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Question: The recount package is not available for R version 3.3.1
0
gravatar for arjunkrish
15 months ago by
arjunkrish0
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.

ADD COMMENTlink modified 15 months ago • written 15 months ago by arjunkrish0
0
gravatar for Steve Lianoglou
15 months ago by
Genentech
Steve Lianoglou12k wrote:

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

Please follow the upgrade instructions found in the "Upgrading installed Bioconductor packages" section of this page.

ADD COMMENTlink written 15 months ago by Steve Lianoglou12k

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)
ADD REPLYlink modified 15 months ago • written 15 months ago by arjunkrish0
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.

ADD REPLYlink written 15 months ago by Martin Morgan ♦♦ 20k

Were you able to install recount following Martin Morgan's feedback? Like others have said, recount is only available via Bioconductor-devel.

ADD REPLYlink written 15 months ago by Leonardo Collado Torres540
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