[BioC] Error with library(limma) with R2.0 devel

[Matthew Hannah]

This does seem to be a problem as now I've come to use affy, it
downloaded ath1121501cdf, but then couldn't use it as built in <2.0.
Tried various (see below) but it's not in CRAN, the local zip from BioC
metaData link is release level, and with Jeffs fix the package can't be
found.....

Can someone suggest a way of getting this to work - build devel
ath1121501 packages?, as without cdf/probe packages there's very little
you can do :(

Cheers,

Matt

> probeset(data,"246863_at")
Note: You did not specify a download type.  Using a default value of:
Win32 
This will be fine for almost all users
 
[1] "Attempting to download ath1121501cdf from
http://www.bioconductor.org/data/cdfenvs/repos/"
[1] "Download complete."
[1] "Installing ath1121501cdf"
Note: Running R version 2.0.0 and package ath1121501cdf was built for R
version 1.8.0
 , installing anyway.
 
[1] "Installation complete"
Error in library("ath1121501cdf", lib.loc =
"C:/PROGRA~1/R/RW2000~2/library") : 
        'ath1121501cdf' is not a valid package -- installed < 2.0.0?

> source("http://www.bioconductor.org/getBioC.R")
> 
> z <- getReposEntry("BIOCDevel")
> install.packages2("ath1121501cdf", repEntry=z, devel=T, type="Win32")
Unable to locate the requested package(s) in any known repository
> install.packages(choose.files('',filters=Filters[c('zip','All'),]),
.libPaths()[1], CRAN = NULL)
package 'ath1121501cdf' successfully unpacked and MD5 sums checked
updating HTML package descriptions
> probeset(data,"246863_at")
Error in library("ath1121501cdf", lib.loc = NULL) : 
        'ath1121501cdf' is not a valid package -- installed < 2.0.0?
> install.packages2("ath1121501", develOK=TRUE)
Note: You did not specify a download type.  Using a default value of:
Win32 
This will be fine for almost all users
 
Unable to locate the requested package(s) in any known repository 

> -----Original Message-----
> From: Gordon K Smyth [mailto:smyth at wehi.EDU.AU] 
> Sent: Mittwoch, 15. September 2004 01:17
> To: Jeff Gentry
> Cc: Matthew Hannah
> Subject: RE: [BioC] Error with library(limma) with R2.0 devel
> 
> >> CRAN actually holds multiple builds of the package for different 
> >> versions of R.  So the R2.0 version is available.
> >
> > I know, that's what I was saying.  We (currently) only have 
> one CRAN 
> > repository and it (currently) is being built off of the 
> 1.9.1 packages.
> >
> > Thus, if one uses the pulldown it will get the one that points 
> > directly at CRAN's 2.0 directory.  If one uses reposTools, it will 
> > wack our CRAN repository which is grabbing the 1.9.1 built packages.
> >
> > Either way, it'd still get it from CRAN as the version # there is 
> > higher then the one on BioC.
> 
> Jeff,
> 
> This seems a serious problem.  As far as I know, no package 
> built for 1.9.1 will run in R 2.0.  So getBioC with 
> develOK=TRUE will install a non-working version of limma.
> 
> This problem will presumably affect not only limma but any 
> BioC package which depends on CRAN packages.
> 
> Gordon
> 
> 
>