[BioC] RMySQL

[Amy Mikhail]

Hi all,

Thanks for the info - it worked with BiocLite.

Cheers,
Amy


> 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)
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>
> --
> 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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-------------------------------------------
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)