Entering edit mode
4.6 years ago
jomagrax
▴
40
Hi everyone!
Im running a pipeline that requires a R (>= 3.6.0) while I have installed (R 3.2.2).
Now, with sudo apt-install r-base
i apparently install the correct version, but everytime i call R with R
command, the 3.2.2 version It´s called. I've tried reinstalling but It doesn´t work either. Any ideas?
Thanks in advance, Jose
what is the output of:
and
Are you sure it installed correctly? According to that you only have 1
R
, and it wasn't installed fromapt
...I would try
conda uninstall r-base
, thensudo apt-get install r-base
and make sure there were no errors or warnings.Alternatively, just upgrade
r-base
inconda
.I did as you say and now It seems that I cant call R, as I obtain;
The point of using conda environments is to make software installation independent of the system. Installing R from the system package manager is not going to have any effect on the R version installed in your conda environment. So if you use conda then install software with conda. If you want to use system software then exit your conda environment. Note that upgrading R usually means re-installing all the previously installed packages.
Hi jomagrax,
Please note that this is not exactly a bioinformatics question. While we can probably help you with this (and will try to if it turns out to be not that complicated), it's not in the scope of biostars to help with typical installation or unix issues. Stackoverflow would probably be a more suitable location, so please keep this in mind for further similar question.
Cheers,
Wouter
What version of Ubuntu are you using? This may be a repository issue if you are using Ubuntu 16.04 or older.
It seems that I have ububtu 16.04
Make sure you have the correct repository for updating R. I also have Ubuntu 16.04 and changed my repository. Check your sources file found here
/ect/apt/sources.list
. I havedeb https://cloud.r-project.org/bin/linux/ubuntu xenial-cran35/
on my list and commented outdeb https://lib.stat.cmu.edu/R/CRAN/bin/linux/ubuntu xenial/
. Instructions for installation can be found here.I have followed the instructions, It seems Its correctly installed in
/usr/lib/R/bin/R
but It does not open when I just typeR
What does your source.list look like?
I'm not quite sure what the error would be. If you followed all the instructions, it should have worked.
If R is installed but can't be found then it's a $PATH problem. It may be because you're still in an isolated conda environment. Get rid of anaconda or at list remove references to it from your .bash_profile.