Installation error - Seurat/SeuratObject/rgeos - in server-based RStudio

Question

[Heidi]

Hey. Today I can't load the Seurat package:

library(Seurat) Error: package or namespace load failed for ‘Seurat’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): namespace ‘SeuratObject’ 4.0.0 is being loaded, but >= 4.0.4 is required

When I try installing SeuratObject I get:

install.packages("SeuratObject") configure: error: geos-config not found or not executable. ERROR: configuration failed for package ‘rgeos’ removing ‘/home/hottesen/R/x86_64-pc-linux-gnu-library/4.0/rgeos’ Warning in install.packages : installation of package ‘rgeos’ had non-zero exit status ERROR: dependency ‘rgeos’ is not available for package ‘SeuratObject’ removing ‘/home/hottesen/R/x86_64-pc-linux-gnu-library/4.0/SeuratObject’ Warning in install.packages : installation of package ‘SeuratObject’ had non-zero exit status

When I then try to install rgeos I get:

install.packages("rgeos") configure: error: geos-config not found or not executable. ERROR: configuration failed for package ‘rgeos’ removing ‘/home/hottesen/R/x86_64-pc-linux-gnu-library/4.0/rgeos’ Warning in install.packages : installation of package ‘rgeos’ had non-zero exit status

What has changed since last week and how do I solve it? I am afraid to do any sudo installations since I'm working on the University server (web-browser RStudio).

Answer 1

[Michael]

Ask local IT support to (re)-install the libgeos++-devel package in your Linux system and explain the situation. (if it has worked before, the library likely has been there before). Alternatively, try to install geos via conda in your home.

I am afraid to do any sudo installations since I'm working on the University server (web-browser RStudio).

If the system is configured correctly, it won't let you.