Question: Can't upgrade to Bioconductor 3.3?
gravatar for enricoferrero
3.5 years ago by
enricoferrero570 wrote:


I'm having troubles in upgrading to Bioconductor 3.3 after installing R 3.3.0. It looks like only Bioconductor 3.2 is available? I'm probably missing something simple here:

$ R --vanilla

R version 3.3.0 (2016-05-03) -- "Supposedly Educational"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> source("")
Bioconductor version 3.2 (BiocInstaller 1.20.2), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
  version of R; see

> biocLite()
Using Bioconductor 3.2 (BiocInstaller 1.20.2), R 3.3.0 (2016-05-03).

> biocLite("BiocUpgrade")
Error: Bioconductor version 3.2 cannot be upgraded with R version 3.3.0


What am I doing wrong? How do I upgrade to Bioconductor 3.3?


ADD COMMENTlink written 3.5 years ago by enricoferrero570

The release version of BiocInstaller is 1.22.1 (see  Somehow you are not getting that loaded.  R CMD REMOVE BiocInstaller might work; followed by the source of biocLite.R as you attempted.  If it doesn't work, check your .libPaths() value.  

ADD REPLYlink written 3.5 years ago by Vincent J. Carey, Jr.6.3k

For removing BiocInstaller I needed to remove it from all libraries, I run R in Linux Terminal:

"sudo R" then I listed my libraries: ".libPaths()", after that I removed all of them:

remove.packages("BiocInstaller",lib = "/usr/lib/R/library")

remove.packages("BiocInstaller",lib = "/home/halil/R/x86_64-pc-linux-gnu-library/3.3)
ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by hioymaci30

Yes, see Troubleshoot BiocInstaller.

Probably you've installed your new R over your old R, .libPaths() is length 1 and points to a system-wide R location. Once you've managed to get the correct version of BiocInstaller, be sure to run biocValid() and update as necessary.

A better strategy is to install R as administrator, but install any additional packages as a regular user. R will then create a version- and user-specific library in your home directory, where you'll have full control over updating packages. It may also be helpful to make an R-and-Bioc version and user-specific directory, as outlined on the Using the ‘Devel’ Version of Bioconductor page.

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by Martin Morgan ♦♦ 24k

Thanks both! Removing BiocInstaller did the trick.

ADD REPLYlink written 3.5 years ago by enricoferrero570
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