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

Jane Fridlyand janef at stat.Berkeley.EDU
Sun Oct 30 21:06:12 CET 2005

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martConnect() it complains about MySQL being out of date (but seems to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the same message of mysql being out of date on his linux but is able to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


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