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

Andreas Tille andreas at an3as.eu
Wed Jan 11 06:15:42 UTC 2017 

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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