It (R, and getBioC) now works but when I tried to load limma I got this > library(limma) Error in library(limma) : 'limma' is not a valid package -- installed < 2.0.0? It works with my previous install of R2.0, but not with the new install (I downloaded everything new, rather than install over the old one). Any ideas? Cheers, Matt > -----Original Message----- > From: Jeff Gentry [mailto:jgentry@jimmy.harvard.edu] > Sent: Freitag, 10. September 2004 17:42 > To: Matthew Hannah > Subject: RE: [BioC] Errors w/ getBioC(develOK =TRUE) with R2.0 devel > > > Hi Matt ... > > Try it now and see if that works. > > > >

Matthew, I have now submitted limma to CRAN, so that users can always get the current version of the package whether or not they're using the development version of R. So just install limma from CRAN. If you're using Windows, just use the drop-down menus: Packages > Install Package(s) from CRAN ... Gordon At 07:21 PM 14/09/2004, Matthew Hannah wrote: >It (R, and getBioC) now works but when I tried to load limma I got this > > > library(limma) >Error in library(limma) : 'limma' is not a valid package -- installed < >2.0.0? > >It works with my previous install of R2.0, but not with the new install >(I downloaded everything new, rather than install over the old one). > >Any ideas? > >Cheers, >Matt

> > library(limma) > Error in library(limma) : 'limma' is not a valid package -- installed < > 2.0.0? > It works with my previous install of R2.0, but not with the new install > (I downloaded everything new, rather than install over the old one). Is this a previous install of limma? After a certain point in the current R-devel cycle, all packages needed to be reinstalled due to changes in the package structure. If this is happening wiht a version that you're downloading, please let me know.

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@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 > > >