[BioC] RMySQL

[Martin Morgan]

Hi Amy --

try this:

> source("http://bioconductor.org/biocLite.R")
> biocLite("RMySQL")

The underlying reason for your problems is that RMySQL is a bit of a
special package that does not usually install 'out of the box' on
Windows computers (which I'm guessing from the error message about
'zip' files is what you have). The bioconductor people have kindly
taken the extra steps to make an installable version of RMySQL
available.

It also sounds like you might want to make sure that the
'Bioconductor' repository is selected under the Packages --> Select
repositories menu, and that the CRAN mirror is USA (WA).

Hope that helps,

Martin

"Amy Mikhail" <a.mikhail at abdn.ac.uk> writes:

> Dear list,
>
> R: 2.2.1, Bioconductor: 1.7, OS: windows XP
>
> I recently downloaded the package BioMArt, which has RMySQL listed as one
> of its dependencies.  Although I can see this package when I go to the
> CRAN website (Bristol mirror), I'm not able to find or download it from R
> and I get this warning:
>
>> install.packages(c("RMySQL"))
> Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
>          no package 'RMySQL' at the repositories
>
> If I try using the pull-down menu (install packages...) the package is not
> even on the list (actually comparing the website and the list, there are
> quite a few packages that don't show up).
>
> Also, if I download RMySQL_0.5-7.tar.gz from the CRAN website and try
> using "install packages from local zip files", it doesn't work either:
>
>> utils:::menuInstallLocal()
> Error in gzfile(file, "r") : unable to open connection
> In addition: Warning messages:
> 1: error 1 in extracting from zip file
> 2: cannot open compressed file 'RMySQL_0.5-7.tar.gz/DESCRIPTION'
>
> So how (and from where) can I get hold of RMySQL?
>
> Regards,
> Amy
>
>
>
>
> -------------------------------------------
> Amy Mikhail
> Research student
> University of Aberdeen
> Zoology Building
> Tillydrone Avenue
> Aberdeen AB24 2TZ
> Scotland
> Email: a.mikhail at abdn.ac.uk
> Phone: 00-44-1224-272880 (lab)
>
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