cppš, 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. Išm not sure why it canšt 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 donšt 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, Išm not sure what R is doing?
> Is R doing the same thing a compiler would do and creating itšs own binary
> instructions for the launch of a function, or is it creating a new
> executable and launching that as itšs 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 Išm 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 itšs 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
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