[Debian-med-packaging] Bug#802867: python-biom-format: FTBFS: _filter.pyx: Incompatible types in conditional expression ((Py_ssize_t, Py_ssize_t); (long, long))

[Chris West (Faux)]

Source: python-biom-format
Version: 2.1+dfsg-1
Severity: serious
Justification: fails to build from source
Tags: sid stretch
User: reproducible-builds at lists.alioth.debian.org
Usertags: ftbfs
X-Debbugs-CC: reproducible-builds at lists.alioth.debian.org

Dear Maintainer,

The package fails to build:

running config
   debian/rules override_dh_auto_build
make[1]: Entering directory '/python-biom-format-2.1+dfsg'
USE_CYTHON=true dh_auto_build
I: pybuild base:170: /usr/bin/python setup.py build 

Error compiling Cython file:
------------------------------------------------------------
...
            offset += end - start
            offset_rows += 1
    arr.data = data[:nnz]
    arr.indices = indices[:nnz]
    arr.indptr = indptr[:m-offset_rows+1]
    arr._shape = (m - offset_rows, n) if m-offset_rows else (0, 0)
                ^
------------------------------------------------------------

biom/_filter.pyx:87:17: Incompatible types in conditional expression ((Py_ssize_t, Py_ssize_t); (long, long))
Compiling biom/_filter.pyx because it changed.
Compiling biom/_transform.pyx because it changed.
Compiling biom/_subsample.pyx because it changed.
[1/3] Cythonizing biom/_filter.pyx
Traceback (most recent call last):
  File "setup.py", line 80, in <module>
    extensions = cythonize(extensions)
  File "/usr/lib/python2.7/dist-packages/Cython/Build/Dependencies.py", line 877, in cythonize
    cythonize_one(*args)
  File "/usr/lib/python2.7/dist-packages/Cython/Build/Dependencies.py", line 997, in cythonize_one
    raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: biom/_filter.pyx
E: pybuild pybuild:262: build: plugin distutils failed with: exit code=1: /usr/bin/python setup.py build 
dh_auto_build: pybuild --build -i python{version} -p 2.7 --dir . returned exit code 13
debian/rules:23: recipe for target 'override_dh_auto_build' failed

Full build log:
https://reproducible.debian.net/rb-pkg/unstable/amd64/python-biom-format.html

-- System Information:
Debian Release: stretch/sid
APT prefers unstable
APT policy: (500, 'unstable')
Architecture: amd64 (x86_64)