[BioC] RMySQL

[James W. MacDonald]

Hi Amy,

Amy Mikhail wrote:
> 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?

I believe this same question was asked and answered earlier today on 
this listserv. Anyway,

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

should do the trick.

Note that with most source packages (xx.tar.gz), you will need quite a 
few tools installed to build on Windows (see the R-FAQ for windows). 
This is even more work for this particular package, so the best bet is 
to get a pre-compiled binary.

Best,

Jim


> 
> 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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-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623



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