[BioC] BioC 2.3 standard installation

[Hervé Pagès]

Hi Tiandao,

What OS do you have? How did you install R? It looks like you cannot
install an R package with native code at all. Please try

   > install.packages("XML")

and show us the complete output.
You could also try the R-help mailing list (r-help at r-project.org)
since your problem doesn't seem to be Bioconductor-specific.

Cheers,
H.


Tiandao Li wrote:
> Hello,
> 
> I tried to install BioC 2.3 on a new laptop (HP AMD Turion x2). However I
> constantly had the following warnings, I tried several times for the last
> few days. I never had this kind of errors before.
> 
> sudo R
> 
>> source("http://bioconductor.org/biocLite.R")
> 
>> biocLite()
> 
>> warnings()
> Warning messages:
> 1: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies, ... :
>   installation of package 'Matrix' had non-zero exit status
> 2: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies, ... :
>   installation of package 'preprocessCore' had non-zero exit status
> 3: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies, ... :
>   installation of package 'IRanges' had non-zero exit status
> 4: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies, ... :
>   installation of package 'affy' had non-zero exit status
> 5: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies, ... :
>   installation of package 'affydata' had non-zero exit status
> 6: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies, ... :
>   installation of package 'Biostrings' had non-zero exit status
> 7: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies, ... :
>   installation of package 'matchprobes' had non-zero exit status
> 8: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies, ... :
>   installation of package 'vsn' had non-zero exit status
> 9: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies, ... :
>   installation of package 'gcrma' had non-zero exit status
> 10: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies, ... :
>   installation of package 'simpleaffy' had non-zero exit status
> 11: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies, ... :
>   installation of package 'affyPLM' had non-zero exit status
> 12: In install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies, ... :
>   installation of package 'affyQCReport' had non-zero exit status
> 
>> sessionInfo()
> R version 2.8.0 (2008-10-20)
> i486-pc-linux-gnu
> 
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
> 
> loaded via a namespace (and not attached):
> [1] tcltk_2.8.0 tools_2.8.0
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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