Problems using R after update in loadNamespace-CodePudding

I am very new to R. Working mostly with Seurat package to evaluate my single-cell RNAseq data. Today I wanted to update the R version and RStudio. After that I had problems using installed packages. This is my problem:

> install.packages("Seurat", dependencies = TRUE)
Installing package into ‘C:/Users/benne/AppData/Local/R/win-library/4.2’
(as ‘lib’ is unspecified)
Warning in install.packages :
  dependencies ‘S4Vectors’, ‘SummarizedExperiment’, ‘SingleCellExperiment’, ‘MAST’, ‘DESeq2’, ‘BiocGenerics’, ‘GenomicRanges’, ‘GenomeInfoDb’, ‘IRanges’, ‘rtracklayer’, ‘monocle’, ‘Biobase’, ‘limma’ are not available
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/Seurat_4.2.0.zip'
Content type 'application/zip' length 2376157 bytes (2.3 MB)
downloaded 2.3 MB

package ‘Seurat’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\benne\AppData\Local\Temp\RtmpIlveV0\downloaded_packages
> library(Seurat)
Error: package or namespace load failed for ‘Seurat’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘spatstat.data’

I think, there is no problem with the installation of Seurat-package but I cannot make the library-function work. I found other topics that tried to solve that problem but they did not help me.

What could be the problem? With the old R/RStudio version everything worked well. After the update I had to install the RTools42 because it said I have to do that. I have never done that before, why today??

I really hope, you guys may help me. I am totally lost!!

Attached my sessionInfo():

> sessionInfo()
R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22000)

Matrix products: default

locale:
[1] LC_COLLATE=German_Germany.utf8  LC_CTYPE=German_Germany.utf8    LC_MONETARY=German_Germany.utf8
[4] LC_NUMERIC=C                    LC_TIME=German_Germany.utf8    

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

loaded via a namespace (and not attached):
 [1] httr_1.4.4           tidyr_1.2.1          viridisLite_0.4.1    jsonlite_1.8.2       splines_4.2.1       
 [6] leiden_0.4.3         shiny_1.7.2          sp_1.5-0             ggrepel_0.9.1        globals_0.16.1      
[11] pillar_1.8.1         lattice_0.20-45      glue_1.6.2           reticulate_1.26      digest_0.6.29       
[16] RColorBrewer_1.1-3   promises_1.2.0.1     colorspace_2.0-3     plyr_1.8.7           cowplot_1.1.1       
[21] htmltools_0.5.3      httpuv_1.6.6         Matrix_1.5-1         pkgconfig_2.0.3      listenv_0.8.0       
[26] purrr_0.3.5          xtable_1.8-4         patchwork_1.1.2      scales_1.2.1         RANN_2.6.1          
[31] later_1.3.0          Rtsne_0.16           spatstat.utils_2.3-1 tibble_3.1.8         generics_0.1.3      
[36] ggplot2_3.3.6        ellipsis_0.3.2       ROCR_1.0-11          pbapply_1.5-0        SeuratObject_4.1.2  
[41] lazyeval_0.2.2       cli_3.4.1            survival_3.3-1       magrittr_2.0.3       mime_0.12           
[46] future_1.28.0        fansi_1.0.3          parallelly_1.32.1    MASS_7.3-57          ica_1.0-3           
[51] progressr_0.11.0     tools_4.2.1          fitdistrplus_1.1-8   data.table_1.14.2    lifecycle_1.0.3     
[56] matrixStats_0.62.0   stringr_1.4.1        plotly_4.10.0        munsell_0.5.0        cluster_2.1.3       
[61] irlba_2.3.5.1        compiler_4.2.1       rlang_1.0.6          scattermore_0.8      grid_4.2.1          
[66] ggridges_0.5.4       RcppAnnoy_0.0.19     htmlwidgets_1.5.4    igraph_1.3.5         miniUI_0.1.1.1      
[71] gtable_0.3.1         codetools_0.2-18     reshape2_1.4.4       R6_2.5.1             gridExtra_2.3       
[76] zoo_1.8-11           dplyr_1.0.10         fastmap_1.1.0        future.apply_1.9.1   rgeos_0.5-9         
[81] utf8_1.2.2           KernSmooth_2.23-20   stringi_1.7.8        parallel_4.2.1       Rcpp_1.0.9          
[86] sctransform_0.3.5    vctrs_0.4.2          png_0.1-7            tidyselect_1.2.0     lmtest_0.9-40

Thank you so much!

I tried to find out what the problem could be. I had hope that the installation of RTools42 may work but that does not make it better. The error still occurs.

CodePudding user response：

I had a similar problem with my installation of R R studio Seurat today (2022/10/26). (I did not have a problem on another computer a few weeks ago). install.packages('Seurat') said that I should install RTools. I did so, and I got a similar error messages as yours with library(Seurat) . Then, I did install.packages('spatstat.data') RTools had to recompile various things (gcc), but at the end, library(Seurat) ran smoothly.

CodePudding user response：

I had the same problem today after updating to R-4.2.1 this week. I found that restarting my computer after installing RTools and then running install.packages('spatstat.data') and install.packages('spatstat.core') worked - RTools had to compile various things as the previous answer from Masa Sato said. Now library(Seurat) is loading fine!