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Question: BioC and genevisR and maftools
0
gravatar for Bogdan
13 months ago by
Bogdan480
Palo Alto, CA, USA
Bogdan480 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 13 months ago • written 13 months ago by Bogdan480
2
gravatar for James W. MacDonald
13 months ago by
United States
James W. MacDonald45k 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 13 months ago by James W. MacDonald45k
0
gravatar for Bogdan
13 months ago by
Bogdan480
Palo Alto, CA, USA
Bogdan480 wrote:

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

ADD COMMENTlink written 13 months ago by Bogdan480
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