GEOquery loading error.

Question

[angus.j.g.campbell]

I started getting a strange error when trying to load GEOquery with library(GEOquery).

Error: package or namespace load failed for ‘GEOquery’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): namespace ‘rlang’ 0.4.9 is already loaded, but >= 0.4.10 is required

When I run

devtools::install_github('r-lib/rlang')

I get ...

Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  namespace ‘rlang’ 0.4.9 is already loaded, but >= 0.4.10 is required

Has anyone dealt with this before? Restarting my R session has no effect.

[ATpoint]

Hello angus.j.g.campbell!

It appears that your post has been cross-posted to another site: https://bioinformatics.stackexchange.com/questions/15486/calling-geoquerry-error-while-loading-the-library

This is typically not recommended as it runs the risk of annoying people in both communities.

Answer 1

[Elucidata]

GEOquery works on the R version (4.0). To update the R version, use the updateR() command. Before running updateR(), install installr package if you don’t have this package installed already. After updating the R version, execute the following command to install GEOquery -

if (!requireNamespace("BiocManager", quietly = TRUE))

install.packages("BiocManager")

BiocManager::install("GEOquery")

Answer 2

[predeus]

I would try un-installing GEOquery and re-installing it again (and updating packages as it's offered).

Alternatively, just do install.packages("rlang") - this should install the newest version. If it doesn't, I'd consider updating R itself.

[angus.j.g.campbell]

Thank you in the end I had to uninstall rlang, and geoquery and then reinstall them and it seems to have fixed the bugs

Angus