Question: recount not available
gravatar for Stephen Henderson
18 months ago by
Stephen Henderson1.0k wrote:


I have the latest R version this morning (R3.3.3) and according to the listed BioC dependencies I believe I should be able to install the 'recount' package (NB I tried installing with R3.3.0 and updated after that didn't work).

Depends R (>= 3.3.0), SummarizedExperiment

However I cannot install it at the moment. A previous mailing list message mentioned using the development version but this doesn't seem to work either:

> BiocInstaller::useDevel()
Error: 'devel' version already in use
> biocLite('recount')
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.3 (2017-03-06).
Installing package(s) ‘recount’
Warning message:
package ‘recount’ is not available (for R version 3.3.3) 


Any ideas?

ADD COMMENTlink modified 18 months ago by Martin Morgan ♦♦ 22k • written 18 months ago by Stephen Henderson1.0k
gravatar for Martin Morgan
18 months ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:

I think you have an old version of BiocInstaller, and it's reporting that, for the version of BiocInstaller that you're using, you are currently using the devel version. Likely when you load your BiocInstaller it says something like

Bioconductor version 3.3 (BiocInstaller 1.22.4), ?biocLite for help
During startup - Warning message:
Bioconductor version 3.3 is too old for R version 3.3.3; see 

with the url pointing you to instructions to remove the current version and re-install BiocInstaller. Hmm I see you have BiocInstaller 1.22.3, which should ask itself to auto-update to 1.22.4 where the message above is activated; regardless, your BiocInstaller is not the most recent version to be used with R-3.3.3.

With an updated BiocInstaller and R-3.3.3, you'd then find that useDevel() would say that you need to use R-3.4 for access to the development version of Bioconductor.

R-3.4 was just released today, and if you were to install it then you'd automatically (until our own release, on Monday) get the devel version of Bioconductor.

But on Monday, with our release, all your 'devel' packages will be out of date compared to the release, so you'll be asked to re-install them.

You might want to wait until after Monday, then simply use R-3.4.

ADD COMMENTlink modified 18 months ago • written 18 months ago by Martin Morgan ♦♦ 22k
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