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Question: BioC and genevisR and maftools
0
gravatar for Bogdan
2.1 years ago by
Bogdan550
Palo Alto, CA, USA
Bogdan550 wrote:

Dear all, I am aiming to install 2 recent BioC packages, ie. GeneVisR and maftools on my Linux ubuntu machine, that runs : Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.3.2 (2016-10-31).

The message I am getting is : 

"package ‘maftools’ is not available (for R version 3.3.2"

or 

"package ‘GeneVisR’ is not available (for R version 3.3.2)" 

Please, could you advise on how to install these packages ? if I need BioC 3.4, how shall I update from BioC 3.2. to 3.4 ?

The error message I am getting is :

>  biocLite("BiocUpgrade")
Error: Bioconductor version 3.2 cannot be upgraded with R version 3.3.2

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by Bogdan550
Answer: BioC and genevisR and maftools
2
gravatar for James W. MacDonald
2.1 years ago by
United States
James W. MacDonald49k wrote:

You have a complete mismatch between your Bioconductor and R versions. BioC 3.2 was intended for R-3.2.x

You should restart R, then do

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

Which should get you the correct version of BiocInstaller, which will then install the correct version of packages.

Also, do note that it's GenVisR, not GeneVisR.

ADD COMMENTlink written 2.1 years ago by James W. MacDonald49k
Answer: BioC and genevisR and maftools
0
gravatar for Bogdan
2.1 years ago by
Bogdan550
Palo Alto, CA, USA
Bogdan550 wrote:

Thank you James, will fix it ;) have a good weekend !

ADD COMMENTlink written 2.1 years ago by Bogdan550
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