Getting Fink to work in OS X Mountain Lion

The Materials:

1. Command Line Tools for ML
2. Fink source code 0.34.0
3. A Mac with Mountain Lion
4. X11

To get your hands on the command line tools, it is necesary to have a Developer account at Apple's site. You don't have to go for the payed-for version. The free ones are good enough. Fink can be obtained at its website.
Now, for reasons that I rather not think off (that is, Apple not caring) X11 is no longer distributed by Apple. X11 (or Xquartz) has been also a open-source project for a while. Now the burden rest with the XQuartz project distributes the X11 for ML.

The Process:

I installed the CLT for ML using the file for July 2012. Then, after unpacking the

fink-0.34.0.tar.gz

I cd into into it

cd fink-0.34.0

and then, following the instructions from the Fink website, cast the command

./boostrap

I got a warning about having to install Xcode up to OS X 10.7. Beyond that version, the command line tools are good enough. After a few minutes ./bootstrap finished its job and all I had to do was to add

. /sw/bin/init.sh

to my .profile.
As usual, I issued the update commands as follows:

fink -y selfupdate-cvs; fink -y update-all; fink -y scanpackages; fink -y index

The

-y

flag tells fink to go for the default options without stopping to query the user. The

;

separates each command so each is performed in sequence. So far everything is going ok. I'll post any updates as they become available.

UPDATE:

As I tried to install gnuplot (yes, gnuplot) a dependencia (lua) turned out to require Xcode. So, I am downloading it and installing it. More to come.

UPDATE 2:

Coot was getting me trouble (0.7-pre-1 (revision 4307)):


Fatal Python error: PyThreadState_Get: no current thread
/sw/bin/coot: line 6:  5976 Abort trap: 6           /sw/bin/coot-real "$@"


I hacked the coot.py located at:

/sw/share/coot/python/coot.py

and got it working. It is worth mentioning that before the hack neither fink nor the standalone precompiled version was working. Now, what I did was add the following lines:


    import sys
        sys.path.append("/sw/bin") # this reflects my fink path

after line 30 in the  /sw/share/coot/python/coot.py file. Remember, this IS a hack. Any coot update is likely to erase it although that same update is likely to fix the original "bug" (if that is what it is).


UPDATE 3:

Annndd my hack breaks MTZ reading capabilities. So, don't try it. Let's wait until a good solutions is out and about.

BTW, on my MBP 4,1 installing PyMol from fink works. But, if after loading a PDB making the window fullscreen screws up the display for good... until a hard restart. Be cautious.