Hi Peter,
many thanks for this information. Since I'd like to reward the user
reporting the bug as fast as possible and to send the message that we
really care about our users I applied the fix right now and uploaded
the package.
Kind regards
Andreas.
On Fri, May 09, 2014 at 01:36:32PM
Hi Jamie,
On Sat, May 10, 2014 at 09:22:29AM +1200, Jamie Norrish wrote:
from .cpairwise2 import rint, _make_score_matrix_fast
should do the trick.
Indeed. This was actually reported and fixed a couple of months ago
upstream[1]; I foolishly didn't check the closed bugs there
Package: python3-biopython
Version: 1.63+dfsg-4
Severity: normal
Dear Maintainer,
After installing this package, the cpairwise2 C implementations of
functions are not available (see the end of Bio/pairwise2.py for the
attempted loading of these):
Python 3.3.5 (default, Mar 22 2014, 13:24:53)
Hi Jamie,
thanks for your bug report. I think this should work out of the box but
I personally not comfortable with cpython to know how this could be
fixed. I keep the Debian Python list in CC - perhaps they might have
some helpful advise.
It seems this module is not affected by the test suite
[Andreas Tille, 2014-05-09]
from cpairwise2 import rint
Traceback (most recent call last):
File stdin, line 1, in module
ImportError: No module named 'cpairwise2'
But some (presumably relevant; I know nothing about how Python
interfaces with C code) files are installed:
$
* Andreas Tille andr...@an3as.eu, 2014-05-09, 13:15:
thanks for your bug report. I think this should work out of the box
but I personally not comfortable with cpython to know how this could be
fixed. I keep the Debian Python list in CC - perhaps they might have
some helpful advise.
The
Hi,
while I have just closed this bug report since I assumed it was a wrong
usage of the import statement I would like to forward this issue to
upstream Biopython developers anyway. It seems there are cases when
cpairwise2 is not used and things might work slower than necessary.
I just forward
Hi Andreas,
This was reported directly to Biopython and fixed two months ago:
https://github.com/biopython/biopython/pull/299
https://github.com/biopython/biopython/commit/daf3e3b5ba317fbbea1f7eebae3c5f8b06a40d6b
If you want to apply the one line fix to Biopython 1.63 for the Debian
Python 3
On Fri, 2014-05-09 at 13:32 +0200, Jakub Wilk wrote:
But in Python 3 imports as always absolute, unless explicitly
requested, so the import fails, and this code snippet is no-op.
Changing the import line to:
from .cpairwise2 import rint, _make_score_matrix_fast
should do the trick.
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