[Bioc-devel] using BiocLite() on Ubuntu Xenial with its default R 3.2.3 release

Jack Howarth howarth.mailing.lists at gmail.com
Thu Jul 20 14:36:42 CEST 2017

I am trying to use the BiocLite() feature of Bioconductor to install
the R modules required by MetaboAnalyst 3.0 under Ubuntu Xenial
16.04LTS with its system R 3.2.3 release. I have added the repo for
Micheal Rutter's cran2deb4ubuntu to provide the missing cran R modules
but have avoided installing any of the r-bioc ones to keep the
installation purely using those installed in /usr/local/lib/R by
BiocLite(). Unfortunately, this is failing on

$ sudo R

> source("https://bioconductor.org/biocLite.R")

> biocLite("‘AnnotationDbi")

BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.2.3 (2015-12-10).
Installing package(s) ‘‘AnnotationDbi’
Warning message:
package ‘‘AnnotationDbi’ is not available (for R version 3.2.3)

Certainly there must be a way to redirect BiocLite to a legacy release
which fully supports the older R 3.2.3 in the current Ubuntu LTS

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