Error/Seurat error with R/Rstudio version 4.1.1
0
0
Entering edit mode
9 weeks ago
akira0714 • 0

Originally, I used Seurat with "R version 4.1.1 (2021-08-10)". However, the package "glmGamPoi" [which requires R (version "4.2") ], so I uninstalled R and Rstudio, and then installed "R-4.2.1.pkg (notarized and signed)"[https://cran.r-project.org/bin/macosx/].

However, this resulted in the situation that Seurat didin't work (I didn't record the detail of the error.)

Then I decided to switch back to uninstall R v4.2.1 and then installed R version 4.1.1 (2021-08-10) again.

Unfortunately, Seurat didn't work again as shown below, although it originally worked with R v4.1.1.

library(Seurat) Warning: package ‘Seurat’ was built under R version 4.1.2Error: package or namespace load failed for ‘Seurat’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):

namespace ‘Matrix’ 1.3-4 is being loaded, but >= 1.5.0 is required

I do appreciate if you advice me what I should do now to run Seurat.

--

[The code below is the R notebook when Seurat worked successfully] R version 4.1.1 (2021-08-10) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Monterey 12.5

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] patchwork_1.1.1 ggplot2_3.3.6 sp_1.4-7 SeuratObject_4.1.0 Seurat_4.1.1

loaded via a namespace (and not attached): [1] Rtsne_0.16 colorspace_2.0-3 ggsignif_0.6.3 deldir_1.0-6
[5] ellipsis_0.3.2 ggridges_0.5.3 rstudioapi_0.13 spatstat.data_2.2-0

seurat rstudio • 434 views
ADD COMMENT
0
Entering edit mode

This error is often fixed by restarting R. Try that first and see if it works.

ADD REPLY

Login before adding your answer.

Traffic: 1962 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6