[Debian-med-packaging] Test failure in biom-format on i386 architecture

Daniel McDonald wasade at gmail.com
Thu Jan 12 01:15:31 UTC 2017 

Does the solution here suffice?

https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=848410

On Wed, Jan 11, 2017 at 9:54 AM, Andreas Tille <andreas at an3as.eu> wrote:

> 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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