[Phylobase-devl] New phylobase build approach using static libncl (Was: Rcpp and OS X compiliation)

[François Michonneau]

It would be really good if we could fix the bugs I reported before
releasing this updated version to CRAN (in particular bug #812).
Indeed, we can't import most nexus trees in phylobase. It looks that
the NCL interface needs to be updated but I don't know C++ and it's
hard for me to investigate the problem. I'm willing to help though and
write the RUnit tests associated with readNexus once the problem is
fixed.

  Cheers,
  -- François


On Sat, Feb 27, 2010 at 14:29, Dirk Eddelbuettel <edd at debian.org> wrote:
>
> On 27 February 2010 at 14:08, Ben Bolker wrote:
> |   fine with me, phylobase passes R CMD check on my system without it.
> | We can always restore it from SVN if it breaks something, right?
>
> Correct. Plus there is a full copy in SVN at the top-level.
>
> So removed as rev741.  Do you think you want to wrap this up as 0.5.1 or
> 0.5.5 or ... for CRAN?
>
> Dirk
>
>
> | Dirk Eddelbuettel wrote:
> | > Hi phylobase'ers,
> | >
> | > On 8 February 2010 at 17:54, Dirk Eddelbuettel wrote:
> | > | On 8 February 2010 at 15:40, Peter Cowan wrote:
> | > | | It appears to be building fine with Mac OS X (i386 & x86_64).  I agreed the
> | > | | commingled approach is the way to go.  I think this will suit the needs of
> | > | | our users best.  In fact, I tried it months ago but didn't have success, so I
> | > | | thank you for your efforts!
> | > |
> | > | Cool! I didn't know that, so thanks for the thumbs up!
> | > |
> | > | | From my understanding, we don't need all of the source files for our NCL commands.
> | > |
> | > | Correct!  But I wanted to be careful here. But in fact I think now that move
> | > | the old
> | > |
> | > |   src/ncl/
> | > |
> | > | into
> | > |
> | > |         src/ncl.original/
> | > |
> | > | and moved the files we need out of it, we can in fact clean up via, say,
> | > |
> | > |         $ svn rm pkg/src/ncl.original
> | > |         $ svn ci pkg -m'remove unused parts of ncl library'
> | > |
> | > | but I think I should leave that to one of the actual phylobase maintainers.
> | >
> | > I think we can do
> | >
> | >           $ svn rm pkg/src/ncl.original
> | >
> | > to clean up a little more.  Comments, anyone?
> | >
> | > Dirk
> | >
> | > | | Down the road, we might be able to clean things up a little.  For example
> | > | | the nxsdistancedatum.cpp file is empty
> | > |
> | > | Hadn't noticed.
> | > |
> | > | | and nxsemptyblock.cpp appears not to be used either.
> | > |
> | > | That one actually blocks building which is why I #ifdef'ed it out.
> | > |
> | > | Oh, the sweet sound of progress :)
> | > |
> | > | Dirk
> | > |
> | > | --
> | > |   Registration is open for the 2nd International conference R / Finance 2010
> | > |   See http://www.RinFinance.com for details, and see you in Chicago in April!
> | >
> |
> |
> | --
> | Ben Bolker
> | Associate professor, Biology Dep't, Univ. of Florida
> | bolker at ufl.edu / people.biology.ufl.edu/bolker
> | GPG key: people.biology.ufl.edu/bolker/benbolker-publickey.asc
> |
> |
> | [GNUPG:] ERRSIG 7395291A3C337A73 17 2 01 1267297727 9
> | [GNUPG:] NO_PUBKEY 7395291A3C337A73
>
> --
>  Registration is open for the 2nd International conference R / Finance 2010
>  See http://www.RinFinance.com for details, and see you in Chicago in April!
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