Question: R error using - BiocManager::install("mygene", version = "3.10")
0
gravatar for jennifer.m.conrad.gr
20 months ago by
jennifer.m.conrad.gr10 wrote:

I am trying to install R package 'mygene' and it is giving me the following error. I am relatively new to R, so any help is appreciated!

BiocManager::install("mygene", version = "3.10")


Bioconductor version 3.10 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)
Installing package(s) 'mygene'

Error in install.packages(pkgs = doing, lib = lib, repos = repos, ...) : 
  This version of R is not set up to install source packages

If it was installed from an RPM, you may need the R-devel RPM
bioconductor R • 1.5k views
ADD COMMENTlink modified 19 months ago by zx875410.0k • written 20 months ago by jennifer.m.conrad.gr10

Why are you trying to install the development version of the package? - currently (July 6, 2019), we are on Bioconductor v3.9. Therefore, Bioconductor v3.10 refers to the current development branch of the packages. Let's first clear that up.

ADD REPLYlink written 20 months ago by Kevin Blighe71k

Ok, here is what I got-

> BiocManager::install("mygene", version = "3.9")
Error: To use Bioconductor version '3.9', first downgrade 26 packages with
"BiocManager::install(version = '3.9')"
> BiocManager::install(version = '3.9')
Downgrade 25 packages to Bioconductor version '3.9'? [y/n]: 
y
Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)
Installing package(s) 'BiocVersion'
Error in install.packages(pkgs = doing, lib = lib, repos = repos, ...) : 
  This version of R is not set up to install source packages
If it was installed from an RPM, you may need the R-devel RPM
ADD REPLYlink modified 20 months ago by Kevin Blighe71k • written 20 months ago by jennifer.m.conrad.gr10

Did you install the version of R that you are currently using? - are you using your own laptop / desktop computer?

What if you restart everything and just do BiocManager::install("mygene")?

ADD REPLYlink written 20 months ago by Kevin Blighe71k

Also, what is the output of this?

R.home("bin")

?

ADD REPLYlink written 20 months ago by Kevin Blighe71k
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