[BioC] Errors using biocLite on Apple OS X

[Steven McKinney]

My apologies - although I had some initial
errors running biocLite, I see now that
I am just getting warnings below, not errors.

New libraries are indeed being installed.

Do I need to be concerned about the warnings
produced below?



Steven McKinney

Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre

email: smckinney at bccrc.ca

tel: 604-675-8000 x7561

BCCRC
Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C. 
V5Z 1L3
Canada




-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch on behalf of Steven McKinney
Sent: Tue 7/18/2006 11:58 AM
To: Bioconductor at stat.math.ethz.ch
Subject: [BioC] Errors using biocLite on Apple OS X
 

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.


> version
               _                         
platform       powerpc-apple-darwin8.6.0 
arch           powerpc                   
os             darwin8.6.0               
system         powerpc, darwin8.6.0      
status                                   
major          2                         
minor          3.1                       
year           2006                      
month          06                        
day            01                        
svn rev        38247                     
language       R                         
version.string Version 2.3.1 (2006-06-01)
> 

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

I see a few others reporting similar errors
when I google this issue, but I see no posted
solutions.  Can anyone see what I am doing wrong,
and is there a solution?

Any info appreciated


Best regards

Steven McKinney

Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre

email: smckinney at bccrc.ca



BCCRC
Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C. 
V5Z 1L3
Canada

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