[Phylobase-devl] bug in phylobase

Ben Bolker bolker at ufl.edu
Tue Jul 13 21:09:31 CEST 2010

  Thanks very much!  I/we will look into this ...


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.

Ben Bolker
***   bbolker at gmail.com , bolker at math.mcmaster.ca
bolker at ufl.edu / people.biology.ufl.edu/bolker
GPG key: people.biology.ufl.edu/bolker/benbolker-publickey.asc

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