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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......

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Tony Xu
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  • Just to check the obvious: Have the commands `source("http://bioconductor.org/biocLite.R"); biocLite()` installed all their packages without any problem or not? Also what platform are you using? – usεr11852 Oct 26 '15 at 20:05
  • I'm using Ubuntu 14.04. I ran the source as you mentioned before the biocLite command, and got the error as I shown above. – Tony Xu Oct 26 '15 at 21:32
  • There is no error message in the bit of output that you posted. Also you are trying to install release packages in an old version of Bioconductor. First o all, what if you just answer 'n' when asked to update packages? Also please edit your post to show any actual errors you are getting, from the output above, it is hard to tell what is happening, and it may be that CNVPanelizer is actually installed fine. – Dan Tenenbaum Oct 26 '15 at 22:13
  • @Dan, please see my edition in the original post. Thanks a lot! – Tony Xu Oct 26 '15 at 22:39

1 Answers1

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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.

Dan Tenenbaum
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  • thanks for your help! Please refer to my edition in my original post. I think your method worked somehow, so I'll up your answer anyway, although I still have some questions. – Tony Xu Oct 27 '15 at 17:43
  • I'm not sure how I am supposed to find your original post. Is there a link to it on this page? I could only find a link to a post by someone else. – Dan Tenenbaum Oct 27 '15 at 21:48
  • I meant the last few lines beginning from "Updates:".... Anyway, I tried and solved the rgl thing, which is the reason why some packages cannot be installed after I upgrade my Bioconductor. Thanks! – Tony Xu Oct 28 '15 at 18:51
  • The rgl thing is not an error. You can ignore it (answer `n`). It's just suggesting you update out of date packages. – Dan Tenenbaum Jan 22 '16 at 22:13