? This should solve the test failures.
Best,
-Michiel.
On Mon, 8/18/14, Andreas Tille wrote:
Subject: Re: Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
To: "Michiel de Hoon" , debian-powe...@lists.debian.org,
debian-m...@lists.
Andreas Tille wrote:
>
> Subject: Re: Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
> To: "Peter Cock"
> Cc: "Dejan Latinovic" , "Michiel de Hoon"
> , "Biopython discussion list"
> , "751...@bugs.debian.org"
> &l
Python 2.7 even with simple strings
rather than unicode?
Thanks,
-Michiel.
On Sat, 8/16/14, Andreas Tille wrote:
Subject: Re: Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
To: "Peter Cock"
Cc: "Dejan Latinovic" , &q
nce_converter function in
Bio/Cluster/clustermodule.c ?
>> For
example, I am really wondering what strlen(data) inside this
function returns on powerpc.
>>
>> Best,
>>
-Michiel.
>>
>>
>> On Sat, 8/16/14, Andreas Tille
wrote:
>>
>>
S
---------------
>> On Sat, 8/16/14, Andreas Tille wrote:
>>
>> Subject: Re: Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
>> To: "Peter Cock"
>> Cc: "Dejan Latinovic" , "Michiel de Hoon"
>> , &
>
> Best,
> -Michiel.
>
>
> On Sat, 8/16/14, Andreas Tille wrote:
>
> Subject: Re: Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
> To: "Peter Cock"
> Cc: "Dejan Latinovic" , "Mi
powerpc.
Best,
-Michiel.
On Sat, 8/16/14, Andreas Tille wrote:
Subject: Re: Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
To: "Peter Cock"
Cc: "Dejan Latinovic" , "Michiel de Hoon"
, "
Hi Peter,
On Thu, Aug 14, 2014 at 09:52:40AM +0100, Peter Cock wrote:
> >
> > 1. waiting for your confirmation / patch
> > 2. deactivating the specific test
> > 3. exclude mips for biopython
> > 4. ? any better idea ?
> >
> > In the current state all the work we spent in biopython over the
On Thu, Aug 14, 2014 at 9:38 AM, Andreas Tille wrote:
> Hi,
>
> On Tue, Aug 05, 2014 Peter Cock wrote
>> > Unfortunately, on mips (BE)
>> > test test_Cluster.py failed under Python 3.4.
>> > Any progress on this issue?
>
>> No. See discussion on https://github.com/biopython/biopython/pull/340
>
>
Hi,
On Tue, Aug 05, 2014 Peter Cock wrote
> > Unfortunately, on mips (BE)
> > test test_Cluster.py failed under Python 3.4.
> > Any progress on this issue?
> No. See discussion on https://github.com/biopython/biopython/pull/340
Do you have any suggestion what to do regarding the Debian package?
Hi Dejan,
thanks for the hint. I'll apply your patch which looks promising. When
checking the wise package I detected some other issues when trying to
run wise's own test suite which I need to fix before an upload. Once
this is done I'll upload biopython with a versioned Build-Depends. This
wo
On Mon, Aug 4, 2014 at 6:10 PM, Dejan Latinovic
wrote:
>
> Hello,
> I took a look at test failures on mips/mipsel.
>
> Test that fails is based on a result of dnal tool.
> dnal is part of a debian package wise.
>
> ...
>
> With this fix, package python-biopython
> successfully builds for mipsel.
>
Hello,
I took a look at test failures on mips/mipsel.
Test that fails is based on a result of dnal tool.
dnal is part of a debian package wise.
In file: Bio/Wise/__init__.py,
an error was raised because the return value from dnal
is greater than 1.
If you look at dnal.c:
> alb = make_align_d
On Mon, Jun 16, 2014 at 5:31 AM, Michiel de Hoon wrote:
> >> This commit verifies the errors are thrown (and they are not
> >> under Python 3 on the Mac):
> >>
> https://github.com/peterjc/biopython/commit/5b99854a82f08321ad78feaf0b362002d2d1fd2b
> >>
> >> I'm going to have to pass this one
>> This commit verifies the errors are thrown (and they are not
>> under Python 3 on the Mac):
>> https://github.com/peterjc/biopython/commit/5b99854a82f08321ad78feaf0b362002d2d1fd2b
>>
>> I'm going to have to pass this one to Michiel to look at... but it
>> looks like a glitch in the bytes v
On Fri, Jun 13, 2014 at 11:05 PM, Andreas Tille wrote:
> Hi Peter,
>
> thanks for your quick response.
>
> On Fri, Jun 13, 2014 at 02:57:37PM +0100, Peter Cock wrote:
>> > I have updated the Debian package to version 1.64 (BTW, it is fine to
>> > ping debian-...@lists.debian.org about new upstream
Hi Peter,
thanks for your quick response.
On Fri, Jun 13, 2014 at 02:57:37PM +0100, Peter Cock wrote:
> > I have updated the Debian package to version 1.64 (BTW, it is fine to
> > ping debian-...@lists.debian.org about new upstream versions - we might
> > become more quick in packaging new versio
* Peter Cock , 2014-06-13, 14:57:
Line 555-557,
clusterid, celldata = somcluster(data=data, mask=mask, weight=weight,
transpose=0, nxgrid=10, nygrid=10,
inittau=0.02, niter=100, dist='e')
This all give the fo
Hi Andreas, Jakub,
On Fri, Jun 13, 2014 at 1:55 PM, Andreas Tille wrote:
> Hi BioPython developers,
>
> I have updated the Debian package to version 1.64 (BTW, it is fine to
> ping debian-...@lists.debian.org about new upstream versions - we might
> become more quick in packaging new versions).
Hi BioPython developers,
I have updated the Debian package to version 1.64 (BTW, it is fine to
ping debian-...@lists.debian.org about new upstream versions - we might
become more quick in packaging new versions). Thanks for adopting the
patches we sended to you.
Since the Debian package is built
* Scott Kitterman , 2014-06-11, 12:46:
All four archs fail with a similar error:
E: pybuild pybuild:256: test: plugin custom failed with: exit code=1: mkdir -p
/«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_2.7/build/Doc; \
cp -a Doc/Tutorial.tex
/«BUILDD
Source: python-biopython
Version: 1.64+dfsg-1
Severity: serious
Justification: fails to build from source (but built successfully in the past)
All four archs fail with a similar error:
E: pybuild pybuild:256: test: plugin custom failed with: exit code=1: mkdir -p
/«BUILDDIR»/python-biopython-1.6
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