[BioC] problems with biomaRt on Mac OS X (10.4.2 = Tiger)

[sdurinck]

Hi Jane,

Which version of RMySQL are you running?  The version you can get from
the CRAN repository is 0.5.5 but there is a newer version (0.5.6) here:

http://stat.bell-labs.com/RS-DBI/download/

Have you tried using that one?

If this also doesn't work, we can contact the maintainer of the RMySQL
package to see if he can provide us with an update.

Note:  If you would want to use biomaRt under Windows, I've put the
latest biomaRt Windows build here:

http://homes.esat.kuleuven.be/~sdurinck/biomaRt_1.5.1.zip

best,
Steffen



Dear Mac users:

more problems with bioC packages on Mac OSX: this time with biomaRt (R
2.2. and latest BioC release). It installs but then when i am doing
martConnect() it complains about MySQL being out of date (but seems to
establish connection). I actually downloaded the latest version of MySQL
(v. 4.1.15, could not find 4.1.14 it is asking for: would that cause a
problem?), reinstalled all the biomaRt dependencies (DBI and RMySQL) and
then biomaRt but message remains the same ).  mysql got installed into
/usr/local/mysql/bin and the location is in the .bashrc path. I would not
mind the message except when i try to do smthg with the package, e.g.
getGene, R session automatically closes. Interestingly, I checked with
Wolfgang Huber, one of the package authors and he says that he observed
the same message of mysql being out of date on his linux but is able to
run the examples without problems.

I hope i am not flooding the list with my "BioC on Mac" questions. biomaRt
was working fine under windows for me , at least in the previous
iterations and was very useful.

Thanks again

Jane


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