[Bioc-devel] Development Versions

[Kasper Daniel Hansen]

I assume you are working under *NIX.

Get the devel version of R and compile it from sources.

Do
   source("http;//www.bioconductor.org/biocLite.R")
   biocLite("affy")
etc.

Note the use of biocLite instead og getBioC and that you need to run  
the script from the devel version of R.

Kasper

On Nov 17, 2005, at 5:44 PM, Ajish wrote:

> To the R Gurus:
>
> I've been searching for about 3 days for some easy way to get the
> developmental packages (specifically the affy, oligo, and makecdfenv
> packages but wouldn't it be nice to have them all) deployed on my  
> machine.
>
> I tried first just updating all the packages on R 2.1 with
> update.packages2(develOK=TRUE). This seemed to choke at some point
> giving me errors about failed to get repListing in BioCRel1.8 --
> apparently something was wrong with 2.1 connecting to the devel
> repository as the current release packages installed and worked fine.
>
> Next, I decided to put the new 2.2 distro of R on my machine and  
> see if
> it could get the devel packages. After installing R 2.2, I conjured up
> the getBioC script at bioconductor.org with getBioC(develOK=TRUE). The
> result:
>
>> getBioC(develOK=TRUE)
> Error in getBioC(develOK = TRUE) : develOK has been deprecated.  If  
> you
> would like to use this script for installing developmental  
> packages, you
> must install the devel version of R.
>
> Sure... Get the devel version of R to get the devel packages -- makes
> some twisted sort of sense to play with all the unstable bits at once.
> So I grab the latest R 2.3 nightly, compile and build it. Trying the
> getBioC script again:
>> getBioC(develOK=TRUE)
> Error in getBioC(develOK = TRUE) : develOK has been deprecated.  If  
> you
> would like to use this script for installing developmental  
> packages, you
> must install the devel version of R.
>
> Huh?! I thought this WAS the devel version of R... Doesn't make too  
> much
> sense. After puttering around looking for all possible permutations  
> and
> substrings of "bioconductor and developmental" I found some  
> reference to
> an isDevel argument for getBioC. Trying that for both 2.2 and 2.3  
> yields:
>> getBioC(isDevel=TRUE)
> Running getBioC version 0.8  with R version  2.3.0
> Error in getBioC(isDevel = TRUE) :
> Please check back soon, currently the BioConductor developmental
> packages are not available for R 2.3 users.
>
> What now? How about trying installing just the BioC 1.7 on the stable
> 2.2 and trying install.packages2 in there?
>> install.packages2("oligo", develOK=TRUE)
> Warning message:
> The develOK option is deprecated and will be ignored.
> If you would like to install development versions of
> Bioconductor packages, please install a development
> version of R. in: install.packages2("oligo", develOK = TRUE)
>
> Wow. That's helpful. I guess the only recourse then is to ... what?
> Install the unstable version of R with BioC 1.7 and then
> install.packages2 or update.packages2 upto the devel versions.  
> After all
> of this I still have some doubt as to whether this will work.
>
>
> Any help or pointers to a HOW-TO for getting all the Devel packages of
> BioC 1.8 working on my box would be much appreciated.
>
> Thanks,
>
> Ajish
> a frustrated newbie
>
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