Your message dated Wed, 13 Feb 2019 21:52:41 +0000
with message-id <e1gu2sp-000irn...@fasolo.debian.org>
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
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immediately.)
--
922258: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=922258
Debian Bug Tracking System
Contact ow...@bugs.debian.org 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.
--- End Message ---
--- 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 922...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (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 ftpmas...@ftp-master.debian.org)
-----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
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
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:
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python-biom-format_2.1.7+dfsg-2.dsc
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python-biom-format_2.1.7+dfsg-2.debian.tar.xz
Checksums-Sha256:
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python-biom-format_2.1.7+dfsg-2.dsc
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python-biom-format_2.1.7+dfsg-2.debian.tar.xz
Files:
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python-biom-format_2.1.7+dfsg-2.dsc
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python-biom-format_2.1.7+dfsg-2.debian.tar.xz
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