From sean.mcguffee at gmail.com  Sat Apr 23 10:03:36 2011
From: sean.mcguffee at gmail.com (Sean Robert McGuffee)
Date: Sat, 23 Apr 2011 04:03:36 -0400
Subject: [Rd] FW: [Rcpp-devel] Question on 5.6 Interfacing C++ code
In-Reply-To: <BC806D73-DE3B-424B-8F57-0A2803286439@r-project.org>
Message-ID: <C9D80018.3E13%sean.mcguffee@gmail.com>

Hi All,

Just to follow up, I finally figured out a way to make a simple test project
I'm working on to compile and install and have access the code inside of R.
It turns out it was related to this "foo" name. I had to make the name of my
dynamic library output have the same name as the "foo" from the DESCRIPTION
file (and useDynLib(foo) ). I had made changes from a sample Rcpp program
where I liked the way args were passed. However, I didn't keep the name of
my dynamic library the same as the name of my directory and the name of my
functions and the name of my code files and the name of my project, and it
seems to me that it matters in about three places that need to match.
Eventually, after weeks of guessing incorrectly that I was doing something
else wrong altogether, I tried renaming the files and got one permutation to
work. After fiddling around with it to get to the bottom of what was going
on, I got one of my old original directories out and simply changed the
dynamic library name between the src/ and the .so part to match with the
name in the DESCRIPTION and the name inside the useDynLib() inside the
NAMESPACE file. Was this obvious to everyone else from reading the manual?
There were so many things I didn't understand that I missed that part.
Anyway, I've learned something about autoconf out of the whole ordeal, so
sometimes it pays off for me to be so silly. Anyway, I'd just like to
confirm that this is correct:

If I want to name a package "MY_PACKAGE_NAME"
then I have to do three things with this name to get Rcpp and/or my package
calling c++ to install and run correctly. I'll call my package directory TOP
1) put the line "Package: MY_PACKAGE_NAME" inside of TOP/DESCRIPTION
2) put the line "useDynLib(MY_PACKAGE_NAME)" inside of TOP/NAMESPACE
3) make sure the final dynamic library is named TOP/src/MY_PACKAGE_NAME.so
Do the experts agree that this is correct and necessary?

I happen to have named TOP to be MY_PACKAGE_NAME too, is that important too?
I also happen to be naming my function MY_PACKAGE_NAME too, is that
important? If I want to add more functions, I assume I can do that as long
as I link them into the TOP/src/MY_PACKAGE_NAME.so file. Is that correct?

Thanks in advance, 

Sean



On 4/21/11 10:57 AM, "Simon Urbanek" <simon.urbanek at r-project.org> wrote:

> 
> On Apr 21, 2011, at 10:52 AM, Sean Robert McGuffee wrote:
> 
>> Thanks,
>> That's great, but I don't know how to determine what foo is.
> 
> It's the name of your package.
> 
> 
>> How do I declare the name of the package?
>> 
> 
> in DESCRIPTION:
> Package: name
> 
> and the directory of your package has to have the same name - please do read
> http://r.research.att.com/man/R-exts.html#Creating-R-packages
> 
> Cheers,
> Simon
> 
> 
>> 
>> On 4/21/11 7:16 AM, "Duncan Murdoch" <murdoch.duncan at gmail.com> 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.
>>> 
>>> 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-fr>>>>
o
>>>> n
>>>> |>>  t_002dends-to-R
>>>> |>>  under the heading:
>>>> |>>  5.6 Interfacing C++ code
>>>> |>>
>>>> |>>  Question 1:
>>>> |>>  If I?m 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 it?s 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
>> 
>> 
> 



[Rd] FW: [Rcpp-devel] Question on 5.6 Interfacing C++ code
Sean Robert McGuffee