[Debian-med-packaging] Bug#806222: pdb2pqr: FTBFS when built with dpkg-buildpackage -A (Directory nonexistent)

[Santiago Vila]

Package: src:pdb2pqr
Version: 2.0.0+dfsg-1
User: sanvila at debian.org
Usertags: binary-indep
Severity: important

Dear maintainer:

I tried to build this package with "dpkg-buildpackage -A"
(i.e. only architecture-independent packages), and it failed:

--------------------------------------------------------------------------------
[...]
 debian/rules build-indep
dh build-indep --with python2
   dh_testdir -i
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/pdb2pqr-2.0.0+dfsg'
dh_auto_configure
python scons/scons.py \
	URL="http://localhost/pdb2pqr/" \
	PREFIX="/usr/share/pdb2pqr"
scons: Reading SConscript files ...
scons: done reading SConscript files.
scons: Building targets ...

[... snipped ...]

For example: "/opt/bin/python scons/scons.py" will setup pdb2pqr to be run with /opt/bin/python

Run "python scons/scons.py install" to install pdb2pqr in /usr/share/pdb2pqr/

Run "python scons/scons.py basic-test" for a basic functionality test
Run "python scons/scons.py advanced-test" for a single test of ligand and PROPKA support. Requires numpy and PDB2PKA support compiled.
Run "python scons/scons.py complete-test" for a complete test of all functionality EXCEPT PDB2PKA. Requires numpy and PDB2PKA support compiled.
Run "python scons/scons.py pdb2pka-test" for a simple test of PDB2PKA functionality.
    Requires numpy, PDB2PKA support compiled AND the APBS python libraries compiled and installed in the pdb2pka directory.

To setup a web service create a symbolic link to /usr/share/pdb2pqr/ that enables you to view http://localhost/pdb2pqr/ after running "scons/scons.py install"

Run "python scons/scons.py msvs" to build Visual Studio projects for the Algorithms and pMC_mult modules.
VS project generation is not well supported in scons. Resulting projects should build using NMAKE but cannot be used for debugging.
The resulting projects will need to modified to use VS natively to compile the code or debug.

Build succeeded.

( cd pdb2pka && \
  cp -a pMC_mult_wrap.cpp pMC_mult_wrap.cpp.saved && \
  cp -a pMC_mult.py pMC_mult.py.saved && \
  swig -c++ -python -o pMC_mult_wrap.cpp pMC_mult.i )
make[1]: Leaving directory '/<<BUILDDIR>>/pdb2pqr-2.0.0+dfsg'
   dh_auto_build -i
   dh_auto_test -i
 fakeroot debian/rules binary-indep
dh binary-indep --with python2
   dh_testroot -i
   dh_prep -i
   debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/pdb2pqr-2.0.0+dfsg'
for app in /usr/share/pdb2pqr/pdb2pqr.py /usr/share/pdb2pqr/src/psize.py; do \
	sed -e "s, at SCRIPT@,${app}," debian/wrapper.sh \
		>debian/pdb2pqr/usr/bin/$(basename ${app} .py) && \
	chmod 0755 debian/pdb2pqr/usr/bin/$(basename ${app} .py); \
done
/bin/sh: 2: cannot create debian/pdb2pqr/usr/bin/pdb2pqr: Directory nonexistent
/bin/sh: 2: cannot create debian/pdb2pqr/usr/bin/psize: Directory nonexistent
debian/rules:43: recipe for target 'override_dh_auto_install' failed
make[1]: *** [override_dh_auto_install] Error 2
make[1]: Leaving directory '/<<BUILDDIR>>/pdb2pqr-2.0.0+dfsg'
debian/rules:15: recipe for target 'binary-indep' failed
make: *** [binary-indep] Error 2
dpkg-buildpackage: error: fakeroot debian/rules binary-indep gave error exit status 2
--------------------------------------------------------------------------------

Sorry not to have a fix, as I am reporting many bugs similar to
this one.

In this case, I see that you are using "dh", which allow
(independently) optional targets override_dh_foo-arch and
override_dh_foo-indep (for several values of "foo").

Maybe using them this problem could be fixed.

Once that both "dpkg-buildpackage -A" and "dpkg-buildpackage -B" work
properly, the package would be suitable to be uploaded in source-only
form if you wish.

Thanks.