[Debian-med-packaging] Bug#922258: python-biom-format: FTBFS (Could not import extension sphinx.ext.pngmath)

[Santiago Vila]

Package: src:python-biom-format
Version: 2.1.7+dfsg-1
Severity: serious
Tags: ftbfs

Dear maintainer:

I tried to build this package in buster but it failed:

--------------------------------------------------------------------------------
[...]
 debian/rules build-indep
dh build-indep --with python2,python3,bash-completion,sphinxdoc --buildsystem=pybuild
   dh_update_autotools_config -i -O--buildsystem=pybuild
   dh_autoreconf -i -O--buildsystem=pybuild
   dh_auto_configure -i -O--buildsystem=pybuild
	pybuild --configure --test-nose -i python{version} -p 2.7
I: pybuild base:217: python2.7 setup.py config 
running config
	pybuild --configure --test-nose -i python{version} -p 3.7
I: pybuild base:217: python3.7 setup.py config 
running config
   debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/python-biom-format-2.1.7+dfsg'
# arch

[... snipped ...]

copying biom/tests/test_data/test.json -> /<<BUILDDIR>>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_data
copying biom/tests/test_data/test.json.gz -> /<<BUILDDIR>>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_data
running build_ext
building 'biom._filter' extension
creating build/temp.linux-amd64-3.7
creating build/temp.linux-amd64-3.7/biom
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-biom-format-2.1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.7m -c biom/_filter.c -o build/temp.linux-amd64-3.7/biom/_filter.o
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from biom/_filter.c:632:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it with " \
  ^~~~~~~
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-biom-format-2.1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.7/biom/_filter.o -o /<<BUILDDIR>>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/_filter.cpython-37m-x86_64-linux-gnu.so
building 'biom._transform' extension
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-biom-format-2.1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.7m -c biom/_transform.c -o build/temp.linux-amd64-3.7/biom/_transform.o
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from biom/_transform.c:632:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it with " \
  ^~~~~~~
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-biom-format-2.1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.7/biom/_transform.o -o /<<BUILDDIR>>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/_transform.cpython-37m-x86_64-linux-gnu.so
building 'biom._subsample' extension
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-biom-format-2.1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.7m -c biom/_subsample.c -o build/temp.linux-amd64-3.7/biom/_subsample.o
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from biom/_subsample.c:632:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it with " \
  ^~~~~~~
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-biom-format-2.1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.7/biom/_subsample.o -o /<<BUILDDIR>>/python-biom-format-2.1.7+dfsg/.pybuild/cpython3_3.7_biom-format/build/biom/_subsample.cpython-37m-x86_64-linux-gnu.so
# indep:
PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -b html doc build/html
Running Sphinx v1.8.3

Extension error:
Could not import extension sphinx.ext.pngmath (exception: No module named 'sphinx.ext.pngmath')
make[1]: *** [debian/rules:25: override_dh_auto_build] Error 2
make[1]: Leaving directory '/<<BUILDDIR>>/python-biom-format-2.1.7+dfsg'
make: *** [debian/rules:19: build-indep] Error 2
dpkg-buildpackage: error: debian/rules build-indep subprocess returned exit status 2
--------------------------------------------------------------------------------

(The above is just how the build ends and not necessarily the most relevant part)

The build was made in my autobuilder with "dpkg-buildpackage -A"
and it also fails here:

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/python-biom-format.html

where you can get a full build log if you need it.

If this is really a bug in one of the build-depends, please use reassign and affects,
so that this is still visible in the BTS web page for this package.

Thanks.