[Phylobase-devl] Compilation woes

Steve Kembel skembel at berkeley.edu
Sun Aug 3 22:33:31 CEST 2008

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  

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?

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