Your message dated Wed, 13 Feb 2019 21:52:41 +0000 with message-id <[email protected]> and subject line Bug#922258: fixed in python-biom-format 2.1.7+dfsg-2 has caused the Debian Bug report #922258, regarding python-biom-format: FTBFS (Could not import extension sphinx.ext.pngmath) to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact [email protected] immediately.) -- 922258: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=922258 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---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.
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--- Begin Message ---Source: python-biom-format Source-Version: 2.1.7+dfsg-2 We believe that the bug you reported is fixed in the latest version of python-biom-format, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <[email protected]> (supplier of updated python-biom-format package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing [email protected]) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Wed, 13 Feb 2019 22:13:47 +0100 Source: python-biom-format Binary: python-biom-format python3-biom-format python-biom-format-doc biom-format-tools Architecture: source Version: 2.1.7+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <[email protected]> Changed-By: Andreas Tille <[email protected]> Description: biom-format-tools - command-line tools for BIOM format python-biom-format - Biological Observation Matrix (BIOM) format (Python 2) python-biom-format-doc - documentation for BIOM format python3-biom-format - Biological Observation Matrix (BIOM) format (Python 3) Closes: 922258 Changes: python-biom-format (2.1.7+dfsg-2) unstable; urgency=medium . * Do not ship *.c and *.pyx cython input files in binary packages * Fix "Could not import extension sphinx.ext.pngmath" Closes: #922258 * Deactivate autopkgtest for the moment since it fails anyway Checksums-Sha1: c244020c89755fe94a84d2ec1b068eac2725256d 2948 python-biom-format_2.1.7+dfsg-2.dsc e824b852b7edfbb34ad4ca8ab2c8128c2a16f3c2 8764 python-biom-format_2.1.7+dfsg-2.debian.tar.xz Checksums-Sha256: 1717d13fc32980549212d10911d9f7d52dd1bb8732e17474983be17361f9a93a 2948 python-biom-format_2.1.7+dfsg-2.dsc 1005075b1b29746566e070be76e8e2f0bc3ecbe1e9ff630ec4f1e0a51da61660 8764 python-biom-format_2.1.7+dfsg-2.debian.tar.xz Files: f3f6384246ddd8aab8cfdf49af62b98e 2948 python optional python-biom-format_2.1.7+dfsg-2.dsc fe3017856fb1038c1c6a99abfcbf876c 8764 python optional python-biom-format_2.1.7+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlxki30RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtESSg//eIY2ENnh4dfwZHEySGAwCsKeHZ4ZeXuo j11sgv0+eCqhzMkgkcBRiZ9GWSAr0R8iK/hqTUdgavYBw2gDUqXOD38k0xPUG+6k yn9eYvFuci6iN78ZQZjoQ91JphKw3zlWjGHMVuPxBVGvkQevK8JxoVq8jovvjUAQ i95kyceSD3palEqD7vP/lREvDrpSlAcA8vLga/hfKrgq4+Ir0OkUvb+0wv4E/NPc S5Jn95dJxFnMIp67Ookr+xL7uVRPLfNzrH+rp8j52NspXmPRY6WiSnEx1womD5ZR WqdV4Izixcb2BoCIpkXGWh8op4OojoT1luNXWXEO+3wU2VObUSFp6MfeGiYHp7xK 0tlnibus+okqaRoh0E3BpIO3CkPL2FbmpHSR3uwgzSjqiY0nDd2efK9iR6fAmTuM GSjRY/ci/wLnbvnpPNcmdnLl9c4t40mb/yZJs1VwBzLfnNGrZUayI+SOA79fag0n PNhXNu9mlP0vkVfFGHK+W1GX8scKNtyv87peR3WwJHxFgNIEsxxdPMA9t9j8Ho1I KuQsIrAUTxRLQIznHmzOGspiJIe+58/18s3zpSdA9/9yRQBuv+HGyKE3cFgHP6+w W/F9IzyPT3W5uk4Pq/IKgNRMTcFbAEbPK5NEGpxS1OD2XHWAWwy56cTXBnoa27SD TL8x5FVrq/w= =SNyE -----END PGP SIGNATURE-----
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