CODEWITHSUNDEEP
rinstallationversionbioconductor
Tony Xu
Tony Xu

Reputation: 3091

Bioconductor DNACopy package xxx is not available (for R version 3.2.1)

I know there are a few similar questions out there, particularly this one: How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning? The answer is bit overwhelming to me, frankly, since I'm not quite familiar with R settings/installation etc. I tried some solutions, but didn't get it work yet.

What I want to do is to install some bioconductor packages from here: https://www.bioconductor.org/packages/release/BiocViews.html#___CopyNumberVariation for example "CNVPanelizer", but I got the following error message:

> biocLite("CNVPanelizer")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.14 (BiocInstaller 1.14.3), R version 3.2.1.
Installing package(s) 'CNVPanelizer'
Old packages: 'PSCBS', 'rgl'
Update all/some/none? [a/s/n]: #--- I tried 'a' and 'n', neither working
Warning message:
package ‘CNVPanelizer’ is not available (for R version 3.2.1) #--- this is the error message I got, as shown in my topic title

For all packages in bioconductor/dnacopy web page, I got the same error message.

Anyone has a simple solution? A step by step guidance will be highly appreciated!

TIA

Try to clarify here (as to answer comments below) I tried both "a" and "n" options when asked "Update all/some/none? [a/s/n]:". Neither works.

> library("CNVPanelizer")
Error in library("CNVPanelizer") :
there is no package called ‘CNVPanelizer’

How to install an old version of Bioconductor? I'll google meanwhile... Thanks.

Update: I tried upgrade R, Bioconductor, biocinstaller. This works for some packages listed on this page: https://www.bioconductor.org/packages/release/BiocViews.html#___CopyNumberVariation such as exomeCopy. some installed with warnings; some with errors, such as CNVPanelizer. and one common error is 

 Old packages: 'rgl'

I saw this 'rgl' before I upgrade R/Bioconductor. And sometime I see messages saying removing 'rgl' and 'rgl' reinstalled. Don't know what this 'rgl' thing is......

Upvotes: 0

Views: 1561

Answers (1)

Dan Tenenbaum
Dan Tenenbaum

Reputation: 1889

You are running Bioconductor 3.1 but according to the landing page for CNVPanelizer, it was introduced in Bioconductor 3.2. So you should upgrade:

library(BiocInstaller)
biocLite("BiocUpgrade")

Then you should be able to install CNVPanelizer:

biocLite("CNVPanelizer")

And actually after upgrading you should upgrade all your existing packages by calling biocLite() without arguments.

Upvotes: 1

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