[Phylobase-devl] [Fwd: phylobase]

François Michonneau francois.michonneau at gmail.com
Thu Dec 10 17:55:14 CET 2009


  I'm planning to do a little bit of hacking on phylobase over the
holidays.

  For various reasons I had to play with libncl a couple of months ago,
and I would be inclined to spend a little bit of time trying to improve
the integration of libncl with phylobase. However, there are a few
things I need to learn to this properly, so I can't guarantee I'll make
much progress. I'll try though...

  Cheers,
  -- François 

On Thu, 2009-12-10 at 11:06 -0500, Brian O'Meara wrote:
> Thanks for the info, Dirk. I was one of the two people responsible for  
> the C++ code in phylobase, and I've consistently had trouble mastering  
> build issues (this has come up in other code I've written, too). For  
> my part, any patches you could provide to make this more robust would  
> be great.
> 
> We included Rcpp sources in phylobase because, as you note, during the  
> week we were first making phylobase Rcpp wasn't being maintained and,  
> more importantly, it was only present on a subset of CRAN mirrors (I  
> think we ended up getting it from Italy). Taking out the Rcpp source  
> from phylobase and just requiring the Rcpp package makes a lot of  
> sense to me, and I will look into doing this after the holidays.
> 
> Best,
> Brian
> 
> On Dec 10, 2009, at 8:37 AM, Ben Bolker wrote:
> 
> >
> >  The C++ interfacing is a fairly regular irritation for us, it would  
> > be
> > great to improve it/clean it up -- I'm cc'ing/forwarding this question
> > to the rest of the dev team, some of whom may have more informed
> > opinions (Brian?)
> >
> >  cheers
> >    Ben
> >
> >
> > -------- Original Message --------
> > Subject: phylobase
> > Date: Wed, 9 Dec 2009 23:07:13 -0500
> > From: Dirk Eddelbuettel <edd at debian.org>
> > To: Bolker,Benjamin Michael <bolker at ufl.edu>
> >
> >
> > Hi Ben,
> >
> > I am writing to you in regards to phylobase for which you are listed  
> > as the
> > maintainer.
> >
> > As you may know, I have been working with a very sharp British (now
> > grad-)student on automtic builds of .deb packages for all of CRAN.  
> > This
> > works
> > already really well for Debian testing -- see
> > http://debian.cran.r-project.org
> > We hope to extend that to Ubuntu one day.  Being able to 'apt-get  
> > install
> > r-cran-ANYTHING' for essentially 2000 values of ANYTHING is pretty  
> > neat, esp
> > as apt et al really do solve dependencies in a reliable way.
> >
> > A few packages fail to build, and phylobase is among them.  We build  
> > these
> > packages (just like normal Debian or Ubuntu packages) in restricted  
> > chroot
> > and that sometimes triggers erros we do not get in interactive  
> > shells. For
> > phylobase it is
> >
> > [...]
> > cendants.o phyloXX.o reorderBinary.o reorderRobust.o -LRcppSrc -lRcpp
> > -Lncl/ncl/.libs -lncl -L/usr/lib/R/lib -lR
> > /usr/bin/ld: cannot find -lncl
> >
> > and I think has to do with ncl using libtool, and the build running
> > configure
> > && make but not make install.  So src/ncl/ncl/.libs -- a temporary  
> > location
> > -- is the only one and that proves too unreliable here.
> >
> > On the other hand, if one also calls, say, in src/ncl/ncl
> >
> >    make install prefix=`pwd`/../..
> >
> > then src/lib/libncl.a is created with about 753kb on an amd64.  We  
> > could
> > then
> > link against this static library which would be easier, and we don;t  
> > need
> > ld.so or LD_LIBRARY_PATH or libtool magic.
> >
> > Another thing I noticed is that the packages uses the older  
> > RcppSrc.  After
> > Dominick stopped working on Rcpp (which he neglected from Nov 2006  
> > to Nov
> > 2009), I took over maintenance about a year ago.  If you look at the  
> > current
> > Rcpp package and say its examples/ directory you may get an idea.  In
> > essence, I maintained the API but made Rcpp a full-fledged CRAN  
> > package.  So
> > update.packages() gets you new versions including a new library that  
> > is
> > ready
> > to get linked against -- no more sources of RcppSrc/ in your  
> > project, no
> > more
> > build from configure etc pp.  I'd be happy to walk you through usage  
> > and
> > builds, and there are other example users.
> >
> > But fixing the build of phylobase w.r.t. nlc is more important.  If  
> > you
> > want,
> > I can work on a patch, or a tentative 0.5.0.1 that changes the build.
> >
> > Cheers, Dirk
> >
> > -- 
> > Three out of two people have difficulties with fractions.
> >
> > -- 
> > Ben Bolker
> > Associate professor, Biology Dep't, Univ. of Florida
> > bolker at ufl.edu / www.zoology.ufl.edu/bolker
> > GPG key: www.zoology.ufl.edu/bolker/benbolker-publickey.asc
> >
> > _______________________________________________
> > 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
> 
> ------------------------------------------------------
> Brian O'Meara
> http://www.brianomeara.info
> Assistant Prof.
> Dept. Ecology & Evolutionary Biology
> U. of Tennessee, Knoxville
> 
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