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

Hi Philip, "Groot, Philip de" <philip.degroot at="" wur.nl=""> writes: > 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, We are able to reproduce this problem and I believe that Martin already has a fix in hand that will be sent to the release branch. We should have an updated annaffy package available within a day. > 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' How did you install the graph package? And what version do you have? Please try using getBioC/biocLite to reinstall the graph package. And send output from sessionInfo(). > 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? I wonder if you are picking up a stale package library when you run your source-built R's? + seth