Question: R error using - BiocManager::install("mygene", version = "3.10")
0
gravatar for jennifer.m.conrad.gr
5 months ago by
jennifer.m.conrad.gr0 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 • 345 views
ADD COMMENTlink modified 4 months ago by zx87548.8k • written 5 months ago by jennifer.m.conrad.gr0

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 5 months ago by Kevin Blighe52k

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 5 months ago by Kevin Blighe52k • written 5 months ago by jennifer.m.conrad.gr0

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 5 months ago by Kevin Blighe52k

Also, what is the output of this?

R.home("bin")

?

ADD REPLYlink written 5 months ago by Kevin Blighe52k
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