[Phylobase-devl] [Fwd: phylobase]

Ben Bolker bolker at ufl.edu
Thu Dec 10 14:37:55 CET 2009

  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?)


-------- 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

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
already really well for Debian testing -- see
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
&& 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
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
to get linked against -- no more sources of RcppSrc/ in your project, no
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
I can work on a patch, or a tentative 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

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