Bug 80464 – [science overlay] sci-chemistry/jana2000-ebuild

• Product: Gentoo Linux
• Status: CONFIRMED ---

[Description Jan Marten Simons 2005-02-02 07:17:32 UTC]

I've checked the ebuild and it's working here.
Suggested category: sci-misc, until there are enough ebuilds to justify sci-xtal (prefered) or sci-crystallography.

JANA2000 is a system for solving and refinement of regular, modulated and composite structures from monocrystal and powder diffraction data. It is a freeware available for most UNIX workstations like FORTRAN77 and C sources and for PC like a compiled program for Windows. JANA2000 has been developed with Lahey Fortran 95 compiler. 

Basic features of JANA2000  
  Integrates all usual tasks of the structure analysis except plotting program and direct methods. 
  For direct methods Jana can directly call SIR97 or EXPO. 
  Works with both single crystal and powder data 
  Works with both X-ray and neutron data 
  Works with ordinary, modulated and composite structures 
  Reads output from many diffractometer types and can merge data sets from various sources 
  Works with various types of twinned crystals and overlapped reflections 
  Can read and export SHELX data and CIF 
  Support for commensurate structures 
  Support for multipole refinement and Anharmonic displacement parameters 
  Enables f' and f'' refinement 
  Enables special modulation functions and orthogonalization method 
  Calculates and plots x4 and t contour maps for modulated structures 
  Calculates and plots (joint) probability density functions 
  Calculates and plots various parameters like a function of t 
  All tools are integrated in a unific user interface 


Limitations  
  No automatic structure solution 
  Does not contain direct methods and plotting program 
  Neutron TOF powder data not supported 

Reproducible: Always
Steps to Reproduce:




Maybe I missed some dependencies.

[Comment 1 Jan Marten Simons 2005-02-02 07:18:21 UTC]

Created attachment 50210 [details]
sci-misc/jana2000-ebuild

[Comment 2 Jan Marten Simons 2005-02-02 07:19:03 UTC]

Created attachment 50211 [details, diff]
patch to select the right CC in the makefile

[Comment 3 Donnie Berkholz (RETIRED) 2006-06-23 20:49:45 UTC]

Perhaps the package should be named jana instead, since they apparently plan to start releasing 2006 versions rather than 2000.

[Comment 4 Jan Marten Simons 2006-06-25 04:49:48 UTC]

To me it rather sounds like we should at least slot both versions then, if not using two seperate packages, as Jana2006 seems to be a new major release in normal linux terms nad some people might actually want to use the old version to reproduce results from older refinements.

[Comment 5 Donnie Berkholz (RETIRED) 2006-06-25 14:36:10 UTC]

Slots are only for using when the actual package itself is installed in a slottable manner. If that's the case, then sure. Otherwise, people are free to upgrade/downgrade/mask as they please.

[Comment 6 Hannes Krüger 2009-07-09 20:28:04 UTC]

Created attachment 197396 [details]
ebuild for jana2000

ebuild for the "final" jana2000 verision (20071218)

[Comment 7 Hannes Krüger 2009-07-09 20:29:51 UTC]

Created attachment 197397 [details, diff]
patch for Makefile

This patch sets up the Makefile for g77

[Comment 8 Hannes Krüger 2009-07-09 20:31:07 UTC]

Created attachment 197398 [details, diff]
patch for Makefile

This patch changes the makefile for using gfortran

[Comment 9 Hannes Krüger 2009-07-09 20:40:47 UTC]

I would suggest sci-chemistry, since all crystallography related packages are there already.

for the package-name I suggest jana2000, since this can stay independent of a future jana2006 package.
Alternatively, the package name could be jana with a slot "2000" (?is that possible?) and the future jana2006 will have its own slot.

[Comment 10 Hannes Krüger 2009-07-20 22:23:42 UTC]

Created attachment 198646 [details, diff]
new patch

includes LDFLAGS now

[Comment 11 Hannes Krüger 2009-07-20 22:24:46 UTC]

Created attachment 198649 [details, diff]
new patch

includes LDFLAGS now

[Comment 12 Justin Lecher (RETIRED) 2009-07-21 06:38:34 UTC]

Looks good, I will commit it tonight.

[Comment 13 Hannes Krüger 2010-12-16 23:37:21 UTC]

The most recent update of the ebuild on 16 Dec 2010
broke it.

The problem is that $(tc-getFC) returns a lengthy string such as "x86_64-pc-linux-gnu-gfortran", therefore the string comparison in src_unpack fail and patches are not applied
Just by replacing "=="  with  "=~"  the ebuild will be repaired.

Can somebody with the permissions to commit plase correct this?!
thanks

[Comment 14 Justin Lecher (RETIRED) 2010-12-17 08:41:02 UTC]

done.