[Debian-med-packaging] Bug#806101: qiime: FTBFS when built with dpkg-buildpackage -A (No such file or directory)

[Santiago Vila]

Package: src:qiime
Version: 1.8.0+dfsg-4
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:

--------------------------------------------------------------------------------
[...]
 fakeroot debian/rules binary-indep
dh binary-indep --with python2
   dh_testroot -i
   dh_prep -i
   dh_auto_install -i
	python setup.py install --force --root=/<<BUILDDIR>>/qiime-1.8.0\+dfsg/debian/tmp --no-compile -O0 --install-layout=deb
make[1]: Entering directory '/<<BUILDDIR>>/qiime-1.8.0+dfsg/qiime/support_files/denoiser/FlowgramAlignment'
rm -f *.o
rm -f *.hi
rm -f FlowgramAli_4frame
rm -f ../../../../scripts/FlowgramAli_4frame
make[1]: Leaving directory '/<<BUILDDIR>>/qiime-1.8.0+dfsg/qiime/support_files/denoiser/FlowgramAlignment'
make[1]: Entering directory '/<<BUILDDIR>>/qiime-1.8.0+dfsg/qiime/support_files/denoiser/FlowgramAlignment'
ghc --make -O2 FlowgramAli_4frame
[1 of 3] Compiling ADPCombinators   ( ADPCombinators.lhs, ADPCombinators.o )
[2 of 3] Compiling FlowgramUtils    ( FlowgramUtils.lhs, FlowgramUtils.o )
[3 of 3] Compiling Main             ( FlowgramAli_4frame.lhs, FlowgramAli_4frame.o )
Linking FlowgramAli_4frame ...
cp FlowgramAli_4frame ../../../../scripts/
make[1]: Leaving directory '/<<BUILDDIR>>/qiime-1.8.0+dfsg/qiime/support_files/denoiser/FlowgramAlignment'
/usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'extras_require'
  warnings.warn(msg)

[... snipped ...]

chmod: cannot access 'debian/qiime/usr/share/qiime/support_files/R/*': No such file or directory
chmod a-x debian/qiime/usr/share/qiime/support_files/js/* || true
chmod: cannot access 'debian/qiime/usr/share/qiime/support_files/js/*': No such file or directory
#Fix lintian warning for jquery
rm debian/qiime/usr/share/qiime/support_files/js/jquery.js && \
    ln -s /usr/share/javascript/jquery/jquery.js debian/qiime/usr/share/qiime/support_files/js
rm: cannot remove 'debian/qiime/usr/share/qiime/support_files/js/jquery.js': No such file or directory
debian/rules:51: recipe for target 'override_dh_install' failed
make[1]: *** [override_dh_install] Error 1
make[1]: Leaving directory '/<<BUILDDIR>>/qiime-1.8.0+dfsg'
debian/rules:16: 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, but I can give some general hints:

* If all the arch-independent packages are dummy transitional packages
released with jessie, the easy fix is to drop them now.
 
* If not, debian/rules should be modified so that the binary-indep
target works in all cases, even when binary-arch is not used (this is
what the "Architecture: all" autobuilder does). For that:
    
* If you are using debhelper, you might want to use options -a and -i
for dh_* commands so that they do not act on packages they do not
have to act.

* Also, if you are using dh, the (independently) optional targets
override_dh_foo-arch and override_dh_foo-indep (for several values
of "foo") may be useful to write a debian/rules which behaves exactly
as desired.


After checking that both "dpkg-buildpackage -A" and "dpkg-buildpackage -B"
work properly, this package will be suitable to be uploaded in
source-only form if you wish (you might want to try it).

Thanks.