Re: [ccp4bb] COOT not connected to PHENIX
Hi, This is why the right way to distribute *nix software is to distribute software itself and ask the end-user to get all the dependencies (not that hard these days). it is a wonderful idea, apart from two tiny nuances: 1) many have no idea about what the command line is, and 2) asking users going through the trouble of installing dependencies will scare them away from the software. Personally, I do not use programs that do not work right out of the box or take more than a minute to make it run. So, I would rather let the majority use whatever works, and let a few gurus count versions of Python in various software and how much space they take. Pavel
Re: [ccp4bb] COOT not connected to PHENIX
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Grand - with every python script one has to distribute a specific python version. More food for my prejudice against python ;-) Tim On 10/26/2011 12:15 AM, Paul Emsley wrote: FYI, from version 0.7, I will not distribute binaries without python. Paul. On 25/10/11 17:02, Yuri wrote: I installed the version with python embedded in coot And it works!! Thanks a lot!! On Tue, 25 Oct 2011 11:41:38 -0700, Nathaniel Echols wrote: On Tue, Oct 25, 2011 at 11:40 AM, Yuriyuri.pom...@ufl.edu wrote: Now here comes the stupid question... How do I fix it? Install a different coot version or is it something in my architecture? Install a different Coot. If you're downloading from Paul Emsley's page, you need a package with python in the file name. I have no idea whether the Linux binaries distributed by CCP4 have Python or not (the Mac version definitely does). -Nat - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFOp8XQUxlJ7aRr7hoRAm9tAKCFFKmPIS+W7puqehbnJYuFhhQR5wCfUo+G ZAeWO1qzOhhW2xXTqLgPMpI= =53xa -END PGP SIGNATURE-
Re: [ccp4bb] COOT not connected to PHENIX
On Wed, 2011-10-26 at 10:33 +0200, Tim Gruene wrote: with every python script one has to distribute a specific python version ... and with every program one has to distribute binaries for every platform... more food for my prejudice against software ;-) This really is not about python, it's about distributing with or without dependencies. And you are absolutely right about that: for example, ccp4-6.2.0 comes with python2.6.7 embedded, and, if one goes with defaults and downloads coot with it, python2.6 in coot's lib folder. Same with phenix - you get python2.7 with it and python2.4 with pymol0.99 that comes with it. By the way, I already have another pymol that I compiled myself (1.4) and the one from ubuntu repositories (1.2). Except for the latter, each carries its own copy of whichever python it needs. Every single python avatar takes 50-100Mb of space, which is fortunately not in short supply. This is why the right way to distribute *nix software is to distribute software itself and ask the end-user to get all the dependencies (not that hard these days). It is fully understood, of course, that people that do this for living find it more troublesome to deal with me whining about how their software is screwing up my matplotlib than to just give me another python copy. What's an extra 50Mb between friends ;-) Cheers, Ed. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] COOT not connected to PHENIX
I experienced this same issue a while ago. When I attempt to reinstall coot using Fink (instructions on Bill Scott's coot page), I receive this error in Terminal: WARNING: While resolving dependency nose-py27 for package numpy-py27-1.5.1-1, package nose-py27 was not found. Reading build dependency for numpy-py27-1.5.1-1... WARNING: While resolving dependency nose-py27 for package numpy-py27-1.5.1-1, package nose-py27 was not found. Can't resolve dependency nose-py27 for package numpy-py27-1.5.1-1 (no matching packages/versions found) Exiting with failure. I had originally downloaded ccp4-6.2.0 (Mac version), and experienced no problems until I tried to open coot from PHENIX. Any suggestions on how to resolve this issue? Jaime From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Ed Pozharski [epozh...@umaryland.edu] Sent: Wednesday, October 26, 2011 9:24 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] COOT not connected to PHENIX On Wed, 2011-10-26 at 10:33 +0200, Tim Gruene wrote: with every python script one has to distribute a specific python version ... and with every program one has to distribute binaries for every platform... more food for my prejudice against software ;-) This really is not about python, it's about distributing with or without dependencies. And you are absolutely right about that: for example, ccp4-6.2.0 comes with python2.6.7 embedded, and, if one goes with defaults and downloads coot with it, python2.6 in coot's lib folder. Same with phenix - you get python2.7 with it and python2.4 with pymol0.99 that comes with it. By the way, I already have another pymol that I compiled myself (1.4) and the one from ubuntu repositories (1.2). Except for the latter, each carries its own copy of whichever python it needs. Every single python avatar takes 50-100Mb of space, which is fortunately not in short supply. This is why the right way to distribute *nix software is to distribute software itself and ask the end-user to get all the dependencies (not that hard these days). It is fully understood, of course, that people that do this for living find it more troublesome to deal with me whining about how their software is screwing up my matplotlib than to just give me another python copy. What's an extra 50Mb between friends ;-) Cheers, Ed. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] COOT not connected to PHENIX
I installed the version with python embedded in coot And it works!! Thanks a lot!! On Tue, 25 Oct 2011 11:41:38 -0700, Nathaniel Echols wrote: On Tue, Oct 25, 2011 at 11:40 AM, Yuri yuri.pom...@ufl.edu wrote: Now here comes the stupid question... How do I fix it? Install a different coot version or is it something in my architecture? Install a different Coot. If you're downloading from Paul Emsley's page, you need a package with python in the file name. I have no idea whether the Linux binaries distributed by CCP4 have Python or not (the Mac version definitely does). -Nat -- Yuri Pompeu
Re: [ccp4bb] COOT not connected to PHENIX
FYI, from version 0.7, I will not distribute binaries without python. Paul. On 25/10/11 17:02, Yuri wrote: I installed the version with python embedded in coot And it works!! Thanks a lot!! On Tue, 25 Oct 2011 11:41:38 -0700, Nathaniel Echols wrote: On Tue, Oct 25, 2011 at 11:40 AM, Yuriyuri.pom...@ufl.edu wrote: Now here comes the stupid question... How do I fix it? Install a different coot version or is it something in my architecture? Install a different Coot. If you're downloading from Paul Emsley's page, you need a package with python in the file name. I have no idea whether the Linux binaries distributed by CCP4 have Python or not (the Mac version definitely does). -Nat
