[BioC] Downgrading R to an older version

[Dan Tenenbaum]

----- Original Message -----
> From: "Chong Kim San Allen" <patcksa at nus.edu.sg>
> To: "Steve Lianoglou" <lianoglou.steve at gene.com>, dtenenba at fhcrc.org
> Cc: bioconductor at r-project.org
> Sent: Wednesday, August 13, 2014 10:21:03 AM
> Subject: RE: [BioC] Downgrading R to an older version
> 
> Dear Dan, Steve,
> Thanks for replying so quickly.
> 
> Initially, I was getting an error message that MeDIPS needs an older
> version of R. However, I decided to re-installed R 3.1.1 and then
> tried installing MeDIPS again and it seems to have installed well
> and is now running.
> 
> I don't know what happened but I am just glad it is now working.
> 

Probably you had somehow installed a version of MeDIPS that was meant for an earlier version of R/Bioconductor.

Dan


> Once again, thank you.
> 
> Best.
> Allen
> 
> 
> ________________________________________
> From: mailinglist.honeypot at gmail.com [mailinglist.honeypot at gmail.com]
> On Behalf Of Steve Lianoglou [lianoglou.steve at gene.com]
> Sent: Wednesday, August 13, 2014 11:05 PM
> To: Chong Kim San Allen
> Cc: bioconductor at r-project.org
> Subject: Re: [BioC] Downgrading R to an older version
> 
> Hi,
> 
> On Tue, Aug 12, 2014 at 10:43 PM, Chong Kim San Allen
> <patcksa at nus.edu.sg> wrote:
> > Hi,
> > My server is running Debian and the most stable version of R for
> > Debian is 2.1.5. I decided to use "apititude install r-base=3.1.0"
> > to install a backport version of R but that command just upgraded
> > it to R 3.1.1. I don't know why it installed 3.1.1 instead of
> > 3.1.0?
> >
> > I have 2 software that I would like to run on my server: ChAMP and
> > MeDIPS. It seems that ChAMP will not run on R 2.1.5 but is fine
> > with R 3.1.1. The reverse is true for MeDIPS. I was told by
> > someone that a compromise is to install R 3.1.0.
> 
> There really shouldn't be any difference between 3.1.1 and 3.1.0 --
> which is to say that you should prefer to use the former.
> 
> The bioconductor folks provide daily build reports for the package in
> the "release" and "devel" branch.
> 
> "release" should be run using R 3.1.x (3.1.1), and their build system
> uses 3.1.1 to build these. Their reports suggest that everything is
> feng shui, so perhaps there's likely something not quite right with
> your server.
> 
> Here are the build reports I'm talking about:
> 
> http://bioconductor.org/checkResults/2.14/bioc-LATEST/
> 
> and you'll see that MeDIPS is being built fine.
> 
> So, we'd need some more info from you to help sort you out. The error
> messages you get when you try to install MeDIPS via biocLite on your
> server would be a good place to start.
> 
> HTH,
> -steve
> 
> --
> Steve Lianoglou
> Computational Biologist
> Genentech
>