Bug 222357

Summary:	[science overlay] sci-chemistry/modeller
Product:	Gentoo Linux	Reporter:	Justin Lecher (RETIRED) <jlec>
Component:	New packages	Assignee:	Default Assignee for New Packages <maintainer-wanted>
Status:	CONFIRMED ---
Severity:	enhancement	CC:	sci-chemistry, weigt.mathias
Priority:	Normal	Keywords:	EBUILD, InOverlay
Version:	unspecified
Hardware:	All
OS:	All
URL:	http://salilab.org/modeller
Whiteboard:	Science overlay
Package list:		Runtime testing required:	---
Attachments:	modeller-9.4.diff modeller-9.4.diff

Description Justin Lecher (RETIRED) gentoo-dev

2008-05-16 09:27:15 UTC

Version bump to 9.4.
The provided diff is adapted to the new version and includes the updates proposed in bug #127628.
Tested on x86 where it runs fine.

Comment 1 Justin Lecher (RETIRED) gentoo-dev

2008-05-16 09:30:41 UTC

Created attachment 153301 [details]
modeller-9.4.diff

Sorry, the ebuild for modeller is still in the science overlay, so I should report it to them. Nevertheless here is the diff towards the new version.

Comment 2 Justin Lecher (RETIRED) gentoo-dev

2008-05-16 11:32:54 UTC

Created attachment 153315 [details]
modeller-9.4.diff

Added python USE Flag,
this is needed if one wants to import python modules, because modeller needs them from version 2.3.

Comment 3 Donnie Berkholz (RETIRED) gentoo-dev

2008-05-16 17:51:34 UTC

Gotta find something to do about python 2.3, it's getting masked.

Comment 4 Justin Lecher (RETIRED) gentoo-dev

2008-05-16 18:05:01 UTC

Thats an upstream thing. Modeller runs fine as long you don't want do use modules from python.

[Quote]
The mod9v4 script uses a built-in copy of the Python 2.3 interpreter, but not the accompanying modules. To fix this problem, you could install Python 2.3 on your system (however, you only need the Python 2.3 modules if you are trying to import non-Modeller modules; you don't need them to run regular Modeller scripts, so you can ignore these warnings). Alternatively, don't use the mod9v4 script to run Modeller, but see the instructions above for running Modeller with Python.
[/Quote]

There is a workaround as mentioned (If you have Python 2.3 or 2.4 installed, then "/opt/mod/bin/modpy.sh python foo.py" will run Python on the same script.). How should this be included in the ebuild? Just a ewarn?

Comment 5 Mathias Weigt 2008-10-22 05:33:00 UTC

Version 9v5 is out
See the Modeller manual for a full change log:
http://salilab.org/modeller/9v5/manual/node38.html

Comment 6 Justin Lecher (RETIRED) gentoo-dev

2010-06-16 11:47:01 UTC

I bumped the version in the overlay.