From duncan at wald.ucdavis.edu  Sun Apr 20 21:42:41 2008
From: duncan at wald.ucdavis.edu (Duncan Temple Lang)
Date: Mon, 21 Apr 2008 07:42:41 +1200
Subject: [Rd] swig 1.3.35 & R - is the R wrapper still maintained and of
 interest?
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Dirk Eddelbuettel wrote:
| 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.

I concur fully. And while it is reasonable for people to wait until there are good examples and a
working tool, it would be helpful if people would express a sense of interest for such potential
projects.  We have built too many "good" things that people haven't used, and it would be
good to evaluate this before committing too much time into them. In the case of something like
interface generators, the idea is well known, so people could express an interest in the concept
without too much learning being necessary.
Indeed, I recall in 2001 asking why people hadn't cried out for SWIG facilities for R
and I got at least one blank look :-)



|
| | 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.

I'm working on that for wxWidgets and Qt at the moment.
And I have some for smaller codebases.

|
| | ~  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?

Well, we are talking about different things. I know Joe had SWIG svn access.
I didn't get the opportunity to discuss how to include my code as Joe included
it before I was ready to make it public in that way given its experimental nature.
Adding it implies some sense of maintenance obligation, potential back compatability,
etc. and that is why it is not particularly helpful to take a project somebody is actively working
on and make decisions about it without that person's approval. It is "water under the bridge",
but helpful to learn from.

|
| 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 ?

One "issue" whether Soeren or anyone else needs the R interface
"immediately" or  whether this would be just a nice thing to have.
Again, chicken and egg, but given the limited amount of time available
of people who know how to do this "properly", whether a stop-gap solution
or whether we can do it properly over a period of time.

It is complex to create the general mechanism for SWIG code generation that covers C and C++
and handles important aspects.  I _might_ be able to get to it
in late summer, but I cannot guarantee it. Once I finish the approach that leverages
GCC, then I should have at least all the issues resolved with how I think the mapping
should generate the code. That should simplify implementing the map in Perl.

I would be very keen to chat with people who are interested in helping or have
examples to try out and are willing to withstand the volatility of development
versions.




|
| | 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,
~ Thanks!
| 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.

I have little doubt that it would be nice to have the RSWIG mechanism functional.
SWIG is excellent. That's why I did the work back in 2005.
However, SWIG does not do everything that we would like it to do, or necessarily do it properly.
We can make things "easier" and better and that is why Michael (Lawrence) and I are exploring
other approaches.  And there is not likely to be one single all-encompassing answer.

And the claim that it is it well understood requires some qualification. There are not many people
who know more than the basics
of the SWIG-specific language used to customize and control the code generation.
And as for widely used - so is MS Windows* :-)
And the idea that "because something is mature and understood and widely used"
is a very worrying attitude that I am seeing more and more with R. Yes, we need usable,
useful things. But we have to continue to innovate or fall further and further behind.

|
| | 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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[Rd] swig 1.3.35 & R - is the R wrapper still maintained and of interest?
Duncan Temple Lang