[Bug 482757] New: Review Request: objcryst-fox - Viewing and solving crystal structures from powder diffraction data - package-review

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Red Hat Bugzilla

27 Jan 2009 27 Jan '09

9:43 p.m.

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Summary: Review Request: objcryst-fox - Viewing and solving crystal structures from powder diffraction data

https://bugzilla.redhat.com/show_bug.cgi?id=482757

Summary: Review Request: objcryst-fox - Viewing and solving crystal structures from powder diffraction data Product: Fedora Version: rawhide Platform: All OS/Version: Linux Status: NEW Severity: medium Priority: low Component: Package Review AssignedTo: nobody@fedoraproject.org ReportedBy: pascal22p@parois.net QAContact: extras-qa@fedoraproject.org CC: notting@redhat.com, fedora-package-review@redhat.com Estimated Hours: 0.0 Classification: Fedora

Spec URL: http://svn.debroglie.net/specs/trunk/objcryst-fox.spec SRPM URL: http://fedora.debroglie.net/SRPMS/9/objcryst-fox-1.8.0-1.fc9.src.rpm

Description: The FOX program was made for the ab initio crystal structure solution from diffraction data (mostly powder diffraction data). Its most interesting features for ab initio structure determination are: * a versatile description of the crystal contents: either isolated atoms, molecules described using a bond length, bond angles and dihedral angles, and polyhedra for inorganic compounds. You can describe your structure by using any combination of groups of atoms, using a chemist's or crystallographer knowledge about the connectivity in your sample to constrain possible solutions; * an automatic correction for special positions and shared atoms between polyhedra, suitable for global optimization algorithms; * the ability to use simultaneously multiple powder patterns (X-rays, neutrons), as well as single crystal data (e.g. extracted from a powder pattern); * smart global optimization algorithms which can get out of false minima; * a graphical interface with a 3D crystal structure view, with live updates during the optimization process. This program can be used also for educational purposes, to show a 3D display of Crystal structures, and the associated powder pattern(s) (see how adding atoms, changing the lattice, or changing the spacegroup affects the powder spectrum and the 3D structure).

webpage : http://vincefn.net/Fox/

rpmlint is quiet.

This package needs libnewmat : https://bugzilla.redhat.com/show_bug.cgi?id=479978

I need a sponsor, these are my first 2 packages.

Cheers, Pascal

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Red Hat Bugzilla

27 Jan 27 Jan

10:23 p.m.

New subject: [Bug 482757] Review Request: objcryst-fox - Viewing and solving crystal structures from powder diffraction data

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https://bugzilla.redhat.com/show_bug.cgi?id=482757

manuel wolfshant wolfy@nobugconsulting.ro changed:

What |Removed |Added ---------------------------------------------------------------------------- Blocks| |177841

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Red Hat Bugzilla

10:24 p.m.

New subject: [Bug 482757] Review Request: objcryst-fox - Viewing and solving crystal structures from powder diffraction data

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https://bugzilla.redhat.com/show_bug.cgi?id=482757

manuel wolfshant wolfy@nobugconsulting.ro changed:

What |Removed |Added ---------------------------------------------------------------------------- Depends on| |479978

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Red Hat Bugzilla

6 Feb 6 Feb

9:08 p.m.

New subject: [Bug 482757] Review Request: objcryst-fox - Viewing and solving crystal structures from powder diffraction data

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https://bugzilla.redhat.com/show_bug.cgi?id=482757

--- Comment #1 from Pascal pascal22p@parois.net 2009-02-06 16:08:23 EDT --- New srpm: http://fedora.debroglie.net/SRPMS/10/objcryst-fox-1.8.0-2.fc10.debroglie.src... New spec: http://svn.debroglie.net/specs/trunk/objcryst-fox.spec

I runned the spec through mock, fedora 9/10 and epel 5 both x86_64 are ok. I corrected some errors on the build require

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Red Hat Bugzilla

14 Feb 14 Feb

1:29 p.m.

New subject: [Bug 482757] Review Request: objcryst-fox - Viewing and solving crystal structures from powder diffraction data

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https://bugzilla.redhat.com/show_bug.cgi?id=482757

--- Comment #2 from Pascal pascal22p@parois.net 2009-02-14 08:29:39 EDT --- Update to match new upstream release.

srpm: http://fedora.debroglie.net/SRPMS/10/objcryst-fox-1.8.0.3-1.fc10.debroglie.s... spec: http://svn.debroglie.net/specs/trunk/objcryst-fox.spec

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Red Hat Bugzilla

11:03 p.m.

New subject: [Bug 482757] Review Request: objcryst-fox - Viewing and solving crystal structures from powder diffraction data

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MERCIER bioinfornatics@gmail.com changed:

What |Removed |Added ---------------------------------------------------------------------------- CC| |bioinfornatics@gmail.com

--- Comment #3 from MERCIER bioinfornatics@gmail.com 2009-02-14 18:03:16 EDT --- what's the rpmlint issue: rpmlint /home/builder/SPEC/objcryst-fox.spec

rpmlint /home/builder/SRPMS/objcryst-fox-1.8.0.3-1.fc10.debroglie.src.rpm

rpmlint /home/builder/RPMS/....

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Red Hat Bugzilla

18 Feb 18 Feb

9:42 a.m.

New subject: [Bug 482757] Review Request: objcryst-fox - Viewing and solving crystal structures from powder diffraction data

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https://bugzilla.redhat.com/show_bug.cgi?id=482757

--- Comment #4 from Pascal pascal22p@parois.net 2009-02-18 04:41:59 EDT --- rpmlint is silent. I runned the spec through mock, fedora 9/10 and epel 5 both x86_64 and i386 are ok.

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Red Hat Bugzilla

4:13 p.m.

New subject: [Bug 482757] Review Request: objcryst-fox - Viewing and solving crystal structures from powder diffraction data

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https://bugzilla.redhat.com/show_bug.cgi?id=482757

Pierre-YvesChibon pingou@pingoured.fr changed:

What |Removed |Added ---------------------------------------------------------------------------- CC| |pingou@pingoured.fr

--- Comment #5 from Pierre-YvesChibon pingou@pingoured.fr 2009-02-18 11:13:43 EDT ---

I cannot do the review since I'm not a sponsor but I looked at the spec file

Several minor points:

* You can use the macro %{name} instead of Fox in a number of places in the spec ie:

...

Source0: http://dfn.dl.sourceforge.net/sourceforge/objcryst/Fox-1.8.0.3-R1088.tar.bz2

becomes

...

Source0: http://dfn.dl.sourceforge.net/sourceforge/objcryst/%%7Bname%7D-%%7Bversion%7...

that can save you some problem for later update

* Please add an extra \n between two change in the changelog (some tool used within Fedora need these white line between the change): ie:

...

Sat Feb 14 2009 Pascal < pascal22p@parois.net > - 1.8.0.3-1

Fixed reading, writing files and display of labels in the linux unicode version of Fox

Fri Feb 06 2009 Pascal < pascal22p@parois.net > - 1.8.0-2

becomes

...

Sat Feb 14 2009 Pascal < pascal22p@parois.net > - 1.8.0.3-1

Fixed reading, writing files and display of labels in the linux unicode version of Fox

It might be nice also to give to the reviewer an input file and an output file so that the software could actually be tested :)

You might also be interested to join the SciTech SIG: https://fedoraproject.org/wiki/Category:SciTech_SIG

...

Fri Feb 06 2009 Pascal < pascal22p@parois.net > - 1.8.0-2

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Red Hat Bugzilla

21 Feb 21 Feb

6:22 p.m.

New subject: [Bug 482757] Review Request: objcryst-fox - Viewing and solving crystal structures from powder diffraction data

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https://bugzilla.redhat.com/show_bug.cgi?id=482757

--- Comment #6 from Pascal pascal22p@parois.net 2009-02-21 13:22:57 EDT --- (In reply to comment #5)

...

You can use the macro %{name} instead of Fox in a number of places in the

The name of the package is not the name of the archive. I used the same name as debian used for their deb: http://packages.debian.org/fr/sid/objcryst-fox

...

Please add an extra \n between two change in the changelog (some tool used

Done in the spec but new srpm/rpm not updated

...

It might be nice also to give to the reviewer an input file and an output file so that the software could actually be tested :)

There are example files in /usr/share/doc/objcryst-fox... A tutorial is here: http://vincefn.net/Fox/Tutorials

...

You might also be interested to join the SciTech SIG: https://fedoraproject.org/wiki/Category:SciTech_SIG

Yes, good idea, I'll see when this get pushed in fedora.

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Red Hat Bugzilla

11 Apr 11 Apr

4:06 p.m.

New subject: [Bug 482757] Review Request: objcryst-fox - Viewing and solving crystal structures from powder diffraction data

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--- Comment #7 from Pascal pascal22p@parois.net 2009-04-11 11:06:21 EDT --- new srpm: http://fedora.debroglie.net/SRPMS/10/objcryst-fox-1.8.1.2-1.fc10.debroglie.s... spec: http://svn.debroglie.net/specs/trunk/objcryst-fox.spec

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Red Hat Bugzilla

8 Jul 8 Jul

6:10 p.m.

New subject: [Bug 482757] Review Request: objcryst-fox - Viewing and solving crystal structures from powder diffraction data

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https://bugzilla.redhat.com/show_bug.cgi?id=482757

Jussi Lehtola jussi.lehtola@iki.fi changed:

What |Removed |Added ---------------------------------------------------------------------------- CC| |jussi.lehtola@iki.fi

--- Comment #8 from Jussi Lehtola jussi.lehtola@iki.fi 2009-07-08 13:10:05 EDT --- - Use %global instead of %define. Put the revision definition at the top of the spec file: %global revision R1119

- Include the revision in the release tag: Release: 2.%{revision}%{?dist} (every time you update the spec file update the release tag if the version hasn't been updated).

- No explicit Requires: are allowed for libraries; drop Requires: wxGTK, fftw, freeglut http://fedoraproject.org/wiki/Packaging/Guidelines#Explicit_Requires

- Drop the commented patch line #%patch0 -p0

- Instead of find . -type d -name .svn -print0 | xargs -0r rm -rf you can just use find . -name *.svn -exec rm -rf {} ; (or maybe even find . -name *.svn -delete; )

- Preserve time stamps by adding -p to install commands.

- Use "rm" instead of "unlink".

- Install the pixmap to /usr/share/pixmaps, drop the hicolor stuff. (Also, you were missing Requires: hicolor-icon-theme.)

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Red Hat Bugzilla

6:24 p.m.

New subject: [Bug 482757] Review Request: objcryst-fox - Viewing and solving crystal structures from powder diffraction data

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--- Comment #9 from Jussi Lehtola jussi.lehtola@iki.fi 2009-07-08 13:24:43 EDT --- (In reply to comment #8)

...

Instead of

find . -type d -name .svn -print0 | xargs -0r rm -rf you can just use find . -name *.svn -exec rm -rf {} ; (or maybe even find . -name *.svn -delete; )

Ugh, the .svn's are directories, so what you want to run is find . -name .svn -exec rm -rf {} ;

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Red Hat Bugzilla

5 Aug 5 Aug

10 a.m.

New subject: [Bug 482757] Review Request: objcryst-fox - Viewing and solving crystal structures from powder diffraction data

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--- Comment #10 from Jussi Lehtola jussi.lehtola@iki.fi 2009-08-05 05:00:28 EDT --- ping?

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Red Hat Bugzilla

6:21 p.m.

New subject: [Bug 482757] Review Request: objcryst-fox - Viewing and solving crystal structures from powder diffraction data

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--- Comment #11 from Pascal Parois pascal22p@parois.net 2009-08-05 13:21:52 EDT --- Sorry, notification mails got lost in my mailbox, I am still here, just very busy.

So I'll look at this later. sometimes this month, as soon as I submit my thesis. As I need newmat-c++, I'll look at this one first (https://bugzilla.redhat.com/show_bug.cgi?id=479978)

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Red Hat Bugzilla

16 Sep 16 Sep

12:16 p.m.

New subject: [Bug 482757] Review Request: objcryst-fox - Viewing and solving crystal structures from powder diffraction data

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--- Comment #12 from Pascal Parois pascal22p@parois.net 2009-09-16 07:16:43 EDT --- I am updating this package and ran into an issue. The release version does not compile, so I would like to use the beta version instead (which is working) but the versioning is 1.8.X

The current version I have is 1.8.1 which is "newer" than 1.8.X. :( I don't if the next version will be 1.8.2 or 1.9.

Any comments welcome

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Red Hat Bugzilla

8 May 8 May

2:01 a.m.

New subject: [Bug 482757] Review Request: objcryst-fox - Viewing and solving crystal structures from powder diffraction data

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--- Comment #13 from MERCIER Jonathan bioinfornatics@gmail.com 2010-05-07 21:01:44 EDT --- nobody for review this package?

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8:32 a.m.

New subject: [Bug 482757] Review Request: objcryst-fox - Viewing and solving crystal structures from powder diffraction data

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--- Comment #14 from Pascal Parois pascal22p@parois.net 2010-05-08 03:32:14 EDT --- By the way, new version: http://fedora.debroglie.net/SRPMS/12/objcryst-fox-1.9.0.2-1.R1215.fc12.src.r... http://fedora.debroglie.net/RPMS/12/x86_64/objcryst-fox-1.9.0.2-1.R1215.fc12...

http://redmine.debroglie.net/projects/debroglie/repository/entry/specs/trunk...

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12 Nov 12 Nov

7:27 p.m.

New subject: [Bug 482757] Review Request: objcryst-fox - Viewing and solving crystal structures from powder diffraction data

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--- Comment #15 from Pascal Parois pascal22p@parois.net 2010-11-12 14:27:48 EST --- http://fedora.debroglie.net/RPMS/14/i386/objcryst-fox-1.9.0.2-1.R1269.fc14.i... http://fedora.debroglie.net/SRPMS/14/objcryst-fox-1.9.0.2-1.R1269.fc14.src.r...

https://redmine.debroglie.net/projects/debroglie/repository/raw/specs/trunk/...

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10 Apr 10 Apr

4:34 a.m.

New subject: [Bug 482757] Review Request: objcryst-fox - Viewing and solving crystal structures from powder diffraction data

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David Nalley david@gnsa.us changed:

--- Comment #16 from David Nalley david@gnsa.us 2011-04-09 23:34:22 EDT --- Pascal are you still interested in this packaging this?? I'll be happy to work to sponsor you if you are.

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9:10 a.m.

New subject: [Bug 482757] Review Request: objcryst-fox - Viewing and solving crystal structures from powder diffraction data

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Pascal Parois pascal22p@parois.net changed:

--- Comment #17 from Pascal Parois pascal22p@parois.net 2011-04-10 04:10:07 EDT --- Yes but I am a bit busy at the moment

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16 Dec 16 Dec

9:57 a.m.

New subject: [Bug 482757] Review Request: objcryst-fox - Viewing and solving crystal structures from powder diffraction data

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--- Comment #18 from Jussi Lehtola jussi.lehtola@iki.fi 2011-12-16 04:57:25 EST --- Ping Pascal?

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10:46 a.m.

New subject: [Bug 482757] Review Request: objcryst-fox - Viewing and solving crystal structures from powder diffraction data

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--- Comment #19 from Pascal Parois pascal22p@parois.net 2011-12-16 05:46:17 EST --- Still here.

Last update (from august): http://depot.debroglie.net/fedora/RPMS/15/repoview/objcryst-fox.html https://svn.parois.net/debroglie/specs/trunk/objcryst-fox.spec

It's outdated, the 1.9.7 is out. I put it on my todo list.

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