any 32bit machines right now...
Peter
On Sat, May 16, 2020 at 2:22 PM Andreas Tille wrote:
> Control: tags -1 upstream
> Control: forwarded -1 Peter Cock
>
> Hi Peter,
>
> it seems the patch applied does not work for 32bit architectures.
>
> Kind regards
>
> An
The small patch on this pull request ought to solve the immediate Debian
testing issue for biopython:
https://github.com/biopython/biopython/pull/2890
Peter
On Wed, May 6, 2020 at 3:06 PM Debian Bug Tracking System <
ow...@bugs.debian.org> wrote:
> Thank you for the additional information you
Thanks for the heads up, logged as:
On Tue, May 5, 2020 at 7:40 PM Andreas Tille wrote:
> Control: tags -1 upstream
> Control: forwarded -1 Peter Cock
>
> Hi Peter,
>
> with the upload of ncbi-blast+ version 2.10 Biopython test is running
> into failures (see
>
>
Thanks for the heads up, logged as:
https://github.com/biopython/biopython/issues/2863
Peter
On Tue, May 5, 2020 at 7:40 PM Andreas Tille wrote:
> Control: tags -1 upstream
> Control: forwarded -1 Peter Cock
>
> Hi Peter,
>
> with the upload of ncbi-blast+ version 2.10
--force
The input file is here (plain text with no extension):
https://github.com/biopython/biopython/blob/master/Tests/Fasta/f002
Peter
On Fri, Apr 10, 2020 at 6:29 AM Andreas Tille wrote:
> Control: forwarded -1 Peter Cock
>
> Hi Peter,
>
> the log that is linked to below
We (upstream) have just released Biopython 1.76 which thanks to
the Debian team's feedback from 1.75 should be less problematic
on alternative CPUs:
https://www.open-bio.org/2019/12/20/biopython-1-76-released/
https://pypi.python.org/pypi/biopython/1.76
These are the commits which I think you mig
, 2019 at 4:22 PM Andreas Tille wrote:
>
> On Wed, Dec 04, 2019 at 01:55:26PM +, Peter Cock wrote:
> > Good. If you are still missing Tests/Fasta/flowers.pro.gz that's odd,
> > since it was in the official tar ball:
> >
> > https://fi
wrote:
>
> Hi Peter,
>
> On Mon, Dec 02, 2019 at 03:42:21PM +, Peter Cock wrote:
> > This was included in Biopython 1.74 and 1.75, yet your copy of
> > Tests/test_psw.py
> > would seem to date from Biopython 1.73 or older.
> >
> > I suspect an old cac
There are indeed a LOT of errors in there (and a sprinkling of
harmless warnings which ought really to be silenced within the test
framework).
Picking on the very last one as a simple case, you got:
```
==
FAIL: test_ColumnUnit (
ython/issues/2350
Peter
Peter
On Tue, Nov 19, 2019 at 10:25 PM Andreas Tille wrote:
>
> On Tue, Nov 19, 2019 at 10:03:25AM +0000, Peter Cock wrote:
> >
> > Do you have a list of things still depending on Biopython & Python 2.7
> > handy? We're discussing w
On Tue, Nov 19, 2019 at 10:03 AM Peter Cock wrote:
>
> I mean I would not worry about this particular test failing - and would
> consider whitelisting this test acceptable.
>
> Without yet being able to reproduce this and test it, does this work?:
>
> https://github.com/pet
On Tue, Nov 19, 2019 at 9:43 AM Andreas Tille wrote:
>
> Hi Peter,
>
> I'd like to give you credit as the fastest upstream answering a
> question. ;-) Thanks a lot for it!
Lucky timing.
> On Tue, Nov 19, 2019 at 09:17:17AM +, Peter Cock wrote:
> > Curious
Curious - do you have the Python 2.7 version and build details?
Missing docstrings are unfortunate (and in this case they are in C
code which is a bit different), but ultimately this is harmless. What
puzzles me is what has triggered this, that we fail to see it on our
own testing.
As an aside, f
The key part of the log
http://aws-logs.debian.net/2017/10/30/python-biopython_1.70+dfsg-2_unstable.log
is this bit:
==
FAIL: test_index (test_BWA_tool.BwaTestCase)
Test for creating index files for the reference genome fasta file
for the quick and helpful response
>
> Andreas.
>
> On Thu, May 19, 2016 at 03:31:59PM +0100, Peter Cock wrote:
>> RE: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=824048
>>
>> I've committed this as "fix",
>>
>> https://github.com/
RE: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=824048
I've committed this as "fix",
https://github.com/biopython/biopython/commit/cb5b8f7cf16dfa9aada8d3c71ab8d588ebf0693f
This was a sanity test which failed due to a change in the NCBI output.
We don't currently try to parse the plain tex
On Mon, Feb 1, 2016 at 12:08 PM, Andreas Tille wrote:
> Hi Peter,
>
> ...
>
> Yes. BioPython is OK - I need to reassign the bug - probably to
> libhmsbeagle-dev which is possibly not featuring the correct
> dependencies. I just wanted to investigate the issue before I
> do the reassigning since
Hi all,
I spotted this via an automated @DebianBug Twitter posting:
https://twitter.com/DebianBug/status/693569490655776768
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=813262
Andreas has dealt with other issues like this in the past, but
I wanted to make this explicit on the issue tracker:
Thanks Andreas,
I've logged this as:
https://github.com/biopython/biopython/issues/623
Which version of phyml is being used here?
Eric - can you look at this please?
Peter
On Wed, Sep 23, 2015 at 12:48 PM, Andreas Tille wrote:
> Hi BioPython developers,
>
> the problem is fixed by the patch y
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 ht
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.
>
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
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 debi
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).
On Wed, Apr 30, 2014 at 2:30 PM, Andreas Tille wrote:
> Hi Peter,
>
> thanks for your super-fast response.
>
> On Wed, Apr 30, 2014 at 02:24:42PM +0100, Peter Cock wrote:
>> Are you specifically asking about Biopython 1.63 here?
>
> Yes. Since I have added python3 bin
Hi Andreas,
Are you specifically asking about Biopython 1.63 here? I think you
can reasonable exclude this DTD file (and any others under the
Bio/Entrez/DTD file). Biopython 1.63 will warn if they are missing
but attempt to download them automatically.
We're looking at dropping all the NCBI Entre
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