[BioC] Biobase/affy installation problem in linux

[Ting-Yuan Liu]

Hi Anja,

If you are using R 2.1.1, could you upgrade to R 2.2.0, which is the 
latest versionof R, please?  

After you upgrade to R 2.2.0, you can use the biocLite script to install 
BioConductor for you.  In an R command window, type the following:

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

Please refer to the "Install - How To" page on the BioConductor official 
website.  

If you still have trouble in installing BioConductor, please report the 
error/warning messages and the result of sessionInfo() to the list again.  

HTH,
Ting-Yuan

______________________________________
Ting-Yuan Liu
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
Seattle, WA, USA
______________________________________

On Sat, 26 Nov 2005, Anja Schiel wrote:

> I have downloaded R version 2.1.1 via apt-get and have now a running R
under Ubuntu Breezy Badger. But now I would like to use the Bioconductor
packages and tried to install with BioC().
No matter if I use the root account or my personal login, I always end
up with at least 11 to 14 warnings and always the problem that all
packages dependent on the Biobase package can not be installed.

I should mention that I gave myself permission to all libraries and
anyhow, other libraries such as limma are not affected.

Warning messages:
1: installation of package 'Biobase' had non-zero exit status in:
install.packages(pkgs = c("affy", "affydata", "affyPLM",
"annaffy",   ...
2: installation of package 'Biostrings' had non-zero exit status in:
install.packages(pkgs = c("affy", "affydata", "affyPLM",
"annaffy",   ...
3: installation of package 'pamr' had non-zero exit status in:
install.packages(pkgs = c("affy", "affydata", "affyPLM",
"annaffy",   ...
4: installation of package 'affy' had non-zero exit status in:
install.packages(pkgs = c("affy", "affydata", "affyPLM",
"annaffy",   ...
5: installation of package 'annaffy' had non-zero exit status in:
install.packages(pkgs = c("affy", "affydata", "affyPLM",
"annaffy",   ...
6: installation of package 'edd' had non-zero exit status in:
install.packages(pkgs = c("affy", "affydata", "affyPLM",
"annaffy",   ...
7: installation of package 'genefilter' had non-zero exit status in:
install.packages(pkgs = c("affy", "affydata", "affyPLM",
"annaffy",   ...
8: installation of package 'multtest' had non-zero exit status in:
install.packages(pkgs = c("affy", "affydata", "affyPLM",
"annaffy",   ...
9: installation of package 'vsn' had non-zero exit status in:
install.packages(pkgs = c("affy", "affydata", "affyPLM",
"annaffy",   ...
10: installation of package 'geneplotter' had non-zero exit status in:
install.packages(pkgs = c("affy", "affydata", "affyPLM",
"annaffy",   ...
11: installation of package 'makecdfenv' had non-zero exit status in:
install.packages(pkgs = c("affy", "affydata", "affyPLM",
"annaffy",   ...
12: installation of package 'matchprobes' had non-zero exit status in:
install.packages(pkgs = c("affy", "affydata", "affyPLM",
"annaffy",   ...
13: installation of package 'gcrma' had non-zero exit status in:
install.packages(pkgs = c("affy", "affydata", "affyPLM",
"annaffy",   ...
14: installation of package 'affyPLM' had non-zero exit status in:
install.packages(pkgs = c("affy", "affydata", "affyPLM",
"annaffy",   ...

So when I try to open affy the following error message appears.

> library(affy)
Loading required package: Biobase
Error in library.dynam(lib, package, package.lib) :
        shared library 'Biobase' not found
In addition: Warning messages:
1: package 'Biobase' contains no R code in: loadNamespace(package,
c(which.lib.loc, lib.loc))
2: S3 method ‘as.data.frame.exprSet’ was declared in NAMESPACE but not
found
Error: package 'Biobase' could not be loaded

I used the woody URL to apt-get install, but I guess that should not
make a difference.

I checked the mail archive, but somehow this particular problem was not
discussed. It seems that something goes wrong during compiling the
Biobase package.
Any suggestions would be very welcome, I am not necessarily an expert on
Linux.

Greetings and thanks in advance,
Anja Schiel

_______________________________________________
Bioconductor mailing list
Bioconductor at stat.math.ethz.ch
https://stat.ethz.ch/mailman/listinfo/bioconductor