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

Daniel McDonald wasade at gmail.com
Wed Jan 11 16:49:25 UTC 2017 

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
>
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