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Question: Upgrading bioconductor - how do I change the contrib.url?
0
2.9 years ago by
ail270
ail270 wrote:

Hello

I was trying to install a new Bioconductor package,using "biocLite" on my Mac but failed.

biocLite("Rcade")
'BiocInstaller' package not in repository
http://bioconductor.org/packages/2.12/bioc, using
'http://bioconductor.org/packages/2.12/bioc'
Error: 'BiocInstaller' package not in repository http://bioconductor.org/packages/2.12/bioc

I think I managed to narrow it down to having to upgrade Bioconductor, because I haven't used it in a while. However, when I tried to use biocLite("BiocUpgrade"), I get the following error (which is basically the same).

'BiocInstaller' package not in repository
http://bioconductor.org/packages/2.12/bioc, using
'http://bioconductor.org/packages/2.12/bioc'
Error: 'BiocInstaller' package not in repository http://bioconductor.org/packages/2.12/bioc.

Having looked it up, I  now that someone else had exactly the same problem, but in theory the solution was upgrading to the newest R version, but I'm already running R 3.1.1. I do realise that I need to change the contributing url. However I do manage to do that? the argument is embedded deep into the biocInstaller and I do not seem to be able to do it. It feels like a circular problem than in order to fix the problem, I need to fix it.

Ana

Here is my sessionInfo()

R version 3.1.1 (2014-07-10)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] BiocInstaller_1.10.4

loaded via a namespace (and not attached):
[1] tools_3.1.1

modified 2.9 years ago by James W. MacDonald48k • written 2.9 years ago by ail270
0
2.9 years ago by
United States
James W. MacDonald48k wrote:

You need to upgrade to the newest version of R, which is 3.2.2, not 3.1.1!