anyone know if upgrading OS X to Leopard might effect Chimera (or have reason to think it might)? -Jeff
I took the plunge and upgraded to Leopard. The Aqua version of Chimera seems to run fine (or at least as well as on Tiger). The X11 version has some problems. In Leopard Apple has made significant changes to X11 (see e.g. http://lists.apple.com/archives/X11-users/2007/Oct/msg00065.html) . If you launch Chimera, it seems to hang (icon keeps bouncing in the dock), but if you quit X11 it will actually run. As soon as you quit X11, it will launch a different version of X11 (/usr/X11/X11.app instead of /Applications/Utilities/X11.app). On Oct 30, 2007, at 2:42 PM, William Jeffrey Triffo wrote:
anyone know if upgrading OS X to Leopard might effect Chimera (or have reason to think it might)?
-- Mark
Just a quick follow-up; I see tons of these messages in /var/log/ system.log: Nov 2 09:50:15 gort [0x0-0x322322].edu.ucsf.cgl.chimera[87740]: Break on __THE_PROCESS_HAS_FORKED_AND_YOU_CANNOT_USE_THIS_COREFOUNDATION_FUNCTIONALITY___YOU_MUST_EXEC__ () to debug. They seem to be happening only on start-up of Chimera. On Nov 2, 2007, at 9:48 AM, Mark Moll wrote:
I took the plunge and upgraded to Leopard. The Aqua version of Chimera seems to run fine (or at least as well as on Tiger). The X11 version has some problems. In Leopard Apple has made significant changes to X11 (see e.g. http://lists.apple.com/archives/X11-users/2007/Oct/msg00065.html) . If you launch Chimera, it seems to hang (icon keeps bouncing in the dock), but if you quit X11 it will actually run. As soon as you quit X11, it will launch a different version of X11 (/usr/X11/ X11.app instead of /Applications/Utilities/X11.app).
On Oct 30, 2007, at 2:42 PM, William Jeffrey Triffo wrote:
anyone know if upgrading OS X to Leopard might effect Chimera (or have reason to think it might)?
-- Mark
Hi Mark, Thanks for reporting the Chimera X11 startup problem on Leopard. We are about to put out a production release of Chimera and will fix this problem before the release. If Chimera detects no X11 server running when you try to start it, then it tries to start it. Maybe there is some fight between the Leopard's new ability to auto-start the X server and Chimera's both trying to act at the same time. Tom
Tom & Mark, Tom, I'm sure you are already aware, but just in case you're not: the build for X11 has changed in Mac OS X Leopard to one based on X.org from an XFree-based effort. There are a number of issues with this at present that are being discussed in Apple's X11 mailing list (Mark's post has a link to this). They are also informally releasing patches there, but I believe the current patch doesn't address the issue Marks refers to. Mark, You could "unwind" back to the X11 used in Tiger--there are instructions on how to do this on the X11 mailing list. Some might argue you're better to wait for updates to the new version--? As for me, I'm staying with Tiger until the X11 issues are resolved as my work on my current contract needs it to be behaving! Grant
Hi Mark,
Thanks for reporting the Chimera X11 startup problem on Leopard. We are about to put out a production release of Chimera and will fix this problem before the release. If Chimera detects no X11 server running when you try to start it, then it tries to start it. Maybe there is some fight between the Leopard's new ability to auto-start the X server and Chimera's both trying to act at the same time.
Tom
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- ------------------------------------------------------------------- Grant Jacobs Ph.D. BioinfoTools ph. +64 3 478 0095 (office, after 10am) PO Box 6129, or +64 27 601 5917 (mobile) Dunedin, gjacobs@bioinfotools.com NEW ZEALAND. Bioinformatics tools: deriving knowledge from biological data Bioinformatics tools - software development - consulting - training 15 years experience in bioinformatics ready to solve your problem Check out the website for more details: http://www.bioinfotools.com The information contained in this mail message is confidential and may be legally privileged. Readers of this message who are not the intended recipient are hereby notified that any use, dissemination, distribution or reproduction of this message is prohibited. If you have received this message in error please notify the sender immed- iately and destroy the original message. This applies also to any attached documents.
The latest Chimera Mac daily build (Nov 5, 2007) works on Mac OS 10.5 Leopard (tested on Intel Mac). http://www.cgl.ucsf.edu/chimera/alpha-downloads.html Earlier Chimera versions did not start-up correctly on Leopard -- no Chimera window was displayed. The problem was that a new Leopard feature is to automatically start the X11 window server. Chimera also tries to automatically start he X11 server. When both Leopard and Chimera tried to start X11 it did not work correctly. The new Chimera code does not try to start X11.app on Leopard, letting Leopard do it. An error message is displayed in the Chimera reply log when Chimera starts on Leopard about an unprocessed Apple event. We believe this is a Python problem. It does not appear to cause any problem in Chimera operation. It will be fixed in a future release. Tom
participants (4)
-
Grant Jacobs
-
Mark Moll
-
Tom Goddard
-
William Jeffrey Triffo