[Phylobase-devl] Rcpp and OS X compiliation

[Mark Holder]

Hi folks,
	I don't mind trying to help out.

	Unfortunately, I haven't done much with R.

	I'm the primary maintainer of NCL these days, and I usually develop  
on OS X.  So if someone sends me a list of steps to perform to  
duplicate any NCL-related problems, then I'd be happy to try to  
diagnose and fix the C++ side of things.

all the best,
Mark


On Jan 12, 2010, at 11:01 AM, Dirk Eddelbuettel wrote:

>
> 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.
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