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Question: The recount package is not available for R version 3.3.1
0
2.3 years ago by
arjunkrish0 wrote:

I'm trying to install the new recount R package.

Now, since recount requires R >= 3.3.0 (according to http://bioconductor.org/packages/devel/bioc/html/recount.html), I installed the latest version of R (3.3.1) and then tries installing recount, but, unfortunately, it doesn't work:

> biocLite("recount")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.5), R version 3.3.1.
Temporarily using Bioconductor version 3.0
Installing package(s) 'recount'
Warning message:
package ‘recount’ is not available (for R version 3.3.1)

Please let me know if recount can be made compatible with 3.3.1. Thanks.

modified 2.3 years ago • written 2.3 years ago by arjunkrish0
0
2.3 years ago by
Denali
Steve Lianoglou12k wrote:

It looks like you are using an old version of bioconductor.

Thanks, Steve. I already tried to no avail:

> biocLite("BiocUpgrade")
Error: Bioconductor version 3.0 cannot be upgraded with R version 3.1.0

Update: Restarting R seems to help, but installation of recount does not go to completion & I still get (among other warnings):

package ‘recount’ is not available (for R version 3.3.1)
1

recount is available in the devel branch, so one last step is

BiocInstaller::useDevel()

Be sure to run BiocInstaller::biocValid() and follow suggestions to bring your packages into the 'devel' version.