[Phylobase-devl] Rcpp and OS X compiliation

[Dirk Eddelbuettel]

Hi Francois,

I hope you don't mind that I added phylobase-dev back as a CC to keep the
list in the loop.

On 12 January 2010 at 17:30, François Michonneau wrote:
| Hi Dirk,
| 
|   I'm willing to help too.

Cool!

|   I run Ubuntu. I can also have access to a machine with Windows XP, but I
| have never tried to compile anything under Windows and I don't really know
| how to do it.

I have those two as well. OS X help and 'mad skillz' are in shorter supply.
 
|   On a side note, I couple of months ago I also tried to learn how to
| package with Ubuntu and created a package for NCL. You can find it here:
| https://launchpad.net/~francois-michonneau/+archive/ppa/+packages (under
| libncl).

Ahh, nice. That may definitely help for OSs where we can do without building
NCL.  But I fear that we may have to play defense and continue to include NCL
as source to keep it self-contained.  I expect that we need to do something
to 'robustify' the build. I got started in this for cran2deb (see
http://debian.cran.r-rpoject.org) and had to do more surgery than I really
wanted to get it to build sanely on i386 and amd64.  But the real isssue may
be OS X where I can't help/

|   I did that while I was down with the flu and never got back to it. The
| package builds and installs but it's not functional. Indeed, the file
| libncl-2.1.06.so after the install is located in /usr/lib/ncl whereas the
| software that depends on it looks for it in /usr/lib. Given your experience
| with packaging, I was wondering if you could indicate me the best way to
| solve this problem (if you have time/if it can help with phylobase).

--prefix=/usr  maybe?  
 
|   At least one thing that needs to be changed in the source code of the
| latest versions of ncl to compile flawlessly with the most recent versions
| of g++ is to include a few additional headers (you can have a look at the
| diff.gz file on my ppa).

Yes, I think updating NCL to a sane and current version may well a good plan
but I can't speak for the phylobase team.

Cheers, Dirk

| 
|   Let me know how I can help.
| 
|   Cheers,
|   -- François
| 
| 
| 
| On Mon, Jan 11, 2010 at 21:37, Dirk Eddelbuettel <edd at debian.org> wrote:
| 
| >
| > On 11 January 2010 at 12:18, Peter Cowan wrote:
| > | On Jan 11, 2010, at 6:55 AM, Dirk Eddelbuettel wrote:
| > |
| > | [snip]
| > |
| > | > I am still game. I see a three-pronged approach:
| > | >
| > | >  i)    Suggestion Let's fix NCL and have a locally built version
| > outside
| > | >        of phylobase on all test platforms
| > |
| > | Is this only for testing purposes, or are you envisioning distributing
| > them separately?
| >
| > Yes, sorry -- just for purposes of squaring this test off.
| >
| > I did not mean to imply we should change phylobase in any way.  I just want
| > to help you make your life easier as Rcpp can actually do that (or so I
| > hope).
| >
| > | >  ii)   With that, fix/simplify Rcpp usage. Should be easy
| > | >
| > | >  iii)  With that, get back to i) and clean up NCL's configure.
| > | >
| > | > I think it would be easier to disentangle Rcpp and NCL inside phylobase
| > while
| > | > we make this more.
| > | >
| > | > Who else can work with us on this, and in particular provide OS X
| > skillz and
| > | > testing?
| > |
| > | I'm happy to help w/ OS X testing, but I'm not very familiar with C++,
| > make or configure files.
| >
| > Thanks for the offer.  Simple 'yay' or 'nay' about the 'does it build and
| > run' will help, but you'd need to have a locally built NCL around so that
| > we
| > can do i).  Can you build one and get to the OS X equivalent of /usr/local
| > --
| > ie somewhere where it will be found unaided?
| >
| > Dirk
| >
| > | Peter
| > |
| > | > Dirk
| > | >
| > | >
| > | > | Brian
| > | > |
| > | > |
| > | > | >
| > | > | > | I'm sure the make files for NCL could be greatly simplified which
| > | > | > could
| > | > | > | help. But, it is currently beyond my abilities, and I don't
| > | > | > currently have
| > | > | > | the time to learn the make.
| > | > | >
| > | > | > Ideally we would able to assume that the user has already installed
| > | > | > ncl. In
| > | > | > the real world down here that may never be the case, alas.
| > | > | >
| > | > | > Dirk
| > | > | >
| > | > | > --
| > | > | > Three out of two people have difficulties with fractions.
| > | > |
| > | > | ------------------------------------------------------
| > | > | Brian O'Meara
| > | > | http://www.brianomeara.info
| > | > | Assistant Prof.
| > | > | Dept. Ecology & Evolutionary Biology
| > | > | U. of Tennessee, Knoxville
| > | > |
| > | >
| > | > --
| > | > Three out of two people have difficulties with fractions.
| > |
| >
| > --
| > Three out of two people have difficulties with fractions.
| > _______________________________________________
| > Phylobase-devl mailing list
| > Phylobase-devl at lists.r-forge.r-project.org
| > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/phylobase-devl
| >

-- 
Three out of two people have difficulties with fractions.