equivalents, for instance by re-creating
records from scratch.
I am not very comfortable with any of the solutions, and was wondering if you
would have suggestions ?
d) Revise Debians guidelines to adequately deal with scientific data.
Cheers,
Morten
--
Morten Kjeldgaard, asc. professor, MSc, PhD
distribute it under the same license as the
program itself.
If you decide at some point to repackage the distribution tarball, it
would be a good idea to include the text of the license in a file
COPYING.
Best wishes,
Morten
--
Morten Kjeldgaard, asc. professor, MSc, PhD
Department
I have updated the packaging of mustang to version 3.2 in the svn repo.
AFAIACS it is ready for upload.
Cheers,
Morten
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Ubuntu MOTU Developer
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What do you think?
Cheers,
Morten
--
Morten Kjeldgaard, asc. professor, MSc, PhD
BiRC - Bioinformatics Research Center, Aarhus University
C. F. Møllers Alle, Building 1110, DK-8000 Aarhus C, Denmark.
Lab +45 8942 3130 * Fax +45 8942 3077 * Home +45 8618 8180
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-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Charles Plessy wrote:
I can upload the new upstream release of biopython, that fixes a bug of
severity important, but for the mmCIF support I would need some hints. Can
you file a bug?
It is ~4 lines commented out in setup.py that needs to be
Hi,
So, consider a package I'm team-maintaining in Debian, john. I'm
currently
applying several patches, something like 17 or so. Should I keep 17
separate
branches for this? And how to handle patches touching the same
files but in
different points? (i.e. what the series, 00list and kinda
Andreas Tille wrote:
On Fri, 21 Nov 2008, Daniel Leidert wrote:
A short look into the manual pages hosted in the debian-med SVN
repository revealed several issues:
Many thanks for your QA effort. Did you used any script to verify
these issues or was it a result of a manual
starting, the Ubuntu developers will by sync'ing and
merging packages from Sid during the next month.
Cheers,
Morten
--
Morten Kjeldgaard, asc. professor, MSc, PhD
BiRC - Bioinformatics Research Center, Aarhus University
C. F. Møllers Alle, Building 1110, DK-8000 Aarhus C, Denmark.
Lab +45 8942
the 2nd paragraph of the DESCRIPTION in Stephane's older manpage transferred
to the new one. Is there some particular reason for not doing this
(copyright)?
This is a trivial modification, so once these points are
clarified, someone :-) should commit the update.
Cheers,
Morten
--
Morten
Nelson wrote:
But even with this, I think that it's wrong.
Applying patch_15Jan2008.mustang will change the version on line 390
of src/CmdLineParser_2.cpp from MUSTANG v.3 Command Line error!\n to
MUSTANG vO.2 Command Line error!\n
The same thing on line 142 of src/superpose_on_core_2.cpp
On 05/02/2008, at 16.37, Nelson A. de Oliveira wrote:
So we have:
3.0.1 3.0+p1 3.0
There won't be problems if using 3.0+p1, for example.
Agreed? :-)
Heh, not quite actually... :-)
The way I've done it is apply upstreams patches via the dpatch system
to the old tarball. When the
On 06/02/2008, at 20.19, Nelson A. de Oliveira wrote:
You need to use 3.0+p1 only if you use the new tarball.
With the old one the version will be 3.0 only.
Of course! It makes absolutely sense! 3.0 it is! I applied the patch
from your mail yesterday. Committed to svn.
Cheers,
Morten
Nelson wrote a short while ago:
There is only one detail: the upstream patch is wrong. It was diffed
wrongly (diff new old instead diff old new).
You can verify by diffing the old tarball against the new one and
comparing to http://www.cs.mu.oz.au/~arun/mustang/
patch_15Jan2008.mustang
The
Hello,
I have committed substantial changes to the mustang package in the
svn repo.
First, the sources have been patched with a patch from upstream.
Unfortunately, upstream has not changed the version number.
Therefore, the patch level has been added to the release. I don't
know if
as per .pdb format version 2.3, all records must start with a HEADER
field.
Actually, a valid PDB format file must start with a HEADER record.
All records must start with a max 6 character long record type, i.e.
HEADER, COMPND, ATOM, etc.
But is the content of the file relevant for the
The existence of /tmp is required by the FHS standard, so I think
it should
be safe to assume it exists.
Sorry to be unclear. I mean safe in the sense of security. A
predictable
*file*name in a world writable directory is unsafe because it can
be used for
a symlink attack to overwrite
On 12/01/2008, at 3.27, Nelson A. de Oliveira wrote:
On Jan 12, 2008 12:13 AM, Nelson A. de Oliveira [EMAIL PROTECTED]
wrote:
And I was thinking if it's not better to use /tmp/mustang (instead
only mustang) in debian/runtest and debian/patches/test_zf-
cchh.dpatch
^^^
On 12/01/2008, at 0.45, Charles Plessy wrote:
This sounds like a good idea, how about proposing it on the
CopyrightFormat wiki page ?
Done!
Cheers,
Morten
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, but I do think that the decision for creating it must come
from upstream.
Cheers,
Morten
--
Morten Kjeldgaard, Asc. professor, Ph.D.
Department of Molecular Biology, Aarhus University
Gustav Wieds Vej 10 C, DK-8000 Aarhus C, Denmark
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Home
Andreas,
you overrode these files. If it was not intentionally we might
move it
back. As I said I might do it tomorrow evening (because at daytime
I have
no SVN access).
Don't worry, I fixed it, and made some further commits. Now I need to
check my mail messages from you and Charles
I just stumbled over this program in Freshmeat. Perhaps it is
something worth considering for debian-med?
http://freshmeat.net/projects/mypatients/?
branch_id=71759release_id=269319
From the project description:
MyPatients is a medical records database that uses OpenOffice.org
Base and
Hello again,
On 09/01/2008, at 22.07, Andreas Tille wrote:
I can see the packages on the bio task page. However, I have
downloaded the svn repo according to the instructions on the wiki,
but I can't see neither mustang or btk-core there. Did you commit
them?
Perhaps the explanation of
On 09/01/2008, at 1.45, Charles Plessy wrote:
For the copyright files, you may be interested by the proposed
machine-parsable format described in the following link. Although no
parser has been written yet, it could be useful to start to use it:
http://wiki.debian.org/Proposals/CopyrightFormat
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