[BioC] How to use biomaRt with RMySQL under Windows

sdurinck@ebi.ac.uk sdurinck at ebi.ac.uk
Fri Jan 27 09:14:19 CET 2006


Normally installing RMySQL under Windows is not extremely difficult, but
indeed you have to manually intervene during the installation process and
move the .dll files from the RMySQL/libs directory to the R/bin directory.
 No MySQL client installation is necessary on Windows.  However on Linux
you need to install a MySQL client.

I'm currently working on a new version of biomaRt that by default will do
the queries over HTTP and not via MySQL (although queries with MySQL will
still be an option).  With this I hope the biomaRt package will be easier
to install and won't have firewall problems.  I expect to put the update
in the repository by early February.


> "James W. MacDonald" <jmacdon at med.umich.edu> wrote
> in message news:43D9335A.3050908 at med.umich.edu...
>> > I'm confused.  There is no libs/libMySQL.dll but only a
> libs/libMySQL.lib
>> > file.
>> Odd. Maybe you got a bum download? I checked my RMySQL installation, and
>> also re-downloaded the binary package, and I have
> Jim, you're absolutely right.  I was having problems downloading the file
> http://stat.bell-labs.com/RS-DBI/download/
> The problem could have been a proxy server problem on my end, a fire wall
> problem somewhere, or a high level of cosmic rays somewhere <g>.  I could
> see the page, but all attempts to download any file from that page timed
> out
> on me earlier today. I gave up after about a dozen attempts.
> Since Google didn't seem to know about any other copies of the file on the
> Internet, I requested one by E-mail from David James.  He was so kind to
> send me one very quickly, but the one I received by E-mail didn't have the
> .DLL your were describing.  So, I found the needed DLL somewhere else.
> <g>.
> The problem preventing my direct downloads has gone away, and yes, I can
> now
> see the DLL file you're describing.  All is well now, and RMySQL and
> biomaRt
> are working quite nicely under Windows -- and installed but not yet tested
> under Linux.  I try to keep the same tools working on both platforms
> whenever possible.
> Thanks again,
> efg
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