[Debian-med-packaging] Test failure in biom-format on i386 architecture
Andreas Tille
andreas at an3as.eu
Wed Jan 11 17:54:11 UTC 2017
Hi Daniel,
thanks for the quick response. Do you have a quick patch I could apply?
Kind regards
Andreas.
On Wed, Jan 11, 2017 at 08:49:25AM -0800, Daniel McDonald wrote:
> Hi Andreas,
>
> It's a stochastic test. Forcing a random seed, or increasing its number of
> iterations would suffice. I've created a new issue as well so that this is
> not an issue going forward as I know it has come up previously with the
> Debian builds.
>
> Best,
> Daniel
>
> On Tue, Jan 10, 2017 at 10:15 PM, Andreas Tille <andreas at an3as.eu> wrote:
>
> > Hi Daniel,
> >
> > as yo umight know biom-format is packaged for Debian. Debian is
> > released for several hardware architectures. It turns out that on i386
> > architecture an error occures on build time tests:
> >
> > I: pybuild pybuild:212: cp -r /«BUILDDIR»/python-biom-format-2.1.5+dfsg/examples
> > /«BUILDDIR»/python-biom-format-2.1.5+dfsg/tests /«BUILDDIR»/python-biom-
> > format-2.1.5+dfsg/.pybuild/pythonX.Y_2.7/build
> > I: pybuild base:184: cd /«BUILDDIR»/python-biom-
> > format-2.1.5+dfsg/.pybuild/pythonX.Y_2.7/build; python2.7 -m nose tests
> > ............................................................
> > ............................................................
> > ............................................................
> > ............................................................
> > ...........S.............
> > ----------------------------------------------------------------------
> > Ran 265 tests in 2.759s
> >
> > OK (SKIP=1)
> > pybuild --test --test-nose -i python{version} -p 3.5
> > I: pybuild pybuild:212: cp -r /«BUILDDIR»/python-biom-format-2.1.5+dfsg/examples
> > /«BUILDDIR»/python-biom-format-2.1.5+dfsg/tests /«BUILDDIR»/python-biom-
> > format-2.1.5+dfsg/.pybuild/pythonX.Y_3.5/build
> > I: pybuild base:184: cd /«BUILDDIR»/python-biom-
> > format-2.1.5+dfsg/.pybuild/pythonX.Y_3.5/build; python3.5 -m nose tests
> > ............................................................
> > ............................................................
> > ..........................F.................................
> > ............................................................
> > ...........S.............
> > ======================================================================
> > FAIL: test_subsample (tests.test_table.SparseTableTests)
> > ----------------------------------------------------------------------
> > Traceback (most recent call last):
> > File "/«BUILDDIR»/python-biom-format-2.1.5+dfsg/.pybuild/
> > pythonX.Y_3.5/build/tests/test_table.py", line 2263, in test_subsample
> > (3, 1, 1)})
> > AssertionError: Items in the second set but not the first:
> > (3, 0, 0)
> >
> > ----------------------------------------------------------------------
> > Ran 265 tests in 3.098s
> >
> > FAILED (SKIP=1, failures=1)
> > E: pybuild pybuild:276: test: plugin distutils failed with: exit code=1:
> > cd /«BUILDDIR»/python-biom-format-2.1.5+dfsg/.pybuild/pythonX.Y_3.5/build;
> > python3.5 -m nose tests
> >
> >
> > Do you have any explanation for this error and any hint how to
> > circumvent it?
> >
> > In addition I'd like to point out that there are some numpy compatibility
> > issues. The build log says:
> >
> > i686-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall
> > -Wstrict-prototypes -fno-strict-aliasing -g -O2
> > -fdebug-prefix-map=/«BUILDDIR»/python-biom-format-2.1.5+dfsg=.
> > -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
> > -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include
> > -I/usr/include/python2.7 -c biom/_filter.c -o build/temp.linux-i686-2.7/
> > biom/_filter.o
> > In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/
> > numpy/ndarraytypes.h:1788:0,
> > from /usr/lib/python2.7/dist-packages/numpy/core/include/
> > numpy/ndarrayobject.h:18,
> > from /usr/lib/python2.7/dist-packages/numpy/core/include/
> > numpy/arrayobject.h:4,
> > from biom/_filter.c:444:
> > /usr/lib/python2.7/dist-packages/numpy/core/include/
> > numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated
> > NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API
> > NPY_1_7_API_VERSION" [-Wcpp]
> > #warning "Using deprecated NumPy API, disable it by " \
> > ^~~~~~~
> > i686-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions
> > -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall
> > -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g
> > -fdebug-prefix-map=/build/python2.7-RPHt3w/python2.7-2.7.13=.
> > -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro
> > -Wl,-z,now -g -O2 -fdebug-prefix-map=/«BUILDDIR»/python-biom-format-2.1.5+dfsg=.
> > -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
> > -D_FORTIFY_SOURCE=2 build/temp.linux-i686-2.7/biom/_filter.o -o
> > /«BUILDDIR»/python-biom-format-2.1.5+dfsg/.pybuild/
> > pythonX.Y_2.7/build/biom/_filter.so
> > building 'biom._transform' extension
> > i686-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall
> > -Wstrict-prototypes -fno-strict-aliasing -g -O2
> > -fdebug-prefix-map=/«BUILDDIR»/python-biom-format-2.1.5+dfsg=.
> > -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
> > -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include
> > -I/usr/include/python2.7 -c biom/_transform.c -o build/temp.linux-i686-2.7/
> > biom/_transform.o
> > In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/
> > numpy/ndarraytypes.h:1788:0,
> > from /usr/lib/python2.7/dist-packages/numpy/core/include/
> > numpy/ndarrayobject.h:18,
> > from /usr/lib/python2.7/dist-packages/numpy/core/include/
> > numpy/arrayobject.h:4,
> > from biom/_transform.c:444:
> > /usr/lib/python2.7/dist-packages/numpy/core/include/
> > numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated
> > NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API
> > NPY_1_7_API_VERSION" [-Wcpp]
> > #warning "Using deprecated NumPy API, disable it by " \
> > ^~~~~~~
> > i686-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions
> > -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall
> > -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g
> > -fdebug-prefix-map=/build/python2.7-RPHt3w/python2.7-2.7.13=.
> > -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro
> > -Wl,-z,now -g -O2 -fdebug-prefix-map=/«BUILDDIR»/python-biom-format-2.1.5+dfsg=.
> > -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
> > -D_FORTIFY_SOURCE=2 build/temp.linux-i686-2.7/biom/_transform.o -o
> > /«BUILDDIR»/python-biom-format-2.1.5+dfsg/.pybuild/
> > pythonX.Y_2.7/build/biom/_transform.so
> > building 'biom._subsample' extension
> > i686-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall
> > -Wstrict-prototypes -fno-strict-aliasing -g -O2
> > -fdebug-prefix-map=/«BUILDDIR»/python-biom-format-2.1.5+dfsg=.
> > -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
> > -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include
> > -I/usr/include/python2.7 -c biom/_subsample.c -o build/temp.linux-i686-2.7/
> > biom/_subsample.o
> > In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/
> > numpy/ndarraytypes.h:1788:0,
> > from /usr/lib/python2.7/dist-packages/numpy/core/include/
> > numpy/ndarrayobject.h:18,
> > from /usr/lib/python2.7/dist-packages/numpy/core/include/
> > numpy/arrayobject.h:4,
> > from biom/_subsample.c:444:
> > /usr/lib/python2.7/dist-packages/numpy/core/include/
> > numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated
> > NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API
> > NPY_1_7_API_VERSION" [-Wcpp]
> > #warning "Using deprecated NumPy API, disable it by " \
> > ^~~~~~~
> > i686-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions
> > -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall
> > -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g
> > -fdebug-prefix-map=/build/python2.7-RPHt3w/python2.7-2.7.13=.
> > -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro
> > -Wl,-z,now -g -O2 -fdebug-prefix-map=/«BUILDDIR»/python-biom-format-2.1.5+dfsg=.
> > -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
> > -D_FORTIFY_SOURCE=2 build/temp.linux-i686-2.7/biom/_subsample.o -o
> > /«BUILDDIR»/python-biom-format-2.1.5+dfsg/.pybuild/
> > pythonX.Y_2.7/build/biom/_subsample.so
> > pybuild --build --test-nose -i python{version} -p 3.5
> > I: pybuild base:184: /usr/bin/python3 setup.py build
> >
> >
> > You can find the full build log here:
> >
> > https://buildd.debian.org/status/fetch.php?pkg=python-
> > biom-format&arch=i386&ver=2.1.5%2Bdfsg-6&stamp=1482186822
> >
> >
> > Kind regards
> >
> > Andreas.
> >
> >
> > --
> > http://fam-tille.de
> >
--
http://fam-tille.de
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