[Phylobase-devl] Rcpp and OS X compiliation

[Brian O'Meara]

Great, thanks, Mark [and Francois, Dirk, and Peter].

Brian

On Jan 12, 2010, at 12:10 PM, Mark Holder wrote:

> 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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>
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------------------------------------------------------
Brian O'Meara
http://www.brianomeara.info
Assistant Prof.
Dept. Ecology & Evolutionary Biology
U. of Tennessee, Knoxville