[Phylobase-devl] bug in phylobase

[François Michonneau]

Hi,

  I believe this is fixed in the current R-forge version (0.5.11).
Indeed, a while back Dirk rewrote the way NCL is built.

  I have limited time to test it now as I'm travelling but if someone
could confirm this it would be great.

  Cheers,
  -- François 

On Tue, 2010-07-13 at 15:09 -0400, Ben Bolker wrote:
> Thanks very much!  I/we will look into this ...
> 
>   cheers
>     Ben
> 
> 
> Simon Urbanek wrote:
> > Ben,
> > 
> > while debugging some other issues I have seen that there is a serious issue in phylobase - it's compiling the wrong architecture of ncl inside so it breaks on all but one architecture (whichever happens to be the default of the OS).
> > 
> > The fix is really trivial - before you make ncl add 
> > 
> > export CXX
> > export CXXFLAGS
> > 
> > to your configure.in. That will make sure that ncl uses the correct compiler.
> > Please consider adding the fix and submitting to CRAN.
> > 
> > Thanks,
> > Simon
> > 
> > 
> > --
> > Although you can trigger the above anywhere with multi-arch R it's beast seen in practice on OS X (example below is on 10.6 with R --arch=i386):
> > 
> > * installing *source* package ‘phylobase’ ...
> > checking for C++ compiler default output file name... rm: a.out.dSYM: is a directory
> > a.out
> > checking whether the C++ compiler works... yes
> > checking whether we are cross compiling... no
> > checking for suffix of executables... 
> > checking for suffix of object files... o
> > checking whether we are using the GNU C++ compiler... yes
> > checking whether g++ -arch i386 accepts -g... yes
> > 
> > [^^-- note this is the correct compiler g++ -arch i386]
> > [...]
> > Building libncl.a in ncl...
> > checking for a BSD-compatible install... /usr/bin/install -c
> > checking whether build environment is sane... yes
> > checking for a thread-safe mkdir -p... config/install-sh -c -d
> > checking for gawk... awk
> > checking whether make sets $(MAKE)... yes
> > checking how to create a ustar tar archive... gnutar
> > checking whether ln -s works... yes
> > checking for a BSD-compatible install... /usr/bin/install -c
> > checking for g++... g++
> >  ^-- this is wring because the default g++ output is x86_64 and not i386 so it will produce 64-bit ncl although phylobase is compiled for 32-bit. By exporting the CXX flags you make sure that ncl uses the correct compiler.
> > 
> > 
> > 
> > 
> 
> 
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