[BioC] Errors using biocLite on Apple OS X

Seth Falcon sfalcon at fhcrc.org
Tue Jul 18 21:38:04 CEST 2006

Hi Steven,

"Steven McKinney" <smckinney at bccrc.ca> writes:

> I've recently started using R and Bioconductor
> on an Apple Mac running OS X (10.4).  I've been
> installing packages from the *nix command line,
> one by one, no trouble.

> I would like to be able to update using
> biocLite from the R gui, but keep getting
> errors.
>> source("http://bioconductor.org/biocLite.R")
>> biocLite("Biobase", destdir = "/Volumes/KilroyHD/kilroy/Software/BioConductor")
> Running getBioC version 0.1.6 with R version 2.3.1 
> Running biocinstall version 1.8.4 with R version 2.3.1 
> Your version of R requires version 1.8 of Bioconductor.
> trying URL 'http://bioconductor.org/packages/1.8/bioc/bin/macosx/powerpc/contrib/2.3/Biobase_1.10.1.tgz'
> Content type 'application/x-gzip' length 1465858 bytes
> opened URL
> ==================================================
> downloaded 1431Kb
> Warning messages:
> 1: number of rows of result
> 	is not a multiple of vector length (arg 2) in: cbind(1, res0, Repository = repos) 
> 2: cannot create HTML package index in: make.packages.html() 

I think that I have seen this error occur when an R package is
installed that is somehow invalid or too old for the current R

I wonder if you could try again but without any additional packages
installed in the libraries on your lib path?

You can inspect and set the lib path using .libPaths().
I suspect that if you start fresh using biocLite things will work.

> I am using version 1.10.1 of Biobase, I presume this is the
> version number for Bioconductor.  

Actually, each package in Bioconductor has its own version number.
Biobase 1.10.1 is the current release version and is part of the BioC
1.8 release.

+ seth

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