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_15PreserveStorageEEEbError: loading failedExecution haltedERROR: loading failedremoving ‘/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 LTSMatrix products: defaultBLAS: /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3locale: [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