Search
Question: recount not available
1
gravatar for Stephen Henderson
5 months ago by
Stephen Henderson1.0k wrote:

Hi

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')
BioC_mirror: https://bioconductor.org
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 5 months ago by Martin Morgan ♦♦ 20k • written 5 months ago by Stephen Henderson1.0k
1
gravatar for Martin Morgan
5 months ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k 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
  https://bioconductor.org/install/#troubleshoot-biocinstaller 

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But on Monday, with our release, all your 'devel' packages will be out of date compared to the release, so you'll be asked to re-install them.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 5 months ago • written 5 months ago by Martin Morgan ♦♦ 20k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 174 users visited in the last hour