From edd at debian.org  Sat Apr 19 22:41:57 2008
From: edd at debian.org (Dirk Eddelbuettel)
Date: Sat, 19 Apr 2008 15:41:57 -0500
Subject: [Rd] swig 1.3.35 & R - is the R wrapper still maintained and
 of	interest?
In-Reply-To: <480A2F66.1080205@wald.ucdavis.edu>
References: <1208515782.11561.27.camel@localhost>
	<509e0620804181208h134706b2r58cdd0307d840dcb@mail.gmail.com>
	<480A2F66.1080205@wald.ucdavis.edu>
Message-ID: <18442.22805.141892.154960@ron.nulle.part>


Duncan,

On 20 April 2008 at 05:44, Duncan Temple Lang wrote:
| ~  I've waited to see if there would be posts from others, but am
| a little surprised to see only your two.  It would seem people aren't
| using SWIG for R and I wonder why this community hasn't used or wanted

AFAICT it is a classic chicken and egg problem.  

"Something" exists, but is not exactly mature, been used mostly just for a
very large and rapidly changing codebase (ie Quantlib, which should stabilise
after the 1.0 release 'real soon now') with moderate success and hence
doesn't get off the ground for more.

| such tools?  Do we not have a need for them, or are we not aware of them, ...?
| or

My conjecture is that it would take off rather forcefully if only there were
one or two use cases for moderately-sized well-known libraries, providing
both use cases and usage templates. 

| ~  So what to do?  Firstly, I don't get that crash on load on my Linux
| box.  So we would have to investigate further, but at least it does work
| somewhere.  And such extreme failures are actually less worrying than the
| potential lack of functionality in the bindings.
| 
| ~  Soeren has already been in touch with me and indeed the
| code in the SWIG distribution comes origially from the RSWIG source on the
| omegahat repository. Unfortunately, the person who took that code
| and put into the SWIG distribution did by himself and didn't seem
| to want to work together to improve it add get it beyond the experimental state
| it was in.  Futher, he apparently listed me as the contributor,
| but haven't communicated at all with the SWIG developers and so I do not have

I think that is not true. Joe Wang had me CCed on a few email he had with the
Swig maintainers. He either has or had write access to the Swig repo, and
that seems to make sense as he was, afaik, the only one showing up there.  Or
did you ever offer your code for inclusion there?

But all that is spilled milk now.  Soeren has an _actual_ issue _right now_
so what can we do to get a proven tool (ie Swig) working and integrated with
R for him to get his work done and R and Shogun integrated ?

| access to the SWIG repository and cannot change the code.
| So we have a little bit of a problem that might have been better dealt with if
| code had continued to be developed outside of SWIG by the R community.
| 
| ~ If there is nobody interested in using SWIG in R, then there is little point
| in fixing it.  I have been working on an alternative way to generate bindings using
| output from GCC (gcc & g++) and exploring how the bindings should work

Sure, that is very well for you as a research project, but Swig is there, is
rather mature, understood and widel y used -- just not as much with R as it
could be.  IMHO we'd better off focussing on getting Swig working.

| generally.  Most of the ideas I think would be able to go back into SWIG
| and that _might_ be an easier tool for people to use who don't want more control
| over the code generation or to do analysis on the code itself.
| But if nobody other than the two of us is interested in using a general interface code
| generation mechanism, then perhaps we shouldn't waste too much time on such
| general resources.  However, I think it is of value and I think
| we can fix up the SWIG module with a little collaboration.

There is definitely interest.  Eg from the Quantlib angle, a few people
expressed interest a few months ago to revive the R/Quantlib integration via
Swig but nothing much has come of it yet. We're all too busy it seems.

Dirk
 
| ~  D.
| 
| 
| Michael Lawrence wrote:
| | I am not sure what is included with swig, but have you seen this?
| |
| | http://www.omegahat.org/RSWIG/
| |
| | I'm not sure if it's actively maintained, but at the very least it might
| | help in your efforts at getting an R swig driver working.
| |
| | Michael
| |
| | On Fri, Apr 18, 2008 at 3:49 AM, Soeren Sonnenburg <r-ml at nn7.de> wrote:
| |
| |> Dear all,
| |>
| |> I was trying to use the R swig wrapper with R 2.7 and shogun
| |> ( http://www.shogun-toolbox.org ) but it fails completely, as in doesn't
| |> even compile and even after patching then though compiling - crashes...
| |>
| |> So I asked on swig-users/swig-devel CC'ing the potential R maintainer
| |> but I never received a reply. I now wonder if anyone here could help or
| |> would be willing to maintain R+swig.
| |>
| |> The compile fix for R 2.7 is here
| |>
| |> http://article.gmane.org/gmane.comp.programming.swig/12697
| |>
| |> and the crash I am now that it compiles see is
| |>
| |> #0  0xb804e201 in _dl_debug_state () from /lib/ld-linux.so.2
| |> #1  0xb8051608 in dl_open_worker () from /lib/ld-linux.so.2
| |> #2  0xb804d5d6 in _dl_catch_error () from /lib/ld-linux.so.2
| |> #3  0xb8050f5e in _dl_open () from /lib/ld-linux.so.2
| |> #4  0xb74c3c19 in dlopen_doit () from /lib/i686/cmov/libdl.so.2
| |> #5  0xb804d5d6 in _dl_catch_error () from /lib/ld-linux.so.2
| |> #6  0xb74c42bc in _dlerror_run () from /lib/i686/cmov/libdl.so.2
| |> #7  0xb74c3b51 in dlopen@@GLIBC_2.1 () from /lib/i686/cmov/libdl.so.2
| |> #8  0xb7efd036 in loadLibrary (path=0xbfa5650c
| |> "/home/sonne/Documents/work/fml/repositories/shogun/trunk/src/features/Features.so",
| |> asLocal=1, now=1, search=0x9a81f20 "") at dynload.c:92
| |> #9  0xb7d6efb3 in AddDLL (path=0xbfa5650c
| |> "/home/sonne/Documents/work/fml/repositories/shogun/trunk/src/features/Features.so",
| |> asLocal=1, now=1, DLLsearchpath=0x9a81f20 "") at Rdynload.c:543
| |> #10 0xb7d6f657 in do_dynload (call=0x9e23998, op=0x9a91e44,
| |> args=0xa60d5e0, env=0xa60d650) at Rdynload.c:904
| |> #11 0xb7e43dba in do_internal (call=0x9e239d0, op=0x9a8798c,
| |> args=0xa60d5e0, env=0xa60d650) at names.c:1129
| |> #12 0xb7e0df21 in Rf_eval (e=0x9e239d0, rho=0xa60d650) at eval.c:463
| |> #13 0xb7e11a3c in Rf_applyClosure (call=0xa60d74c, op=0x9e23a94,
| |> arglist=0xa60d6dc, rho=0x9a9a720, suppliedenv=0x9a9a73c) at eval.c:669
| |> #14 0xb7e0de19 in Rf_eval (e=0xa60d74c, rho=0x9a9a720) at eval.c:507
| |> #15 0xb7e31a00 in Rf_ReplIteration (rho=0x9a9a720, savestack=0,
| |> browselevel=0, state=0xbfa589a8) at main.c:257
| |> #16 0xb7e31ddc in run_Rmainloop () at main.c:306
| |> #17 0xb7e31e1c in Rf_mainloop () at main.c:974
| |> #18 0x08048776 in main (ac=1, av=0xb805b668) at Rmain.c:35
| |> #19 0xb7be8450 in __libc_start_main () from /lib/i686/cmov/libc.so.6
| |> #20 0x08048691 in _start ()
| |>
| |> To reproduce
| |>
| |> ???wget http://nn7.de/debugging/shogun-0.6.1+svn2882.tar.bz2
| |> tar xjf shogun-0.6.1+svn2882.tar.bz2
| |> cd shogun-0.6.1+svn2882/src
| |> ./configure --interface=R-modular
| |> make
| |>
| |> (wait a few minutes)
| |>
| |> R
| |> dyn.load('features/Features.so')
| |> #source("features/Features.R") # not even necessary.
| |>
| |> Note that shogun works for both python and octave nicely...
| |>
| |> ???So the question for me is, will this be better maintained in the future
| |> or should I stop investing time on getting R supported?
| |>
| |> Desperate,
| |> Soeren
| |>
| |> ______________________________________________
| |> 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
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-- 
Three out of two people have difficulties with fractions.



[Rd] swig 1.3.35 & R - is the R wrapper still maintained and of interest?
Dirk Eddelbuettel