[Bioc-devel] Problem loading Biobase in newest R2.4 for windows

[Seth Falcon]

"James W. MacDonald" <jmacdon at med.umich.edu> writes:

> Oosting, J. (PATH) wrote:
>> When I try to load Biobase 1.11.32 in the latest versions of R (from
>> about 3 sep onwards) I get the following error message. I'm not sure
>> whether this is a R problem or a Biobase problem. This doesn't happen
>> to a july version of R2.4, and looking at the check page for 1.9 it
>> doesn't happen with the aug 31 version either. I have now tried it on
>> different systems and a few versions (even compiled R for windows on
>> the latest src snapshot). It does not happen on a linux system with
>> the latest R.
>
> This is because of some changes in S4 objects in R-devel. You can't just 
> use the win32 binaries from BioC right now (the release 1.9 binaries 
> that is) because they have to be rebuilt using a newer version of 
> R-devel that has the changes (which are still being made AFAIK). If you 
> can build source packages on your windows box, you can always use
>
> biocLite("packagename", type = "source")
>
> which will download and install the source packages, which will then 
> work. Unfortunately this doesn't work for certain packages because they 
> need special babying on windows (XML, RCurl, RMySQL, maybe some others). 
> These have to be installed by hand.

Yes, what Jim said.  We plan to update (most of) our build systems
today to the most recent R 2.4.0 alpha.  By Monday, we should have
updated Windows binaries.

+ seth