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
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
>
>
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
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 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
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
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
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
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
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
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 (
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
, 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
--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
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
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/
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
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:
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
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
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
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
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.
>
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 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
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
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