[BioC] Problems installing bioconductor

Martin Morgan mtmorgan at fhcrc.org
Tue Jun 17 17:48:19 CEST 2008

Hi Daniel --

Daniel Silberschmidt wrote:
> Hello everybody,
> 	tried to install bioconductor from three different machines (all 64
> bits) and different OS (Linux different kernels, Windows XP)  but always
> got a message like this one:
>>> source("http://bioconductor.org/biocLite.R")
>>> biocLite()
>> Running biocinstall version 2.2.9 with R version 2.7.0 
>> Your version of R requires version 2.2 of BioConductor.
>> Will install the following packages:
>>  [1] "affy"         "affydata"     "affyPLM"      "annaffy"      "annotate"    
>>  [6] "Biobase"      "Biostrings"   "DynDoc"       "gcrma"        "genefilter"  
>> [11] "geneplotter"  "hgu95av2.db"  "limma"        "marray"       "matchprobes" 
>> [16] "multtest"     "ROC"          "vsn"          "xtable"       "affyQCReport"
>> Please wait...
>> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  :
>>   argument 'lib' is missing: using '/home/xxxxxxxx'
>> Error: subscript out of bounds
>> In addition: There were 15 warnings (use warnings() to see them)
> 	Think that is something related to the  place because at home (linux ubuntu 8.04, 32 bits) I was able to  install it without problem

Hard to know for sure. After the error, what does traceback() say?

Also,  is /home/xxxxxxx really the directory where you are installing 
libraries? Perhaps a helpful system administrator has written a Rprofile 
file for the site that sets 'your' home directory to this. What does 
.libPaths() say? The packages will be installed in the first directory 
returned by .libPaths(), and you must have write permissions. If this is 
the issue, you'll want to configure R to know about a more sensible 
directory; see ?Startup and ?.libPaths for more.

Hope that helps...


> 	Any idea? 
> Thanks
> Daniel Silberschmidt
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Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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PO Box 19024 Seattle, WA 98109

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Phone: (206) 667-2793

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