From OS X Scientific Computing

You can install my Fink Pre-Compiled Binaries to save yourself some time

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.

What is Available

First, please make certain you understand that these are not official fink packages. They are mine, and are provided informally, as-is, with no warranty or guarantee of anything. If this worries you, you are better off compiling your own software.

Make certain you use the right one for your processors and operating system.

Fink binary 64-bit distribution for 10.6 intel only

This is a live fink distribution that absolutely must be installed into /sw64 on a 64-bit-capable intel machine with OS X 10.6 Here is what is currently available in my

fink_intel_10.6_64bit repository.

Fink binary 32-bit distribution for 10.6 intel only

This is a live fink distribution that must be installed into /sw on any intel machine with OS X 10.6. Here is what is currently available in my

fink_intel_10.6_32bit repository.

This was the result of an upgrade from 10.5 using the procedure described on the Fink project web page.

I've copied this verbatim, but check the link in case of revisions:

To upgrade, follow a four step process. 

Step 1: edit the file /sw/etc/fink.conf, adding a line to it which reads NoAutoIndex: true 
(You may need to use sudo to obtain the correct permissions to edit this file.) 

Step 2: run the command fink reinstall fink in order to tell fink that you are now on 10.6. 
(If you encounter a message about package database corruption, run fink index -f and try this step again.) 

Step 3: run the command fink update fink to get the latest fink for 10.6. 

Step 4: run the command fink install perl588-core to replace the version of perl 
which Apple changed during the OS X upgrade, in case you have fink packages which depend on it.

Fink binary 32-bit distribution for 10.5 ppc only

This is a live fink distribution that must be installed into /sw on any PPC machine with OS X 10.5. Here is what is currently available in my

fink_ppc_10.5 repository.

Fink binary 32-bit distribution for 10.5 intel only

This is a frozen fink distribution that must be installed into /sw on any intel machine with OS X 10.5. I'm keeping this on the server only to avoid breakage for users who haven't updated. If you have 10.5 intel, you should upgrade to 10.6.

I have no way to update or trouble-shoot older operating system versions. Sorry.

Here is what is currently available in my

fink_intel_10.5_only FROZEN repository.

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 the most current OS X release. (10.6 on intel, or 10.5.8 on ppc)

2. Make sure you have installed the most current Xcode (compilers, etc) from the install disk or from Apple's web site.

3. If you are on 10.5 ppc, install the latest X11 from here: http://xquartz.macosforge.org/trac/ (The one originally distributed with 10.5 is badly broken). For intel, use the X11.app that comes with 10.6 and gets installed by default.

All of this is summarized, with links, on the Quick Start page.

Install Fink at /sw (default basepath) or /sw64 for the 64-bit version

Unless you plan to use my 64-bit fink distribution, you should install fink into /sw, which is the default location. This is what happens normally when you install the fink binary. Follow the directions on that webpage.

If you want to install the 64-bit version and use my repositories, you must install into /sw64. I have to do this since /sw is already taken on my machine. The only way to do this is to Bootstrap Install from Sourcecode into /sw64 as directed on the link.

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:

source /sw*/bin/init.sh

where /sw* is either /sw or /sw64.

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

Edit the file /sw/etc/apt/sources.list

(or /sw64/etc/apt/sources.list ) and add the following sets lines to the bottom of that file:

Specific to 10.6

sources.list for 10.6 intel only

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


sudo apt-get update
sudo apt-get install ccp4


fink -b  install coot


sudo apt-get install coot


sudo apt-get dist-upgrade

The first or third command installs or updates ccp4, the fourth or fifth installs or updates coot, and the final 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, but sadly it seems you can't use it if you have the head directory named /sw64 (so use sudo apt-get instead)."

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.

Getting your fink installation to use packages that I have pre-compiled