[Biopython] upgrade problems on Mac

[Peter Cock]

On Fri, Jul 18, 2014 at 7:03 AM, Mark Budde <markbudde at gmail.com> wrote:
> Hi Peter,
> Xcode 5.1.1 is installed on my machine, and I have successfully installed
> older versions of Biopython. I have followed the instructions about
> installing xcode command line tools, but that also doesn't solve the
> problem.

Does xcode-select give any output? There are a few more options
like --reset which might be useful...

On my Mac OS X 10.9.3 machine with Xcode 5.1.1,

$ xcode-select --print-path
/Applications/Xcode.app/Contents/Developer
$ xcode-select --version
xcode-select version 2333.

$ which gcc
/usr/bin/gcc
$ gcc -v
Configured with:
--prefix=/Applications/Xcode.app/Contents/Developer/usr
--with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 5.1 (clang-503.0.40) (based on LLVM 3.4svn)
Target: x86_64-apple-darwin13.3.0
Thread model: posix

$ which clang
/usr/bin/clang
$ clang -v
Apple LLVM version 5.1 (clang-503.0.40) (based on LLVM 3.4svn)
Target: x86_64-apple-darwin13.3.0
Thread model: posix

> I installed EPD over a year ago, so I might have to try a fresh
> install, but was hoping to avoid that if this is a known problem. Since
> nobody else seems to have run into this problem, I guess it must be specific
> to something about my machine.
> Thanks again,
> Mark

Maybe Joao's reply is relevant, but updating EPD sound worth
trying too. However, not having gcc available at the command
line is the immediate problem.

Peter