<div dir="ltr">This is 32-bit Python running on Windows 8.1. Were you interested in the 64-bit version?<div><br></div><div>The issue is not that "echo" is missing, but that platform.win32_ver()[0] rather than "7" or "8" returns "post2012Server", which in turn causes the Popen call to run with shell=false. I think this indicates a bug in Python itself.</div><div><br></div><div>Are people available to look at the skipping errors?</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Sun, Aug 30, 2015 at 8:37 AM, Peter Cock <span dir="ltr"><<a href="mailto:p.j.a.cock@googlemail.com" target="_blank">p.j.a.cock@googlemail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Thanks Ben,<br>
<br>
I'm not 100% clear if your machine is running Python in 32 or 64 bit<br>
mode. How did you install Python 3.5.0rc2 itself?<br>
<br>
At first glance there are main two issues here,<br>
<br>
First the "echo" command does not seem to be available on your Windows<br>
machine causing test_Application.py to fail. This is odd, but perhaps<br>
depends on the version of Windows? What version of Windows is this?<br>
<br>
Second some of the missing dependencies are not being skipped, but<br>
treated as errors. e.g. Missing reportlab in test_KGML_graphics.py<br>
raises MissingExternalDependencyError (it could use the more precise<br>
subclass MissingPythonDependencyError), and missing MySQLdb in<br>
test_DocSQL.py correctly raises MissingPythonDependencyError - but<br>
this is not being detected in run_tests.py - we need to try the Python<br>
3.5.0rc2 on another OS to investigate this.<br>
<br>
There are also a lot more warnings in the output from the PDB code<br>
that I would expect...<br>
<span class="HOEnZb"><font color="#888888"><br>
Peter<br>
</font></span><div class="HOEnZb"><div class="h5"><br>
On Fri, Aug 28, 2015 at 8:36 PM, Ben Fulton <<a href="mailto:ben@benfulton.net">ben@benfulton.net</a>> wrote:<br>
> It turned out to be not very difficult. I installed Visual Studio, Numpy<br>
> from Christoph Gohlke's wheel, and downloaded BioPython-1.65 and ran setup.<br>
> I ran the offline tests, which told me:<br>
><br>
> Python version: 3.5.0rc2 (v3.5.0rc2:cc15d736d860, Aug 25 2015, 04:45:41)<br>
> [MSC v.1900 32 bit (Intel)]<br>
> Operating system: nt win32<br>
><br>
> The most recent Windows XP - Python 3.3 build report had 240 tests, all<br>
> passing; I had 237 tests with seven failures. I'll look further into the<br>
> differences. The test report is available here:<br>
><br>
> <a href="https://iu.box.com/biopython-win-python35-test" rel="noreferrer" target="_blank">https://iu.box.com/biopython-win-python35-test</a><br>
><br>
><br>
><br>
><br>
> On Fri, Aug 28, 2015 at 9:05 AM, Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com">p.j.a.cock@googlemail.com</a>><br>
> wrote:<br>
>><br>
>> Thanks Ben, any help here would be great:<br>
>> <a href="https://github.com/biopython/biopython/issues/601" rel="noreferrer" target="_blank">https://github.com/biopython/biopython/issues/601</a><br>
>><br>
>> If you can make notes on this, that would be wonderful.<br>
>><br>
>> In the medium term, ideally we'd get another volunteer<br>
>> Windows machine setup as a buildslave.<br>
>> <a href="http://testing.open-bio.org/biopython/tgrid" rel="noreferrer" target="_blank">http://testing.open-bio.org/biopython/tgrid</a><br>
>> <a href="http://biopython.org/wiki/Continuous_integration" rel="noreferrer" target="_blank">http://biopython.org/wiki/Continuous_integration</a><br>
>><br>
>> Also note this may have implications for 32 vs 64 bit<br>
>> Windows builds, where AFAIK NumPy don't yet have<br>
>> an official binary release (we would likely follow their<br>
>> lead for 64bit builds).<br>
>><br>
>> <a href="http://biopython.org/wiki/64-bit_Windows_Biopython" rel="noreferrer" target="_blank">http://biopython.org/wiki/64-bit_Windows_Biopython</a><br>
>><br>
>> Peter<br>
>><br>
>> On Fri, Aug 28, 2015 at 1:43 PM, Ben Fulton <<a href="mailto:ben@benfulton.net">ben@benfulton.net</a>> wrote:<br>
>> > I can have a go at getting this running on my Windows 8 machine. Not<br>
>> > sure<br>
>> > how much work it will be. Is there an issue open for it or anything?<br>
>> ><br>
>> > On Wed, Aug 26, 2015 at 10:57 AM, Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com">p.j.a.cock@googlemail.com</a>><br>
>> > wrote:<br>
>> >><br>
>> >> Hi Chris,<br>
>> >><br>
>> >> I'd like to retire this WinXP box, but not until I have another<br>
>> >> Windows development machine setup (perhaps a VM).<br>
>> >> For now it is handy for building our Biopython installers<br>
>> >> for 32-bit windows, and as a buildbot slave, but its days<br>
>> >> are numbered.<br>
>> >><br>
>> >> I've not looked into how to install MSCV 14.0 but it would<br>
>> >> not surprise me that it isn't available on Windows XP.<br>
>> >><br>
>> >> Biopython would benefit from one or more developers<br>
>> >> working primarily on Windows (which is what I did when<br>
>> >> I first started).<br>
>> >><br>
>> >> Peter<br>
>> >><br>
>> >> On Wed, Aug 26, 2015 at 3:38 PM, Fields, Christopher J<br>
>> >> <<a href="mailto:cjfields@illinois.edu">cjfields@illinois.edu</a>> wrote:<br>
>> >> > Peter, Just a note on Windows XP and Python 3.5 support (under<br>
>> >> > 'Unsupported<br>
>> >> > Operating Systems’):<br>
>> >> ><br>
>> >> > <a href="https://docs.python.org/3.6/whatsnew/3.5.html" rel="noreferrer" target="_blank">https://docs.python.org/3.6/whatsnew/3.5.html</a><br>
>> >> ><br>
>> >> > Not sure how this affects whether it actually would work on XP using<br>
>> >> > MS<br>
>> >> > Visual C++ 14.0 though; is it supported on that platform?<br>
>> >> ><br>
>> >> > chris<br>
>> >> ><br>
>> >> > On Aug 26, 2015, at 3:52 AM, Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com">p.j.a.cock@googlemail.com</a>><br>
>> >> > wrote:<br>
>> >> ><br>
>> >> > Hello all,<br>
>> >> ><br>
>> >> > Python 3.5.0 rc 2 is out now, so we ought to be testing<br>
>> >> > Biopython with it:<br>
>> >> ><br>
>> >> > <a href="https://www.python.org/downloads/release/python-350rc2/" rel="noreferrer" target="_blank">https://www.python.org/downloads/release/python-350rc2/</a><br>
>> >> ><br>
>> >> > However, this has deeper implications for compiling on<br>
>> >> > Windows - in addition to the email forwarded below, I<br>
>> >> > also saw this via Guido van Rossum's Twitter,<br>
>> >> ><br>
>> >> > <a href="https://twitter.com/gvanrossum/status/636279572938428416" rel="noreferrer" target="_blank">https://twitter.com/gvanrossum/status/636279572938428416</a><br>
>> >> > <a href="http://stevedower.id.au/blog/building-for-python-3-5/" rel="noreferrer" target="_blank">http://stevedower.id.au/blog/building-for-python-3-5/</a><br>
>> >> ><br>
>> >> > The key point is for Python 3.5 on Windows builds now use<br>
>> >> > Microsoft Visual C++ 14.0, and extension modules should<br>
>> >> > use the same.<br>
>> >> ><br>
>> >> > He notes that for the short term, there are likely to be<br>
>> >> > compatibility problems with mingw32 which we have also<br>
>> >> > used previously.<br>
>> >> ><br>
>> >> > Unless someone else volunteers, at some point I will have<br>
>> >> > to try installing MSVC 14.0 on my old Windows XP machine<br>
>> >> > which has been used for all our recent Biopython Windows<br>
>> >> > installers.<br>
>> >> ><br>
>> >> > Regards,<br>
>> >> ><br>
>> >> > Peter<br>
>> >> ><br>
>> >> > ---------- Forwarded message ----------<br>
>> >> > From: Fernando Perez <<a href="mailto:fperez.net@gmail.com">fperez.net@gmail.com</a>><br>
>> >> > Date: Wed, Aug 26, 2015 at 6:24 AM<br>
>> >> > Subject: [Numpy-discussion] Python extensions for Python 3.5 - useful<br>
>> >> > info...<br>
>> >> > To: Discussion of Numerical Python <<a href="mailto:numpy-discussion@scipy.org">numpy-discussion@scipy.org</a>>,<br>
>> >> > SciPy<br>
>> >> > Developers List <<a href="mailto:scipy-dev@scipy.net">scipy-dev@scipy.net</a>>, Core developer mailing list of<br>
>> >> > the Cython compiler <<a href="mailto:cython-devel@python.org">cython-devel@python.org</a>><br>
>> >> ><br>
>> >> ><br>
>> >> > Just an FYI for the upcoming Python release, a very detailed post<br>
>> >> > from<br>
>> >> > Steve Dower, the Microsoft developer who is now in charge of the<br>
>> >> > Windows releases for Python, on how the build process will change in<br>
>> >> > 3.5 regarding extensions:<br>
>> >> ><br>
>> >> > <a href="http://stevedower.id.au/blog/building-for-python-3-5/" rel="noreferrer" target="_blank">http://stevedower.id.au/blog/building-for-python-3-5/</a><br>
>> >> ><br>
>> >> > Cheers,<br>
>> >> ><br>
>> >> > f<br>
>> >> > --<br>
>> >> > Fernando Perez (@fperez_org; <a href="http://fperez.org" rel="noreferrer" target="_blank">http://fperez.org</a>)<br>
>> >> > fperez.net-at-gmail: mailing lists only (I ignore this when swamped!)<br>
>> >> > fernando.perez-at-berkeley: contact me here for any direct mail<br>
>> >> ><br>
>> >> > _______________________________________________<br>
>> >> > NumPy-Discussion mailing list<br>
>> >> > <a href="mailto:NumPy-Discussion@scipy.org">NumPy-Discussion@scipy.org</a><br>
>> >> > <a href="http://mail.scipy.org/mailman/listinfo/numpy-discussion" rel="noreferrer" target="_blank">http://mail.scipy.org/mailman/listinfo/numpy-discussion</a><br>
>> >> > _______________________________________________<br>
>> >> > Biopython-dev mailing list<br>
>> >> > <a href="mailto:Biopython-dev@mailman.open-bio.org">Biopython-dev@mailman.open-bio.org</a><br>
>> >> > <a href="http://mailman.open-bio.org/mailman/listinfo/biopython-dev" rel="noreferrer" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biopython-dev</a><br>
>> >> ><br>
>> >> ><br>
>> >><br>
>> >> _______________________________________________<br>
>> >> Biopython-dev mailing list<br>
>> >> <a href="mailto:Biopython-dev@mailman.open-bio.org">Biopython-dev@mailman.open-bio.org</a><br>
>> >> <a href="http://mailman.open-bio.org/mailman/listinfo/biopython-dev" rel="noreferrer" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biopython-dev</a><br>
>> ><br>
>> ><br>
><br>
><br>
</div></div></blockquote></div><br></div>