[Bioc-devel] Failing to installing prada in 1.9 release

[Wolfgang Huber]

Hi Florian & Biocore,

I just installed an R-2.4.1 from scratch,  then ran

  source("http://www.bioconductor.org/biocLite.R")
  biocLite("cellHTS")

I get errors that seem to do with the usage of classes from Biobase in 
prada that hasn't kept up with the moving target that these classes have 
been...

-- 
* Installing *source* package 'prada' ...
** libs
gcc -std=gnu99 -I/homes/huber/p/R-2.4.1/include 
-I/homes/huber/p/R-2.4.1/include  -I/usr/local/include    -fpic  -O3 -c 
inPolygon.c -o inPolygon.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o prada.so inPolygon.o
** 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: RColorBrewer
Loading required package: grid
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Error in setIs(class2, cli, extensionObject = obji, doComplete = FALSE,  :
         Unable to find package environment for class "VersionedBiobase" 
to revise subclass information
Error in setClass("ddCtSet", contains = "eSet", validity = 
function(object) { :
         error in contained classes ("eSet") for class "ddCtSet"; class 
definition removed from "prada"
Error: unable to load R code in package 'prada'
Execution halted
ERROR: execution of package source for 'prada' failed
** Removing '/panfs/panda1/huber/users/huber/R-2.4.1/library/prada'
* Installing *source* package 'cellHTS' ...
** R
** data
** inst
** preparing package for lazy loading
Error: package 'prada' required by 'cellHTS' could not be found
Execution halted
ERROR: lazy loading failed for package 'cellHTS'
** Removing '/panfs/panda1/huber/users/huber/R-2.4.1/library/cellHTS'

The downloaded packages are in
         /tmp/RtmprJRgHs/downloaded_packages
Warning messages:
1: installation of package 'prada' had non-zero exit status in: 
install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,
2: installation of package 'cellHTS' had non-zero exit status in: 
install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,


 > sessionInfo()
R version 2.4.1 (2006-12-18)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"
[7] "base"


------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber