[phenixbb] python issues

Graeme Winter graeme.winter at googlemail.com
Wed Mar 10 08:25:48 PST 2010

Hi Folks,

Regarding these errors I do remember seeing these when I did a binary
installation, but forgot to run binary.setup. I'm not sure if you need
to do the same on a mac though - I don't remember doing such on my Mac
OS X.5 installation.

Certainly used to happen on Linux if you just downloaded the binary
tarball, unpack and then edit and source the setup script.

Best wishes,


On 10 March 2010 16:20, Ralf W. Grosse-Kunstleve <rwgk at cci.lbl.gov> wrote:
> Hi Pat,
>> source /sw*/bin/init.csh       (where /sw* is either /sw64 on the
>> machine running 10.6, or /sw on the machine running 10.5)
>> gives the error:
>>     *******************************************
>>     Fatal Error: Incomplete libtbx environment!
>>     *******************************************
>>     Please re-run the libtbx/configure.py command.
> I wrote the script which produces this error, but I'm not sure I can
> help much...
> The message comes from an auto-generated "setpaths.csh" file which
> contains full path names to the Python used to configure the cctbx-based
> build, and a utility script. Apparently, those full path names aren't
> valid on your system. If you can find the "setpaths.csh" script maybe
> the pathnames will give you a clue what's wrong.
> Under 10.6 there are several things that can go wrong in addition,
> related to 32-bit vs. 64-bit.
>> If I go to ...ccp4.../src/phaser/phaser-2.1.4/libtbx/ and type
>> python configure.py
> Users shouldn't have to run this command themselves. It is meant to
> be part of the package-specific installation scripts.
> If you run it manually you have to have the "build" directory as
> your current working directory, i.e. the same directory where you
> find the "setpaths.csh" script (which will be overwritten). Also,
> importantly, you have to get the right python executable, matching
> the pre-compiled binaries.
> I hope you'll get better help from the people who made the ccp4
> installer you're using.
> Ralf
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