issues installing seurat in R v4.2

satijalab / seurat

R toolkit for single cell genomics

http://www.satijalab.org/seurat

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issues installing seurat in R v4.2 #5962

Closed carlosaya2 closed 2 years ago

carlosaya2 commented 2 years ago

my admin renewed my R to 4.2 and I lost all the installed packages. when reinstalling seurat, it failed to install as it needed rgeos. I tried to install rgeos but it required geos-config which I cannot install as there is no version for R v4.2.

The problem is I cannot use sudo install as I do not have admin rights. is there a way that i can solve this issue or I can download the right package?

I tried to install libgeos through CRAN and did not work.

will highly appreciate your help with this.

Cheers,

carlos

longmanz commented 2 years ago

Hi,

It is likely a problem with package "rgeos". Is it possible to ask your admin to help sudo install?
Alternatively, you may use Anaconda to install your own R and packages. It also helps avoid R being renewed on your cluster.

Longda

mojaveazure commented 2 years ago

SeuratObject depends on rgeos for spatial support, has a requirement of libgeos. You can have your admin install libgeos, or you can get the source from https://libgeos.org/

skchronicles commented 2 years ago

Hey @mojaveazure @longmanz,

I am also able to replicate this error/issue on a fresh install of ubuntu/20.04 using R/4.2.

Here is a screenshot of the error when trying to install Seurat:

I was able to resolve the issue by installing libgeos-dev with apt, as you suggested:

DEBIAN_FRONTEND=noninteractive apt-get install -y libcairo2-dev

Do you think it might be worth suggesting this C/C++ library should be installed in your documentation?

I did not see it mentioned anywhere here: https://satijalab.org/seurat/articles/install.html

Even just a small blurb could be helpful.

Best, @skchronicles