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.