[Bioc-devel] Development Versions

[Ajish]

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