Checking Version of Bioconductor
3
2
Entering edit mode
6.8 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 • 15k views
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9
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4.3 years ago
apa@stowers ▴ 580

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.

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1
Entering edit mode
6.8 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.

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2
Entering edit mode
6.8 years ago

Just read the instructions at bioconductor.org:

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