<div>Indeed, plenty of warnings.. I'll check here as well, there should be a ignore statement somewhere in the code. </div>
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<br><br><div class="gmail_quote"><p>On Sun, Aug 30, 2015 at 2:09 PM, 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></p><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><p>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><br>Peter<br><br>On Fri, Aug 28, 2015 at 8:36 PM, Ben Fulton <ben@benfulton.net> 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>> https://iu.box.com/biopython-win-python35-test<br>><br>><br>><br>><br>> On Fri, Aug 28, 2015 at 9:05 AM, Peter Cock <p.j.a.cock@googlemail.com><br>> wrote:<br>>><br>>> Thanks Ben, any help here would be great:<br>>> https://github.com/biopython/biopython/issues/601<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>>> http://testing.open-bio.org/biopython/tgrid<br>>> http://biopython.org/wiki/Continuous_integration<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>>> http://biopython.org/wiki/64-bit_Windows_Biopython<br>>><br>>> Peter<br>>><br>>> On Fri, Aug 28, 2015 at 1:43 PM, Ben Fulton <ben@benfulton.net> 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 <p.j.a.cock@googlemail.com><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>>> >> <cjfields@illinois.edu> wrote:<br>>> >> > Peter, Just a note on Windows XP and Python 3.5 support (under<br>>> >> > 'Unsupported<br>>> >> > Operating Systems’):<br>>> >> ><br>>> >> > https://docs.python.org/3.6/whatsnew/3.5.html<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 <p.j.a.cock@googlemail.com><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>>> >> > https://www.python.org/downloads/release/python-350rc2/<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>>> >> > https://twitter.com/gvanrossum/status/636279572938428416<br>>> >> > http://stevedower.id.au/blog/building-for-python-3-5/<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 <fperez.net@gmail.com><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 <numpy-discussion@scipy.org>,<br>>> >> > SciPy<br>>> >> > Developers List <scipy-dev@scipy.net>, Core developer mailing list of<br>>> >> > the Cython compiler <cython-devel@python.org><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>>> >> > http://stevedower.id.au/blog/building-for-python-3-5/<br>>> >> ><br>>> >> > Cheers,<br>>> >> ><br>>> >> > f<br>>> >> > --<br>>> >> > Fernando Perez (@fperez_org; http://fperez.org)<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>>> >> > NumPy-Discussion@scipy.org<br>>> >> > http://mail.scipy.org/mailman/listinfo/numpy-discussion<br>>> >> > _______________________________________________<br>>> >> > Biopython-dev mailing list<br>>> >> > Biopython-dev@mailman.open-bio.org<br>>> >> > http://mailman.open-bio.org/mailman/listinfo/biopython-dev<br>>> >> ><br>>> >> ><br>>> >><br>>> >> _______________________________________________<br>>> >> Biopython-dev mailing list<br>>> >> Biopython-dev@mailman.open-bio.org<br>>> >> http://mailman.open-bio.org/mailman/listinfo/biopython-dev<br>>> ><br>>> ><br>><br>><br><br>_______________________________________________<br>Biopython-dev mailing list<br>Biopython-dev@mailman.open-bio.org<br>http://mailman.open-bio.org/mailman/listinfo/biopython-dev</p></blockquote></div><br>