Dear Jason,
Thank you very much for your help.
On Wed, Oct 30, 2013 at 2:50 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Wed, Oct 30, 2013 at 5:52 AM, M. Reza Ganjalikhany <
> ganjalikhany.gmail.com> wrote:
>
> > Dear Amber Users,
> >
> > I am trying to compile Amber 12 on Arch linux (latest kernel 3.11.6),
> but I
> > get the error message from the biginig when updater tries to autoupdate
> > Amber as below. Also, the rest of check points pass successfully at
> > configuration step.
> >
> > Any help will be greatly appreciated,
> >
> > [root.localhost amber12]# ./configure gnu
> > Checking for updates...
> > File "./update_amber", line 30
> > except AmberUpdaterError, err:
> > ^
> > SyntaxError: invalid syntax
> >
>
> This is valid syntax for Python 2, but not for Python 3. We are reaching a
> point where newer Linux distributions are starting to finally retire Python
> 2 as their main system Python and they are moving to Python 3. According
> to the Arch Linux Wiki, Python 3 is now the default Python version shipped
> with that Linux distribution. Because Python 2.4 is still a commonly-used
> default Python version on RHEL 5 -- which is still popular for some larger
> clusters -- it was important for update_amber to support Python 2.4 through
> 2.7 (but at the time of writing, no distros had fully switched to Python
> 3). The upcoming AmberTools 14 will feature an update_amber that uses
> syntax fully compatible with both Python 2 (2.4+) and Python 3
> (significantly trickier than it would seem). For the time being, though,
> Python 2 is required for AmberTools 13's updating script.
>
> Long story short, change the shebang line of update_amber from
>
> #!/usr/bin/env python
>
> to
>
> #!/usr/bin/env python2
>
> See the Arch Linux wiki page on Python for more information:
> https://wiki.archlinux.org/index.php/python
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Sat Nov 02 2013 - 06:00:02 PDT
