[Phylobase-devl] Compilation woes

Ben Bolker bolker at zoology.ufl.edu
Sun Aug 3 22:53:49 CEST 2008

    Hmmm.  I didn't have trouble compiling on x86_32, presumably
that's more likely to be by accident -- that I happen to have
a clean copy -- than a 32/64 bit difference -- but I'm not going
to spend a lot of time trying to reproduce the error. (Steve,
can you make it happen reproducibly?)

   I'd say it's Brian's call what to do about NCL.  I'm a little
bit worried about taking it out, just because it will
decrease the urgency of doing anything about it -- but on the
other hand, it seems more or less on Brian's shoulders to fix it.
It would be nice if we could come up with a repeatable way of
making the errors happen -- I know from experience how frustrating
it is to try to debug something on a remote build server that only
builds once a day ... (it would be neat if the R-forge guys could
set up a build-on-demand server analogous to win-builder.r-project.org).

  The other question would be how much of our potential user
base (ha!) is interested in the capabilities that NCL offers
beyond the ape stuff ...


Steve Kembel wrote:
> Hi Brian,
> I just tried to build phylobase 0.3-1 on my Linux x86_64 box and got 
> similar errors to R-Forge (warnings about out of scope declarations and 
> then some fatal errors in the vignettes). I tried a bunch of different 
> things, and eventually got the package to build by simply checking out a 
> fresh copy of the code from the repository. Logs from the successful 
> build are attached. The cruft that accumulates as the NCL C++ code is 
> compiled multiple times in a local directory seems to cause mysterious 
> build errors. My guess is that this is what is happening on R-Forge. I 
> wonder if there's a way to make sure the package is being built from a 
> clean copy of the svn code every time on R-Forge?
> I know that an awful lot of work went into getting the NCL code working 
> with phylobase, but the ongoing issues with getting phylobase to compile 
> and install are a bit of a show-stopper for the package. Could I suggest 
> that we move the NCL-related code into its own package for now, until we 
> sort out why the package isn't building on R-Forge? As far as I can 
> tell, the NCL code isn't actually being used to read trees (we're 
> already using Brian's modified version of the ape read.nexus R code to 
> read Nexus trees), the NCL is just being used to read character data 
> from nexus files in the NexusToPhylo4D function, right? If we split the 
> NCL code off into its own package, we'd hopefully eliminate the problems 
> with compiling and installing phylobase. It might also make it easier to 
> troubleshoot compiling the NCL code. It would however require writing a 
> new function or modifying ape's read.nexus.data function if we want to 
> be able to seamlessly read a tree + data into a phylo4d object from a 
> Nexus file in phylobase.
> What do you think of this idea?
> Cheers,
> Steve
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