[BioC] Problems with BioConductor 1.9 in R-2.4.1

[Groot, Philip de]

Hello,
 
I want to report 2 problems.
 
The first problem is encountered when installing bioconductor 1.9 in R-2.4.1 (Linux: g++ (GCC) 3.3.3 (SuSE Linux)). When executing the getBioC.R script, everything installs fine EXCEPT annaffy. I obtain the following warning:
 
Warning message:
installation of package 'annaffy' had non-zero exit status in: install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,
 
When I try to install this package manually, the following happens:
 
R CMD INSTALL ./annaffy_1.6.0.tar.gz
* Installing *source* package 'annaffy' ...
** R
** data
** inst
** save image
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
    Vignettes contain introductory material. To view, type
    'openVignette()' or start with 'help(Biobase)'. For details
    on reading vignettes, see the openVignette help page.
Loading required package: GO
Loading required package: KEGG
Error in setIs(class2, cli, extensionObject = obji, doComplete = FALSE,  :
        Unable to find package environment for class "AssayData" to revise subclass information
Error in setClass("aafGO", "aafList", prototype = list()) :
        error in contained classes ("aafList") for class "aafGO"; class definition removed from "annaffy"
Error: unable to load R code in package 'annaffy'
Execution halted
ERROR: execution of package source for 'annaffy' failed
** Removing '/mnt/geninf01/prog64/R/R-2.4.1/lib64/R/library/annaffy'
 
This problem only occurs with the latest R-release. In R-2.4.0 everything works fine (I just checked it). It is the same version of annaffy: 1.6.0. What is going on and how can it be fixed?
 
The second problem that I have applies to both R-2.4.0 and R-2.4.1. I compile the win32 RGui myself from source using the mingw-5.1.1 compiler (and msys).  R works fine. Bioconductor installs etc. But last week, I found that in R-2.4.0 the library 'graph' won't load. This is the error message that I obtain:
 
> library(graph)
Error in `parent.env<-`(`*tmp*`, value = NULL) : 
        use of NULL environment is defunct
Error: package/namespace load failed for 'graph'

The same error occurs for R-2.4.1 (which makes sense off course). However, if I install the pre-compiled binary this problem does not occur. I do not know where this problem comes from, but I followed everything in the administration guide on compiling R in Windows. Someone any suggestion?
 
Thanks!
 
Dr Philip de Groot
Wageningen University