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Due to different time zones, I'm not sure Lincoln's comment was before or after our exchange on the mailing list. It also seemed like a good idea to put these notes on the bug tracker.
Today (19 Dec 2008) I updated a working Linux installation of GBrowse 1.69+ under apache to the latest stable code using:
$ sudo perl gbrowse_netinstall.pl --gbrowse_dev --build_param_str="--SELINUX=1"...
2008-12-19 11:14:51 UTC in Generic Model Organism System Database
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I would favour writing these additional lines to standard error (ideally all the time, but at very least when -filter is used).
2008-12-17 12:18:19 UTC in EMBOSS Suite
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I've just check using EMBOSS 6.0.1 on Mac OS X, and the warnings are still present.
Was this bug closed because it was fixed in CVS?
Thanks
Peter.
2008-12-17 11:30:04 UTC in EMBOSS Suite
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This has been reported on the mailing list and should be fixed in SVN.
https://sourceforge.net/mailarchive/forum.php?thread_name=d9bfa52b0812011537x63b3e541g4ba46ae97af3abc4%40mail.gmail.com&forum_name=rpy-list
According to Laurant, "An immediate workaround is to put the right R in the path, and a fix should appear a little later.".
2008-12-07 14:49:00 UTC in RPy (R from Python)
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The MySQLdb/__init__.py update works for me on Python 2.6 (using MySQLdb 1.2.2 plus MySQLdb/__init__.py revision 554).
That leaves MySQLdb/converters.py still using the deprecated sets module. When I originally filed this bug I have noticed you imported BaseSet,
from sets import BaseSet, Set
However, you are not actually using BaseSet, but just Set in the Str2Set function. This means...
2008-10-17 09:10:44 UTC in MySQL for Python
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This was reported on the mailing list, and Lincoln suggested filing a bug.
Tested on Linux and MacOS, using GBrowse 1.69 and the then current SVN stable branch.
Using BioSQL with GenBank files loaded using either BioPerl or Biopython.
GenBank files with revision/version equal to one work fine, e.g.
ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Nanoarchaeum_equitans/NC_005213.gbk...
2008-10-15 14:15:57 UTC in Generic Model Organism System Database
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As of python 2.6, the sets module is deprecated. This is currently used in MySQLdb/__init__.py and MySQLdb/converters.py - on both the 1.2 branch and the trunk.
Fixing the ImmutableSet usage is fairly easy. Currently:
from sets import ImmutableSet
class DBAPISet(ImmutableSet):
...
I think the new built in frozenset (added in python 2.4) should be used instead. Suggested short...
2008-10-10 09:29:02 UTC in MySQL for Python
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No, MySQL-python doesn't use SWIG.
However, MySQLdb does use an old version of setuptools, which clashes with the version of pyrex on my machine due to a mismatch in the swig_sources() argument signature.
The tiny change to ez_setup.py does seem to resolve this issue neatly.
2008-06-26 09:14:03 UTC in MySQL for Python
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I'm trying to install MySQLdb 1.2.2 from source on Mac OS X Leopard. I have downloaded and unzipped the tar ball, and edited site.cfg to include:
mysql_config = /usr/local/mysql/bin/mysql_config
Then, from the MySQL-python-1.2.2 directory:
$ python setup.py build
running build
running build_py
creating build
creating build/lib.macosx-10.3-i386-2.5
copying _mysql_exceptions.py ->...
2008-06-24 15:32:39 UTC in MySQL for Python
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Try running R, which on your machine appears to be version 2.4.1, and typing:
library(mgcv)
I predict this will fail after giving the warning message:
package 'mgcv' was built under R version 2.5.0
i.e. Where ever you got your copy of mgcv from, it appears to be intended for R 2.5.0 not 2.4.1
If this does fail in R, then your problem is nothing to do with rpy.
2007-05-17 13:57:37 UTC in RPy (R from Python)
