Getting your fink installation to use packages that I have pre-compiled
From OS X Scientific Computing
Please Note: I only have packages available for 10.5.x
I have no way to update or trouble-shoot older operating system versions. Sorry.
- I have a "live" (continuously updated) set of packages now for intel and a separate set for ppc. Do not mix them up.
Jump-start
I've backed up my 10.5.4 /sw directories for intel and ppc which you might be able to use if what is described below is problematic. I have no way to troubleshoot this.
For PowerPC and Intel Macs running OS X 10.5.x:
Introduction
This page describes how to get your current fink installation to look to mine for packages that I have pre-compiled. There are two reasons you might want to do this. The first is that fink officially only distributes pre-compiled binary (debian) packages for a subset of packages, i.e., those in the "stable" branch that have unrestricted licenses like GPL and LGPL. For that reason, none of the crystallography programs are distributed in pre-compiled form officially by fink. (Almost all of them are in the "unstable" branch of fink and many have restrictive licenses.) The second reason is that I have made some packages that are not available officially in fink. CNS is one such example. These are packages that exist in my personal "local" branch.
How-To
Here is all you need to do to configure your fink installation to automatically install my pre-compiled fink packages for crystallography (and other) programs. If you would rather manually install one or two packages, follow the linked example (in general a bad idea).
Before you begin
Please do the following three things in the order below:
1. Update to 10.5.4 (or the most current OS X release).
2. Make sure you have Xcode 3.0 or newer.
3. Install the latest X11 from here: http://xquartz.macosforge.org/trac/ (The one originally distributed with 10.5 is badly broken).
Install Fink at /sw (default basepath).
This is what happens normally when you install the fink binary. Follow the directions on that webpage.
Edit the file /sw/etc/fink.conf
You will have to activate the "unstable" branch of fink to do anything useful. ("Unstable" is paranoia-speak for "current".)
To do so, edit the file /sw/etc/fink.conf and add the final two entries to the line "Trees" so that it looks like this:
Trees: local/main stable/main stable/crypto unstable/main unstable/crypto
Update Fink Immediately
Be sure to issue all of the following commands:
fink selfupdate-rsync
or, alternatively
fink selfupdate-cvs
Make sure that worked. You should see a long string of output. On some restricted servers (like our campus wireless) this won't work. So pay attention to the output.
fink scanpackages; fink index fink update-all
Then, if you don't already have fink local directories, do this (it can't hurt, even if you never make use of this):
sudo mkdir -p /sw/fink/dists/local/main/finkinfo
sudo mkdir -p /sw/fink/dists/local/main/binary-darwin-powerpc
Run fink configure and enable the option to download packages from the binary distribution
Alternatively, you can edit the /sw/etc/fink.conf file and put the line
UseBinaryDist: true
at the bottom of the file.
Edit the file /sw/etc/apt/sources.list
and add the following sets lines to the bottom of that file:
Specific to 10.5
Use this only if you are running 10.5.X on intel.
sources.list for 10.5 intel only
or
sources.list for 10.5 ppc only
For 10.4 and earlier?
Sorry. I can no longer distribute ppc 10.4 packages.'
Run the following four commands:
fink scanpackages sudo apt-get update sudo apt-get dist-upgrade fink scanpackages
Install or update programs as with the following examples:
fink -b install ccp4
fink -b install coot
sudo apt-get dist-upgrade
The first command installs or updates ccp4, the second installs or updates coot, and the third command updates (or upgrades) all the packages to the most currently available version. "fink -b install" essentially means use "sudo apt-get install" where possible, and then build anything missing from the binary distribution that is needed as a dependency. So "fink -b install" is slightly more robust and foolproof than "sudo apt-get install"
These instructions are modified from those available in Fink's documentation.
Note to G4 PPC users
The package gmp that is built on my G5 PPC is incompatible with G4 processors. You will have to force-rebuild it manually:
fink rebuild gmp fink reinstall gmp gmp-shlibs
This bug causes coot to fail when running the "tips-gui.scm" file.
