[Debichem-devel] Bug#835224: pymol: FTBFS in every autobuilder (No such file or directory)

[Santiago Vila]

Package: src:pymol
Version: 1.8.2.1+dfsg-1
Severity: serious

Dear maintainer:

I tried to build this package in stretch with "dpkg-buildpackage -A"
(which is what the "Arch: all" autobuilder would do to build it)
but it failed:

--------------------------------------------------------------------------------
[...]
 debian/rules build-indep
dh build-indep --with python2 --parallel
   dh_testdir -i -O--parallel
   dh_update_autotools_config -i -O--parallel
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/pymol-1.8.2.1+dfsg'
dh_auto_configure -Spython_distutils
make[1]: Leaving directory '/<<BUILDDIR>>/pymol-1.8.2.1+dfsg'
   debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/pymol-1.8.2.1+dfsg'
dh_auto_build -Spython_distutils
	python setup.py build --force

[... snipped ...]

copying build/lib.linux-x86_64-2.7/chempy/champ/amber99.py -> /<<BUILDDIR>>/pymol-1.8.2.1+dfsg/debian/tmp/usr/lib/python2.7/dist-packages/chempy/champ
creating /<<BUILDDIR>>/pymol-1.8.2.1+dfsg/debian/tmp/usr/lib/python2.7/dist-packages/chempy/bmin
copying build/lib.linux-x86_64-2.7/chempy/bmin/util.py -> /<<BUILDDIR>>/pymol-1.8.2.1+dfsg/debian/tmp/usr/lib/python2.7/dist-packages/chempy/bmin
copying build/lib.linux-x86_64-2.7/chempy/bmin/state.py -> /<<BUILDDIR>>/pymol-1.8.2.1+dfsg/debian/tmp/usr/lib/python2.7/dist-packages/chempy/bmin
copying build/lib.linux-x86_64-2.7/chempy/bmin/realtime.py -> /<<BUILDDIR>>/pymol-1.8.2.1+dfsg/debian/tmp/usr/lib/python2.7/dist-packages/chempy/bmin
copying build/lib.linux-x86_64-2.7/chempy/bmin/commands.py -> /<<BUILDDIR>>/pymol-1.8.2.1+dfsg/debian/tmp/usr/lib/python2.7/dist-packages/chempy/bmin
copying build/lib.linux-x86_64-2.7/chempy/bmin/__init__.py -> /<<BUILDDIR>>/pymol-1.8.2.1+dfsg/debian/tmp/usr/lib/python2.7/dist-packages/chempy/bmin
copying build/lib.linux-x86_64-2.7/chempy/water_residues.py -> /<<BUILDDIR>>/pymol-1.8.2.1+dfsg/debian/tmp/usr/lib/python2.7/dist-packages/chempy
creating /<<BUILDDIR>>/pymol-1.8.2.1+dfsg/debian/tmp/usr/lib/python2.7/dist-packages/pmg_wx
copying build/lib.linux-x86_64-2.7/pmg_wx/__init__.py -> /<<BUILDDIR>>/pymol-1.8.2.1+dfsg/debian/tmp/usr/lib/python2.7/dist-packages/pmg_wx
running install_egg_info
Writing /<<BUILDDIR>>/pymol-1.8.2.1+dfsg/debian/tmp/usr/lib/python2.7/dist-packages/pymol-1.8.2.1.egg-info
creating /<<BUILDDIR>>/pymol-1.8.2.1+dfsg/debian/tmp/usr/bin
   debian/rules override_dh_install
make[1]: Entering directory '/<<BUILDDIR>>/pymol-1.8.2.1+dfsg'
pdflatex -output-directory debian -jobname pymol-ref-card debian/pymolRef.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./debian/pymolRef.tex
LaTeX2e <2016/03/31> patch level 3
Babel <3.9r> and hyphenation patterns for 3 language(s) loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))
(/usr/share/texlive/texmf-dist/tex/latex/tools/multicol.sty)
No file pymol-ref-card.aux.

Underfull \hbox (badness 10000) in paragraph at lines 78--79

[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]
(/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [2]
(debian/pymol-ref-card.aux) )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/amsfonts/cm/cmitt10.pfb></usr/share/texlive/texmf-dist/fonts/t
ype1/public/amsfonts/cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/pu
blic/amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am
sfonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmr9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy9
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti9.pfb></
usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb>
Output written on debian/pymol-ref-card.pdf (2 pages, 108274 bytes).
Transcript written on debian/pymol-ref-card.log.
sed -e s/@PYTHON_VERSION@/2.7/g < debian/pymol.launch.in > debian/pymol.launch
dh_numpy
dh_install data/shaders usr/lib/python2.7/dist-packages/pymol/data/
install -m 755 debian/pymol.launch debian/pymol/usr/bin/pymol
install: cannot create regular file 'debian/pymol/usr/bin/pymol': No such file or directory
debian/rules:37: recipe for target 'override_dh_install' failed
make[1]: *** [override_dh_install] Error 1
make[1]: Leaving directory '/<<BUILDDIR>>/pymol-1.8.2.1+dfsg'
debian/rules:14: recipe for target 'binary-indep' failed
make: *** [binary-indep] Error 2
dpkg-buildpackage: error: fakeroot debian/rules binary-indep gave error exit status 2
--------------------------------------------------------------------------------

To reproduce, please try to build the package with "dpkg-buildpackage -A".

This happens because debian/pymol/[...] does not exist, because pymol
is arch-dependent and we are creating only arch-independent packages.

To fix this, try splitting override_dh_install into
override_dh_install-arch and override_dh_install-indep.

BTW: Not even "dpkg-buildpackage -B" works:

https://buildd.debian.org/status/package.php?p=pymol

Once you make dpkg-buildpackage -B and dpkg-buildpackage -A to work
again, the package would be suitable to be uploaded in source-only
form.

Thanks.