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ScienceParkMadrid / SinglePointRNA

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Error in irlba::irlba: function 'as_cholmod_sparse' not provided by package 'Matrix' #5

Open nick-youngblut opened 1 month ago

nick-youngblut commented 1 month ago

Selecting UMAP in the 2d visualizations tab results in the following error:

Warning: Error in irlba::irlba: function 'as_cholmod_sparse' not provided by package 'Matrix'
  1: runApp

I tried installing irlba (irlba [2.3.5.1]), which is not in the list dependencies, but that didn't help.

Screenshot 2024-08-14 at 11 06 22 AM

sessionInfo

R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.4.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

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

time zone: America/Los_Angeles
tzcode source: internal

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

other attached packages:
 [1] scCATCH_3.2.2        glmGamPoi_1.14.3     sctransform_0.4.1    BiocParallel_1.36.0  stringr_1.5.1       
 [6] HH_3.1-52            multcomp_1.4-26      TH.data_1.1-2        MASS_7.3-60          survival_3.5-5      
[11] mvtnorm_1.2-5        latticeExtra_0.6-30  lattice_0.21-8       hdf5r_1.3.11         SeuratObject_5.0.2  
[16] Seurat_4.3.0         readxl_1.4.3         zoo_1.8-12           openxlsx_4.2.6.1     ggalluvial_0.12.5   
[21] plotly_4.10.4        gridExtra_2.3        ggplot2_3.5.1        dplyr_1.1.4          shinyFiles_0.9.3    
[26] shinydashboard_0.7.2 shinyjs_2.1.0        shiny_1.9.1         

loaded via a namespace (and not attached):
  [1] RcppAnnoy_0.0.22            splines_4.3.1               later_1.3.2                
  [4] bitops_1.0-8                tibble_3.2.1                cellranger_1.1.0           
  [7] polyclip_1.10-7             rpart_4.1.19                lifecycle_1.0.4            
 [10] globals_0.16.3              backports_1.5.0             magrittr_2.0.3             
 [13] vcd_1.4-12                  sass_0.4.9                  Hmisc_5.1-3                
 [16] rmarkdown_2.27              jquerylib_0.1.4             httpuv_1.6.15              
 [19] spam_2.10-0                 zip_2.3.1                   sp_2.1-4                   
 [22] spatstat.sparse_3.1-0       reticulate_1.38.0           cowplot_1.1.3              
 [25] pbapply_1.7-2               RColorBrewer_1.1-3          zlibbioc_1.48.2            
 [28] abind_1.4-5                 GenomicRanges_1.54.1        Rtsne_0.17                 
 [31] purrr_1.0.2                 BiocGenerics_0.48.1         RCurl_1.98-1.16            
 [34] nnet_7.3-19                 sandwich_3.1-0              GenomeInfoDbData_1.2.11    
 [37] IRanges_2.36.0              S4Vectors_0.40.2            ggrepel_0.9.5              
 [40] irlba_2.3.5.1               listenv_0.9.1               spatstat.utils_3.0-5       
 [43] goftest_1.2-3               spatstat.random_3.3-1       fitdistrplus_1.2-1         
 [46] parallelly_1.38.0           DelayedMatrixStats_1.24.0   DelayedArray_0.28.0        
 [49] leiden_0.4.3.1              codetools_0.2-19            tidyselect_1.2.1           
 [52] farver_2.1.2                gmp_0.7-4                   matrixStats_1.3.0          
 [55] stats4_4.3.1                base64enc_0.1-3             spatstat.explore_3.3-1     
 [58] jsonlite_1.8.8              progressr_0.14.0            Formula_1.2-5              
 [61] ggridges_0.5.6              progress_1.2.3              tools_4.3.1                
 [64] ica_1.0-3                   Rcpp_1.0.13                 glue_1.7.0                 
 [67] SparseArray_1.2.4           xfun_0.46                   MatrixGenerics_1.14.0      
 [70] GenomeInfoDb_1.38.8         withr_3.0.1                 BiocManager_1.30.23        
 [73] fastmap_1.2.0               fansi_1.0.6                 digest_0.6.36              
 [76] R6_2.5.1                    mime_0.12                   colorspace_2.1-1           
 [79] scattermore_1.2             tensor_1.5                  jpeg_0.1-10                
 [82] spatstat.data_3.1-2         utf8_1.2.4                  tidyr_1.3.1                
 [85] generics_0.1.3              renv_1.0.2                  data.table_1.15.4          
 [88] prettyunits_1.2.0           S4Arrays_1.2.1              httr_1.4.7                 
 [91] htmlwidgets_1.6.4           uwot_0.2.2                  pkgconfig_2.0.3            
 [94] gtable_0.3.5                Rmpfr_0.9-5                 lmtest_0.9-40              
 [97] XVector_0.42.0              htmltools_0.5.8.1           dotCall64_1.1-1            
[100] Biobase_2.62.0              scales_1.3.0                leaps_3.2                  
[103] png_0.1-8                   spatstat.univar_3.0-0       knitr_1.48                 
[106] rstudioapi_0.16.0           reshape2_1.4.4              checkmate_2.3.2            
[109] nlme_3.1-162                cachem_1.1.0                KernSmooth_2.23-21         
[112] parallel_4.3.1              miniUI_0.1.1.1              foreign_0.8-84             
[115] pillar_1.9.0                vctrs_0.6.5                 RANN_2.6.1                 
[118] promises_1.3.0              xtable_1.8-4                cluster_2.1.4              
[121] htmlTable_2.4.3             evaluate_0.24.0             cli_3.6.3                  
[124] compiler_4.3.1              crayon_1.5.3                rlang_1.1.4                
[127] future.apply_1.11.2         labeling_0.4.3              interp_1.1-6               
[130] plyr_1.8.9                  fs_1.6.4                    stringi_1.8.4              
[133] viridisLite_0.4.2           deldir_2.0-4                munsell_0.5.1              
[136] lazyeval_0.2.2              spatstat.geom_3.3-2         Matrix_1.6-5               
[139] hms_1.1.3                   patchwork_1.2.0             sparseMatrixStats_1.14.0   
[142] bit64_4.0.5                 future_1.34.0               SummarizedExperiment_1.32.0
[145] ROCR_1.0-11                 fontawesome_0.5.2           memoise_2.0.1              
[148] igraph_2.0.3                bslib_0.8.0                 bit_4.0.5
nick-youngblut commented 1 month ago

This very long thread might help with solving this issue