Hi Andreas,
I managed to reproduce conditions when that strange message with pdb2pqr
appears and when not:
It appears if I download, build, and call tests.
It doesn't appear if I download, *call quilt push -a*, build, call tests.
It also appears if I build project at first time, then *call quilt push
-a*, and then build again.
This happens because of rules defined in debian/rules, and
pMC_mult_wrap.cpp and *.saved files in pdb2pka folder.
How can be solved manually?
after call quilt push -a, cd to pdb2pka, when remove *.saved files and run
command
swig -c++ -python -o pMC_mult_wrap.cpp pMC_mult.i
The same command as in `override_dh_auto_configure` in debian/rules. When I
noticed that, I run build in verbose mode.
Scons also builds all .cpp files, so, when it is run after swig regenerates
pMC_mult_wrap.cpp, it uses version of that file which correspond to
unpatched sources, Because in any previous run of `override_dh_auto_clean`
it is reset to version which is stored in .saved. That's why I think there
should be different order of commands, and this should fix that problem. At
least I tried to reproduce, it doesn't appear any more. Please check my
recent commit, and tell me if the error still appears.
There is also 1 problem with this package - in last test it can't load apbs
package, even if it is installed. pdb2pqr doesn't fail, still some
functionality which involves apbs call, is not available. For the moment I
worked on that package I decided to postpone it and to fix later. Now I'll
try to install apbs from sources and check where the problem is - if you
don't mind.
2016-06-29 15:54 GMT+03:00 Andreas Tille <[email protected]>:
> Hi Tanya,
>
> On Wed, Jun 29, 2016 at 01:35:38PM +0300, merlettaia wrote:
> >
> > 2016-06-22 11:39 GMT+03:00 Andreas Tille <[email protected]>:
> >
> > > > Conservation-code,
> > >
> > > I realised that there is no such matrix blosum63.bla even in the source
> > > package (only 62). Similarliy with swissprot1.distribution - we just
> > > have swissprot.distribution (without "1"). Do you have any explanation
> > > for this?
> >
> > I removed this from test and added some description (describing this
> > behavior) to README.test instead.
>
> Good. Package is uploaded now.
>
> > > > * pdb2pqr - added 3 tests, fixed lintian warnings.
> > >
> > > At first I need to say that I'm very happy about your engaged work on
> > > the packages your are touching. It is a proof of deeper understanding
> > > of Debian packaging. Your changelog regarding non-test issues is
> > > impressing and very appreciated. I wonder whether you are interested
> in
> > > staying in the Debian Med team even after this outreachy project and to
> > > apply as Debian Maintained. I would definitely support this intention.
> >
> > Yes, I'm interested :)
>
> Very good. Feel free to decide yourself if you apply right now and may
> be do the first upload your own at the end of the outreachy program or
> wait a bit and apply afterwards. Its your decision how you are feeling
> about it.
>
> > > I consider it a sensible strategy to provide other tests than those
> that
> > > are done at build time if it turns out as to complex for the moment.
> > > Your tests are looking sensible and we can keep on working on even more
> > > fine grained tests later if necessary.
> > >
> > > $ sh pdb2pka-test
> > > Run pdb2pqr...
> > > ...
> > > This smells like a missing Dependency. Could you please investigate
> > > which package might provide this?
> > >
> >
> > Pdb2pqr uses SWIG (http://www.swig.org/), so this error is
> SWIG-specific.
> > For me this error appeared when one of interface files, which should be
> > regenerated, was replaced by backup file (and it simply dissapeared when
> it
> > was regenerated). I'll check this package again now and describe in next
> > letter how to avoid this.
>
> OK.
>
> Thanks for your work on this
>
> Andreas.
>
> --
> http://fam-tille.de
>
--
Best wishes,
Tanya.
