<div dir="ltr">Does the solution here suffice?<div><br></div><div><a href="https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=848410">https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=848410</a><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Jan 11, 2017 at 9:54 AM, Andreas Tille <span dir="ltr"><<a href="mailto:andreas@an3as.eu" target="_blank">andreas@an3as.eu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Daniel,<br>
<br>
thanks for the quick response. Do you have a quick patch I could apply?<br>
<br>
Kind regards<br>
<br>
Andreas.<br>
<div><div class="h5"><br>
On Wed, Jan 11, 2017 at 08:49:25AM -0800, Daniel McDonald wrote:<br>
> Hi Andreas,<br>
><br>
> It's a stochastic test. Forcing a random seed, or increasing its number of<br>
> iterations would suffice. I've created a new issue as well so that this is<br>
> not an issue going forward as I know it has come up previously with the<br>
> Debian builds.<br>
><br>
> Best,<br>
> Daniel<br>
><br>
> On Tue, Jan 10, 2017 at 10:15 PM, Andreas Tille <<a href="mailto:andreas@an3as.eu">andreas@an3as.eu</a>> wrote:<br>
><br>
> > Hi Daniel,<br>
> ><br>
> > as yo umight know biom-format is packaged for Debian. Debian is<br>
> > released for several hardware architectures. It turns out that on i386<br>
> > architecture an error occures on build time tests:<br>
> ><br>
> > I: pybuild pybuild:212: cp -r /«BUILDDIR»/python-biom-<wbr>format-2.1.5+dfsg/examples<br>
> > /«BUILDDIR»/python-biom-<wbr>format-2.1.5+dfsg/tests /«BUILDDIR»/python-biom-<br>
> > format-2.1.5+dfsg/.pybuild/<wbr>pythonX.Y_2.7/build<br>
> > I: pybuild base:184: cd /«BUILDDIR»/python-biom-<br>
> > format-2.1.5+dfsg/.pybuild/<wbr>pythonX.Y_2.7/build; python2.7 -m nose tests<br>
> > ..............................<wbr>..............................<br>
> > ..............................<wbr>..............................<br>
> > ..............................<wbr>..............................<br>
> > ..............................<wbr>..............................<br>
> > ...........S.............<br>
> > ------------------------------<wbr>------------------------------<wbr>----------<br>
> > Ran 265 tests in 2.759s<br>
> ><br>
> > OK (SKIP=1)<br>
> > pybuild --test --test-nose -i python{version} -p 3.5<br>
> > I: pybuild pybuild:212: cp -r /«BUILDDIR»/python-biom-<wbr>format-2.1.5+dfsg/examples<br>
> > /«BUILDDIR»/python-biom-<wbr>format-2.1.5+dfsg/tests /«BUILDDIR»/python-biom-<br>
> > format-2.1.5+dfsg/.pybuild/<wbr>pythonX.Y_3.5/build<br>
> > I: pybuild base:184: cd /«BUILDDIR»/python-biom-<br>
</div></div>> > format-2.1.5+dfsg/.pybuild/<wbr>pythonX.Y_3.5/build; python3.5 -m nose tests<br>
> > ..............................<wbr>..............................<br>
> > ..............................<wbr>..............................<br>
> > ..........................F...<wbr>..............................<br>
> > ..............................<wbr>..............................<br>
<div class="HOEnZb"><div class="h5">> > ...........S.............<br>
> > ==============================<wbr>==============================<wbr>==========<br>
> > FAIL: test_subsample (tests.test_table.<wbr>SparseTableTests)<br>
> > ------------------------------<wbr>------------------------------<wbr>----------<br>
> > Traceback (most recent call last):<br>
> > File "/«BUILDDIR»/python-biom-<wbr>format-2.1.5+dfsg/.pybuild/<br>
> > pythonX.Y_3.5/build/tests/<wbr>test_table.py", line 2263, in test_subsample<br>
> > (3, 1, 1)})<br>
> > AssertionError: Items in the second set but not the first:<br>
> > (3, 0, 0)<br>
> ><br>
> > ------------------------------<wbr>------------------------------<wbr>----------<br>
> > Ran 265 tests in 3.098s<br>
> ><br>
> > FAILED (SKIP=1, failures=1)<br>
> > E: pybuild pybuild:276: test: plugin distutils failed with: exit code=1:<br>
> > cd /«BUILDDIR»/python-biom-<wbr>format-2.1.5+dfsg/.pybuild/<wbr>pythonX.Y_3.5/build;<br>
> > python3.5 -m nose tests<br>
> ><br>
> ><br>
> > Do you have any explanation for this error and any hint how to<br>
> > circumvent it?<br>
> ><br>
> > In addition I'd like to point out that there are some numpy compatibility<br>
> > issues. The build log says:<br>
> ><br>
> > i686-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall<br>
> > -Wstrict-prototypes -fno-strict-aliasing -g -O2<br>
> > -fdebug-prefix-map=/«BUILDDIR»<wbr>/python-biom-format-2.1.5+<wbr>dfsg=.<br>
> > -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time<br>
> > -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python2.7/dist-<wbr>packages/numpy/core/include<br>
> > -I/usr/include/python2.7 -c biom/_filter.c -o build/temp.linux-i686-2.7/<br>
> > biom/_filter.o<br>
> > In file included from /usr/lib/python2.7/dist-<wbr>packages/numpy/core/include/<br>
> > numpy/ndarraytypes.h:1788:0,<br>
> > from /usr/lib/python2.7/dist-<wbr>packages/numpy/core/include/<br>
> > numpy/ndarrayobject.h:18,<br>
> > from /usr/lib/python2.7/dist-<wbr>packages/numpy/core/include/<br>
> > numpy/arrayobject.h:4,<br>
> > from biom/_filter.c:444:<br>
> > /usr/lib/python2.7/dist-<wbr>packages/numpy/core/include/<br>
> > numpy/npy_1_7_deprecated_api.<wbr>h:15:2: warning: #warning "Using deprecated<br>
> > NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API<br>
> > NPY_1_7_API_VERSION" [-Wcpp]<br>
> > #warning "Using deprecated NumPy API, disable it by " \<br>
> > ^~~~~~~<br>
> > i686-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions<br>
> > -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall<br>
> > -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g<br>
> > -fdebug-prefix-map=/build/<wbr>python2.7-RPHt3w/python2.7-2.<wbr>7.13=.<br>
> > -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro<br>
> > -Wl,-z,now -g -O2 -fdebug-prefix-map=/«BUILDDIR»<wbr>/python-biom-format-2.1.5+<wbr>dfsg=.<br>
> > -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time<br>
> > -D_FORTIFY_SOURCE=2 build/temp.linux-i686-2.7/<wbr>biom/_filter.o -o<br>
> > /«BUILDDIR»/python-biom-<wbr>format-2.1.5+dfsg/.pybuild/<br>
> > pythonX.Y_2.7/build/biom/_<wbr>filter.so<br>
> > building 'biom._transform' extension<br>
> > i686-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall<br>
> > -Wstrict-prototypes -fno-strict-aliasing -g -O2<br>
> > -fdebug-prefix-map=/«BUILDDIR»<wbr>/python-biom-format-2.1.5+<wbr>dfsg=.<br>
> > -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time<br>
> > -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python2.7/dist-<wbr>packages/numpy/core/include<br>
> > -I/usr/include/python2.7 -c biom/_transform.c -o build/temp.linux-i686-2.7/<br>
> > biom/_transform.o<br>
> > In file included from /usr/lib/python2.7/dist-<wbr>packages/numpy/core/include/<br>
> > numpy/ndarraytypes.h:1788:0,<br>
> > from /usr/lib/python2.7/dist-<wbr>packages/numpy/core/include/<br>
> > numpy/ndarrayobject.h:18,<br>
> > from /usr/lib/python2.7/dist-<wbr>packages/numpy/core/include/<br>
> > numpy/arrayobject.h:4,<br>
> > from biom/_transform.c:444:<br>
> > /usr/lib/python2.7/dist-<wbr>packages/numpy/core/include/<br>
> > numpy/npy_1_7_deprecated_api.<wbr>h:15:2: warning: #warning "Using deprecated<br>
> > NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API<br>
> > NPY_1_7_API_VERSION" [-Wcpp]<br>
> > #warning "Using deprecated NumPy API, disable it by " \<br>
> > ^~~~~~~<br>
> > i686-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions<br>
> > -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall<br>
> > -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g<br>
> > -fdebug-prefix-map=/build/<wbr>python2.7-RPHt3w/python2.7-2.<wbr>7.13=.<br>
> > -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro<br>
> > -Wl,-z,now -g -O2 -fdebug-prefix-map=/«BUILDDIR»<wbr>/python-biom-format-2.1.5+<wbr>dfsg=.<br>
> > -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time<br>
> > -D_FORTIFY_SOURCE=2 build/temp.linux-i686-2.7/<wbr>biom/_transform.o -o<br>
> > /«BUILDDIR»/python-biom-<wbr>format-2.1.5+dfsg/.pybuild/<br>
> > pythonX.Y_2.7/build/biom/_<wbr>transform.so<br>
> > building 'biom._subsample' extension<br>
> > i686-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall<br>
> > -Wstrict-prototypes -fno-strict-aliasing -g -O2<br>
> > -fdebug-prefix-map=/«BUILDDIR»<wbr>/python-biom-format-2.1.5+<wbr>dfsg=.<br>
> > -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time<br>
> > -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python2.7/dist-<wbr>packages/numpy/core/include<br>
> > -I/usr/include/python2.7 -c biom/_subsample.c -o build/temp.linux-i686-2.7/<br>
> > biom/_subsample.o<br>
> > In file included from /usr/lib/python2.7/dist-<wbr>packages/numpy/core/include/<br>
> > numpy/ndarraytypes.h:1788:0,<br>
> > from /usr/lib/python2.7/dist-<wbr>packages/numpy/core/include/<br>
> > numpy/ndarrayobject.h:18,<br>
> > from /usr/lib/python2.7/dist-<wbr>packages/numpy/core/include/<br>
> > numpy/arrayobject.h:4,<br>
> > from biom/_subsample.c:444:<br>
> > /usr/lib/python2.7/dist-<wbr>packages/numpy/core/include/<br>
> > numpy/npy_1_7_deprecated_api.<wbr>h:15:2: warning: #warning "Using deprecated<br>
> > NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API<br>
> > NPY_1_7_API_VERSION" [-Wcpp]<br>
> > #warning "Using deprecated NumPy API, disable it by " \<br>
> > ^~~~~~~<br>
> > i686-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions<br>
> > -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall<br>
> > -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g<br>
> > -fdebug-prefix-map=/build/<wbr>python2.7-RPHt3w/python2.7-2.<wbr>7.13=.<br>
> > -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro<br>
> > -Wl,-z,now -g -O2 -fdebug-prefix-map=/«BUILDDIR»<wbr>/python-biom-format-2.1.5+<wbr>dfsg=.<br>
> > -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time<br>
> > -D_FORTIFY_SOURCE=2 build/temp.linux-i686-2.7/<wbr>biom/_subsample.o -o<br>
> > /«BUILDDIR»/python-biom-<wbr>format-2.1.5+dfsg/.pybuild/<br>
> > pythonX.Y_2.7/build/biom/_<wbr>subsample.so<br>
> > pybuild --build --test-nose -i python{version} -p 3.5<br>
> > I: pybuild base:184: /usr/bin/python3 setup.py build<br>
> ><br>
> ><br>
> > You can find the full build log here:<br>
> ><br>
> > <a href="https://buildd.debian.org/status/fetch.php?pkg=python-" rel="noreferrer" target="_blank">https://buildd.debian.org/<wbr>status/fetch.php?pkg=python-</a><br>
> > biom-format&arch=i386&ver=2.1.<wbr>5%2Bdfsg-6&stamp=1482186822<br>
> ><br>
> ><br>
> > Kind regards<br>
> ><br>
> > Andreas.<br>
> ><br>
> ><br>
> > --<br>
> > <a href="http://fam-tille.de" rel="noreferrer" target="_blank">http://fam-tille.de</a><br>
> ><br>
<br>
</div></div><span class="HOEnZb"><font color="#888888">--<br>
<a href="http://fam-tille.de" rel="noreferrer" target="_blank">http://fam-tille.de</a><br>
</font></span></blockquote></div><br></div>