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Question: Can't upgrade to Bioconductor 3.3?
3
gravatar for enricoferrero
2.4 years ago by
enricoferrero570
Switzerland
enricoferrero570 wrote:

Hello,

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

> biocLite()
BioC_mirror: https://bioconductor.org
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?

Thanks,

ADD COMMENTlink written 2.4 years ago by enricoferrero570
1

The release version of BiocInstaller is 1.22.1 (see http://bioconductor.org/packages/release/bioc/html/BiocInstaller.html).  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 2.4 years ago by Vincent J. Carey, Jr.6.2k
3

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 2.2 years ago • written 2.2 years ago by hioymaci30
1

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 2.4 years ago • written 2.4 years ago by Martin Morgan ♦♦ 22k

Thanks both! Removing BiocInstaller did the trick.

ADD REPLYlink written 2.4 years ago by enricoferrero570
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