[Bug 497622] Review Request: apbs - adaptive poisson boltzmann solver

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https://bugzilla.redhat.com/show_bug.cgi?id=497622





--- Comment #36 from Tim Fenn <fenn at stanford.edu>  2009-07-27 15:02:56 EDT ---
(In reply to comment #33)
> (In reply to comment #32)
> > > Package does not build:
> > > RPM build errors:
> > >     File not found:
> > > /builddir/build/BUILDROOT/apbs-1.1.0-5.fc11.x86_64/usr/bin/ApbsClient.pyc
> > >     File not found:
> > > /builddir/build/BUILDROOT/apbs-1.1.0-5.fc11.x86_64/usr/bin/ApbsClient.pyo
> > > 
> > > This is due to RPM in Fedora 11 not byte compiling files in %{_bindir}. Instead
> > > of %exclude you could just delete the files after %install with rm -f which
> > > doesn't complain about possible non-existing files.  
> > 
> > I just removed the %exclude statement and built using F11 (since I won't be
> > packaging this for F10 anyway).
> > 
> > Spec URL: http://www.stanford.edu/~fenn/packs/apbs.spec
> > SRPM URL: http://www.stanford.edu/~fenn/packs/apbs-1.1.0-6.fc11.src.rpm  
> 
> .. but won't you be building for EPEL, if you need this for pymol?
> 

Right... in that case, using rm -f in %install isn't enough -
brp-python-bytecompile runs after %install, so it just recreates the .pyc/.pyo
files. The other option is to rename the files so they don't have a .py
extension, but I'm not sure if that will break other tools. Could I just use a
different spec file for the F-10 and EPEL branches?

> 
> We usually don't add license files ourselves.
> 

The package doesn't include a LGPL license file (for some reason, they included
the GPL license file with LGPL licensed code) - I'll mention this to upstream.

> 
> You're using ATLAS for ARPACK? You might want to use it for blas, too:
>  --with-blas="-L%{_libdir}/atlas -lf77blas -latlas"
> should do it.
> 

Yes - the tools/arpack/ folder makes calls to ATLAS, even though the configure
script doesn't look for it (grrr).  Added the recommended flags.

> 
> For the tools installation I suggest using a loop:
> 
> for bin in tools/manip/{psize.py,coulomb,born}
> tools/mesh/{mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis}
> arpack/driver; do
>  install -p -m 755 $bin %{buildroot}%{_bindir}/apbs-`basename $bin`
> done  

thanks for all the pointers on this package, its been a challenge!

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