I’ve been having issues trying to install monocle3 for trajectory analysis of our single cell data. I’m currently remoted into a server and I’m not able to sudo anything. The particular error I’m getting is the following:
`> Error: package or namespace load failed for ‘sf’ in dyn.load(file, DLLpath = DLLpath, …):

unable to load shared object ‘/home/R/x86_64-pc-linux-gnu-library/4.2/00LOCK-sf/00new/sf/libs/sf.so’:
/home/R/x86_64-pc-linux-gnu-library/4.2/00LOCK-sf/00new/sf/libs/sf.so: undefined symbol: _Z16CPL_set_data_dirN4Rcpp6VectorILi16ENS_15PreserveStorageEEEb
Error: loading failed
Execution halted
ERROR: loading failed
removing ‘/home/R/x86_64-pc-linux-gnu-library/4.2/sf’
ERROR: dependency ‘sf’ is not available for package ‘spdep’
removing ‘/home/R/x86_64-pc-linux-gnu-library/4.2/spdep’

The downloaded source packages are in
‘/tmp/Rtmpo8MM4X/downloaded_packages’`

I’m not sure why I’m getting this issue or how to create the sf.so shared object. I’m on a Windows OS and have the environment I’m working in listed below.
Thanks in advance for helping me figure this out.

R version 4.2.3 (2023-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods  
[9] base     

other attached packages:
 [1] RColorBrewer_1.1-3          ROCR_1.0-11                 KernSmooth_2.23-20         
 [4] fields_16.2                 viridisLite_0.4.2           spam_2.10-0                
 [7] edgeR_3.40.2                limma_3.54.2                EnhancedVolcano_1.16.0     
[10] ggrepel_0.9.5               doBy_4.6.22                 GSA_1.03.3                 
[13] fgsea_1.24.0                Cairo_1.6-2                 DoubletFinder_2.0.4        
[16] cowplot_1.1.3               harmony_1.2.0               Rcpp_1.0.13                
[19] sctransform_0.4.1           glmGamPoi_1.10.2            ggpubr_0.6.0               
[22] ggplotify_0.1.2             ggplot2_3.5.1               scCustomize_2.1.2          
[25] MAST_1.24.1                 SingleCellExperiment_1.20.1 DESeq2_1.38.3              
[28] SummarizedExperiment_1.28.0 Biobase_2.58.0              MatrixGenerics_1.10.0      
[31] matrixStats_1.4.0           GenomicRanges_1.50.2        GenomeInfoDb_1.34.9        
[34] IRanges_2.32.0              S4Vectors_0.36.2            BiocGenerics_0.44.0        
[37] HGNChelper_0.8.14           readxl_1.4.3                Seurat_5.1.0               
[40] SeuratObject_5.0.2          sp_2.1-4                    dplyr_1.1.4                
[43] patchwork_1.2.0             devtools_2.4.5              usethis_2.2.3              

loaded via a namespace (and not attached):
  [1] ggprism_1.0.5          scattermore_1.2        tidyr_1.3.1           
  [4] bit64_4.0.5            irlba_2.3.5.1          DelayedArray_0.24.0   
  [7] data.table_1.16.0      KEGGREST_1.38.0        RCurl_1.98-1.16       
 [10] generics_0.1.3         callr_3.7.6            RSQLite_2.3.7         
 [13] RANN_2.6.2             future_1.34.0          bit_4.0.5             
 [16] spatstat.data_3.1-2    lubridate_1.9.3        httpuv_1.6.15         
 [19] promises_1.3.0         fansi_1.0.6            igraph_2.0.3          
 [22] DBI_1.2.3              geneplotter_1.76.0     htmlwidgets_1.6.4     
 [25] spatstat.geom_3.2-9    paletteer_1.6.0        purrr_1.0.2           
 [28] ellipsis_0.3.2         RSpectra_0.16-2        backports_1.5.0       
 [31] annotate_1.76.0        deldir_2.0-4           vctrs_0.6.5           
 [34] remotes_2.5.0          abind_1.4-5            cachem_1.1.0          
 [37] withr_3.0.1            progressr_0.14.0       presto_1.0.0          
 [40] goftest_1.2-3          cluster_2.1.4          dotCall64_1.1-1       
 [43] lazyeval_0.2.2         crayon_1.5.3           spatstat.explore_3.2-7
 [46] labeling_0.4.3         pkgconfig_2.0.3        nlme_3.1-162          
 [49] vipor_0.4.7            pkgload_1.4.0          rlang_1.1.4           
 [52] globals_0.16.3         lifecycle_1.0.4        miniUI_0.1.1.1        
 [55] fastDummies_1.7.3      modelr_0.1.11          ggrastr_1.0.2         
 [58] cellranger_1.1.0       polyclip_1.10-7        RcppHNSW_0.6.0        
 [61] lmtest_0.9-40          Matrix_1.6-5           carData_3.0-5         
 [64] boot_1.3-28            zoo_1.8-12             beeswarm_0.4.0        
 [67] processx_3.8.4         ggridges_0.5.6         GlobalOptions_0.1.2   
 [70] png_0.1-8              bitops_1.0-8           splitstackshape_1.4.8 
 [73] Biostrings_2.66.0      blob_1.2.4             shape_1.4.6.1         
 [76] stringr_1.5.1          parallelly_1.38.0      spatstat.random_3.2-3 
 [79] rstatix_0.7.2          gridGraphics_0.5-1     ggsignif_0.6.4        
 [82] scales_1.3.0           memoise_2.0.1          magrittr_2.0.3        
 [85] plyr_1.8.9             ica_1.0-3              zlibbioc_1.44.0       
 [88] compiler_4.2.3         fitdistrplus_1.1-11    snakecase_0.11.1      
 [91] cli_3.6.3              XVector_0.38.0         urlchecker_1.0.1      
 [94] listenv_0.9.1          ps_1.7.6               pbapply_1.7-2         
 [97] MASS_7.3-58.3          tidyselect_1.2.1       stringi_1.8.3         
[100] forcats_1.0.0          locfit_1.5-9.10        grid_4.2.3            
[103] fastmatch_1.1-4        tools_4.2.3            timechange_0.3.0      
[106] future.apply_1.11.2    circlize_0.4.16        rstudioapi_0.16.0     
[109] janitor_2.2.0          gridExtra_2.3          farver_2.1.2          
[112] Rtsne_0.17             digest_0.6.37          shiny_1.9.1           
[115] microbenchmark_1.4.10  car_3.1-2              broom_1.0.6           
[118] later_1.3.2            RcppAnnoy_0.0.22       httr_1.4.7            
[121] AnnotationDbi_1.60.2   Deriv_4.1.3            colorspace_2.1-1      
[124] XML_3.99-0.17          fs_1.6.4               tensor_1.5            
[127] reticulate_1.38.0      splines_4.2.3          uwot_0.2.2            
[130] yulab.utils_0.1.4      rematch2_2.1.2         spatstat.utils_3.0-5  
[133] plotly_4.10.4          sessioninfo_1.2.2      xtable_1.8-4          
[136] jsonlite_1.8.8         R6_2.5.1               profvis_0.3.8         
[139] pillar_1.9.0           htmltools_0.5.8.1      mime_0.12             
[142] glue_1.7.0             fastmap_1.2.0          BiocParallel_1.32.6   
[145] codetools_0.2-19       maps_3.4.2             pkgbuild_1.4.4        
[148] utf8_1.2.4             lattice_0.20-45        spatstat.sparse_3.1-0 
[151] tibble_3.2.1           curl_5.2.2             ggbeeswarm_0.7.2      
[154] leiden_0.4.3.1         survival_3.5-5         desc_1.4.3            
[157] munsell_0.5.1          GenomeInfoDbData_1.2.9 reshape2_1.4.4        
[160] gtable_0.3.5