Error/Seurat error with R/Rstudio version 4.1.1
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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)"[].

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


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