Snow Leopard upgrade notes

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Snow Leopard Upgrade Notes


Link to a 23 page Arse Technica review

Any reason to wait?

No show-stoppers that I am aware of.

Adobe no longer supports CS3, but it still seems to work fine for me. Which is good, because it seems like I just bought the thing the other day (they came out with CS4 within a few weeks.)

Apple has a list of incompatibilities.

Intel Only

The first thing you need to know is this is an intel-only upgrade. Your ppc will forever be frozen at 10.5.X.


Here is some advice I found using google: Installing Snow Leopard. In general, the installation is as seamless as an OS X point update.


Annoyances that are tripping points which fall well short of genuine problems (like the kind of thing that would cause you to file a bug report) are listed below. Real problems (if any) will be listed in the subsequent section.

Pre-ordering was a HUGE mistake

I "pre-ordered" 10.6 from Apple the day they started accepting orders (within hours of the announcement). On August 29th, I received this email:

   Dear Apple Education Customer,

   Thank you for your recent order.

        Purchase Order#:   X
        Sales Order#:      X
        Ship-to Zip Code:  95064

   Due to an unexpected delay, we are unable to ship the following item(s)
   by the date that you were originally quoted:

     will now ship on or before
     Sep 08, 2009

I purchased one at my local campus bookstore and am trying to cancel this "pre-order."

Moral: Never give anyone money for anything in advance.

Previously updating to 2.4.0 in 10.5 created problems

If you compiled anything against 2.4.0 in 10.5, you might have a problem after upgrading to 10.6. The installation clobbers and installs something near to 2.3.3, which downgrades a few of the libraries.

This bit me for coot. Recompiling is the best solution (but see below for a dirty fix).

/etc/zshenv gets clobbered

This isn't really a complaint, but just a heads up. Probably this is similar for the other shell configuration files that live in /etc.

See ZSH on OS X if you need to replace anything.

Input Managers no longer work

If you used input managers (for example, "Edit in TextMate" would normally permit me to write this in a TextMate editor window and save to the Safari web page input window), you will find they no longer work, as this functionality is apparently no longer present in the operating system. Hopefully there will be some work-around. My guess is that it was a security hole.


For the above, simply set to open in 32-bit mode using the Get Info menu item in the Finder.

Similarly, doing so for System will permit use of preference panes and screen savers that are not yet 64-bit compatible.

Contextual Menu Items and Services

Services and Contextual Menu Items behave differently. The good news is you can edit the Services menu and remove a bunch of useless junk. The bad news is that the services are context-dependent, which is a great idea, but there is no over-ride when the OS guesses wrongly about the relevance of a service. Similarly, third-part Contextual Menu Items may not appear where you want them. (My workaround is to use ShortCuts or right-click over an open iTerm window).


None yet.


You have a choice:

Upgrade your 32-bit fink distribution

The original advantage was that more packages are available than in 64-bit fink, but this is no longer a significant difference.

My recommendation is that you install a 64-bit version of fink from scratch if you have 64-bit compatible hardware (which is everything intel apart from the first generation iMac (white) and ibooks (black and white)).

On some computers (macbook, first-generation intel iMacs), this is the only option.

I did an upgrade from 10.5 using the procedure described on the web page.

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

Upgrading 32-bit Fink from 10.5 to 10.6

Start a 64-bit fink installation from scratch

If you have a 64-bit capable machine, another option is to install a fully 64-bit fink. Not all fink packages are present in this distribution, and it is less tested.

You can have both on one machine. In that case, you can install 64-bit fink into a directory such as /sw64 so it can coexist but not interfere with what is in /sw.

For further details and discussion of the options, please visit the 64-bit Fink for 10.5 and 10.6 wiki page.

Specific to Crystallography

Pretty much everything you have compiled on 10.5 should work without intervention on 10.6.


If you have a binary version of coot that requires 2.4.0, you are out of luck. The upgrade downgraded, with no way to recover except to use a version of coot compiled with the earlier version of X-windows (or grab the missing library, see below).

How do I know, short of upgrading?

Use the otool -L command:

 % otool -L /usr/X11/lib/libfontconfig.1.dylib | grep fontconfig
        /usr/X11/lib/libfontconfig.1.dylib (compatibility version 5.0.0, current version 5.0.0)

% otool -L /sw/bin/coot-real   | grep fontconfig
        /usr/X11/lib/libfontconfig.1.dylib (compatibility version 5.0.0, current version 5.0.0)

As long as the compatibility version that appears for this library in coot-real is less than or equal to the one in /usr/X11/lib, you should be fine.

Dirty, unofficial fix

If you don't mind messing with your system files, you can move your copy of /usr/X11/lib/libfontconfig.1.dylib out of the way and replace it with one from 10.5 2.4.0. You can grab a copy of /usr/X11/lib/libfontconfig.1.dylib with the required compatibility version here.

This will restore coot's functionality until the next OS X point upgrade (which is why this is not a recommended solution).

CCP4 and Mosflm

Everything previously compiled should just work. Mosflm fails to compile with the new gcc4.2 compiler supplied by Apple. You can fix this by editing the file


and commenting out or otherwise removing the line

char *strcat( char *, const char *)

Then it compiles, and runs, even for 64-bit.

Having said that, the newest version mosflm 7.0.5 and the accompanying imosflm work better (albeit as 32-bit).

As an added bonus, imosflm works with the 10.6-supplied tcl/tk (aqua version) and /usr/bin/wish8.4 so you don't have to install anything else.

I found making an alias like this helpful (bash and zsh):

alias imosflm='CCP4_BROWSER=Safari    MOSFLM_WISH=/usr/bin/wish8.4    MOSDIR=${PWD}    ${CBIN}/imosflm'

although you might prefer simply to export these variables.

64-bit fink

If you use the 64-bit version of fink, you will be able to install fully 64-bit versions of coot and ccp4 with no extra effort. The 32-bit fink will still work if you prefer not to inhabit the cutting edge.

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