Bug 505813 - Review Request: ballview - Molecule and protein visualisation and analysis
Summary: Review Request: ballview - Molecule and protein visualisation and analysis
Alias: None
Product: Fedora
Classification: Fedora
Component: Package Review
Version: rawhide
Hardware: All
OS: Linux
Target Milestone: ---
Assignee: Nobody's working on this, feel free to take it
QA Contact: Fedora Extras Quality Assurance
Depends On:
TreeView+ depends on / blocked
Reported: 2009-06-14 04:24 UTC by D Haley
Modified: 2010-03-29 06:08 UTC (History)
3 users (show)

Fixed In Version:
Doc Type: Bug Fix
Doc Text:
Clone Of:
Last Closed: 2010-02-19 21:19:53 UTC
Type: ---

Attachments (Terms of Use)

Description D Haley 2009-06-14 04:24:05 UTC
SPEC URL: http://dhd.selfip.com/427e/ballview-1.spec
SRPM URL: http://dhd.selfip.com/427e/ballview-1.2-1.fc10.src.rpm 

Koji Build:
F10: http://koji.fedoraproject.org/koji/taskinfo?taskID=1410847

RPMLint output:
]$ rpmlint  ../SRPMS/ballview-1.2-1.fc10.src.rpm ../RPMS/i386/ballview-*2-1.* ../RPMS/noarch/ballview-doc-1.2-1.fc10.noarch.rpm 
ballview.i386: E: explicit-lib-dependency libXmu
ballview.i386: W: shared-lib-calls-exit /usr/lib/libVIEW.so.1.2 exit@GLIBC_2.0
ballview-devel.i386: W: no-documentation
ballview-doc.noarch: W: file-not-utf8 /usr/share/doc/ballview/doxygen/latex/classBALL_1_1CreateSpectrumProcessor.tex
ballview-doc.noarch: W: file-not-utf8 /usr/share/doc/ballview/doxygen/latex/classBALL_1_1RotationalEntropyLoss.tex
5 packages and 0 specfiles checked; 1 errors, 4 warnings.

Without the libXmu requires, the build fails at configure time. Not sure what requires I should use here. As for the UTF-8 errors, I will fix them along with whatever comments are made here for -2. Sorry about that, limited time to spend on this and the build takes my poor little machine a long time to complete.

Bugs have been opened upstream :
-regarding the use of the exit() function
-Missing LGPL boilerplate on source files.
-Incorrectly written unit test
-Header file patches

Possible problems:
*The include subdir of the tarball has .iC files, which I have no idea what they are for. They appear to be C++ like, with heavy use of preprocessor macros, but why should this be in include? 
*One of the unit tests hangs (on the actual test itself, not the component being tested, as far as I can tell). I have therefore disabled make test, and opened an upstream bug.
*I removed smpflag support, as I suspect the makefiles of not being reliable when run in this fashion (I had a few problems building with -j 2, which were intermittent, which have not re-occurred since removal of smpflags).
*Enabling GSL and FFTW support modifies the licence to GPLv3. This can be disabled at configure time to match the closer upstream LGPL. However I wasn't entirely sure of fedora policy here, so I just enabled them and set the licence field accordingly.
*Ballview complains about missing python import "BALL" on startup and subsequently disables in-app python support. Wasn't sure how to fix this at this stage.

I would appreciate a co-maintainer if possible, as I am not entirely familiar with QT & SIP, and the package is somewhat large.

Comment 1 Susi Lehtola 2009-08-06 13:05:08 UTC
A few notes:

- The license of GSL, FFTW &c does not affect the license tag (Fedora policy). License should be lgpl.

- Drop the explicit Requires, they're automatically picked up by rpm.

- You can only define subpackages
 BuildArch:	noarch
on >= F11 and >= RHEL6.

- You can change
 find ./data/ -name \*.data -exec chmod 644 {} \;
 chmod 644 ./data/structures/test.btf
 chmod 644 ./source/STRUCTURE/smartsParserParser.y
 chmod 644 ./source/STRUCTURE/smartsParserLexer.l
 find ./ -name \*.h -executable -exec chmod 644 {} \;
 find ./ -name \*.C -executable -exec chmod 644 {} \;
 find data/ -name \*.data -exec chmod 644 {} \;
 chmod 644 data/structures/test.btf \
  source/STRUCTURE/smartsParserParser.y \
 find . -name \*.h -executable -exec chmod 644 {} \;
 find . -name \*.C -executable -exec chmod 644 {} \;

- Change
 BuildRequires:	qt-devel
 BuildRequires: qt4-devel
to get qt4. 

- Why do you remove header documentation? You could place them in the -doc package.

- Don't add an soversion yourself. This has to be done by upstream.

- Drop
 #Install documentation
 mkdir -p  %{buildroot}%{_docdir}/%{name}
 cp -Rp ./doc/BALLView %{buildroot}%{_docdir}/%{name}
 cp -Rp ./doc/doxygen %{buildroot}%{_docdir}/%{name}/doxygen
instead list these in the %doc of -doc.

- Instead of
as %{_libdir} starts with a /. Same thing with other directories.

Comment 2 Bug Zapper 2009-11-18 12:05:53 UTC
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Approximately 30 (thirty) days from now Fedora will stop maintaining
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Comment 3 D Haley 2009-11-19 12:11:06 UTC
I'm sorry, work has caught up to me, and I will not be able to attend to this package for the next two months. I have marked it FE-DEADREVIEW until then. If someone needs/wants it urgently, feel free to take the package over. 

I did make some of the changes you suggested, and will post this in the next few days.

Comment 4 Jason Tibbitts 2009-11-19 17:40:56 UTC
FYI, FE-DEADREVIEW is what we put in the "Blocks" field after we close a ticket due to inactivity.  I suspect you just wanted to drop this out of the review queue, which I've done with "NotReady".

BTW, the original package fails to build for me in mock on rawhide.  I get quite a lot of build output, and then:

creating dependencies for PYTHON/EXTENSIONS...
pyBALLSipHelper.C:8:30: error: sipBALLComposite.h: No such file or directory

and several similar errors.  I've also indicated the build failure in the whiteboard.  All of these whiteboard and blocker strings are documented in https://fedoraproject.org/wiki/Package_Review_Process if you're curious.

Comment 5 Jason Tibbitts 2010-01-25 23:13:07 UTC
This is still marked as failing to build; I'll close this ticket soon if that's not rectified.

Comment 6 D Haley 2010-02-19 21:19:53 UTC
Closing. I have no fedora machine at this time. For interest, I have uploaded a spec to fedorapeople.

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