Checking Version of Bioconductor
3
2
Entering edit mode
9.4 years ago

I am trying to update my bioconductor to the latest version (3.0+). I currently have R 3.2.1 and Bioconductor 2.28. When I run BiocUpdate, it just reinstalls 2.28. I tried uninstalling and reinstalling Bioconductor, but still only got 2.28.

The reasoning is that a package I am running (phyloseq) is having an error that the developer doesn't recognize. He suggested updating to the latest version of Bioconductor & R to fix it. I have updated my R version, but am unable to update my Bioconductor.

Any suggestions to install Bioconductor 3.0 or 3.1?

Edit: There was a misunderstanding in how to tell what version of Bioconductor I have.

The best way to check the version of Bioconductor is to compare your version of BiocInstaller (a package within R once Bioconductor is installed) with the Bioconductor website.

bioconductor R • 25k views
ADD COMMENT
10
Entering edit mode
6.8 years ago
apa@stowers ▴ 600

As of about R 3.2.0, the way to get the associated Bioconductor version is to run the non-exported built-in function:

> tools:::.BioC_version_associated_with_R_version()
[1] '3.1'

Mind the . in front of the BioC.

That said, it may be possible for some installed packages to have been sourced from a different BioC version.

ADD COMMENT
1
Entering edit mode
9.4 years ago

The best way to check the version of Bioconductor is to compare your version of BiocInstaller (a package within R once Bioconductor is installed) with the Bioconductor website.

ADD COMMENT
2
Entering edit mode
9.4 years ago

Just read the instructions at bioconductor.org:

source("http://bioconductor.org/biocLite.R")
biocLite()
ADD COMMENT

Login before adding your answer.

Traffic: 1706 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6