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.
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gaiusjaugustus
3 answers
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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apa@stowers
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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gaiusjaugustus
Just read the instructions at bioconductor.org:
source("http://bioconductor.org/biocLite.R")
biocLite()
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