[Biopython] upgrade problems on Mac

[João Rodrigues]

Hi Mark,

Recent versions of osx changed the location of the sdks and have been known
to cause some issues.. Did you upgrade the machine to Mavericks from a
previous version or was it a clean install?

I would try reinstalling xcode and checking your profile or bashrc files
for clues. It might be a broken installation of gcc where its include and
lib paths are still pointing to the old locations, or just old definitions
in these files.

Cheers,
João
Em 18/07/2014 09:57, "Mark Budde" <markbudde at gmail.com> escreveu:

> 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. 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
>
>
> On Thu, Jul 17, 2014 at 3:00 AM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
>
>> On Wed, Jul 16, 2014 at 8:03 PM, Mark Budde <markbudde at gmail.com> wrote:
>> > Hi all,
>> > I am trying to upgrade to the current version on my Mac, but get an
>> error.
>> > I've tried the suggestions online about
>> >
>> > $ xcode-select --install
>> >
>> > but that doesn't work.
>> >
>> > ...
>> >
>> > error: command 'gcc' failed with exit status 1
>>
>> Hi Mark,
>>
>> Those problems suggest that XCode itself is not installed. Since
>> you are running OSX 10.9 this is available for free from the Apple
>> App Store (but it is a large download).
>>
>> i.e. You need to install XCode, *then* the command line tools by
>> running 'xcode-select --install', or equivalently via the XCode GUI.
>>
>> Can you suggest a clearer phrasing for our instructions here?
>> http://biopython.org/wiki/Download
>>
>> Also, since you are using enthought's Python they may offer a
>> Biopython packaged installation route instead?
>>
>> Regards,
>>
>> Peter
>>
>
>
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