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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