Error in irlba(A = t(x = object), nv = n, work = irlba.work, tol = tol) : function 'as_cholmod_sparse' not provided by package 'Matrix'

[ykugo95]

Hello.
I have been encountering a difficulty at RunSVD() with an error;

Error in irlba(A = t(x = object), nv = n, work = irlba.work, tol = tol) :
function 'as_cholmod_sparse' not provided by package 'Matrix'

I searched for a solution including (#1530) https://github.com//issues/1535 tried them, but they all did not work.

Actually, I reinstalled "Matrix" ver 1.6.1 to meet dependency, but it conflict SeuratObject that requires >=1.6.
Of course latest versions of each packages did not work, showing the error message.

I am sure I passed the difficulty of compilation of "Matrix" package.

Could you please tell me how to solve this?

• I have a list of 6 SeuratObjects to be passed preprocessing according to the vignette for the 10X multiome.

`> multiome_subset_list <- lapply(multiome_subset_list, function(obj){

• obj <- FindTopFeatures(obj, min.cutoff = 5)
• obj <- RunTFIDF(obj)
• obj <- RunSVD(obj)
• return(obj)
• })
  Performing TF-IDF normalization
  Running SVD
  Error in irlba(A = t(x = object), nv = n, work = irlba.work, tol = tol) :
  function 'as_cholmod_sparse' not provided by package 'Matrix'`

`> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.2

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: Asia/Tokyo
tzcode source: internal

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

other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg38_1.4.5 BSgenome_1.70.1
[3] rtracklayer_1.62.0 BiocIO_1.12.0
[5] Biostrings_2.70.1 XVector_0.42.0
[7] EnsDb.Hsapiens.v86_2.99.0 ensembldb_2.26.0
[9] AnnotationFilter_1.26.0 GenomicFeatures_1.54.1
[11] AnnotationDbi_1.64.1 Signac_1.12.0
[13] scCustomize_2.0.1 png_0.1-8
[15] SingleCellExperiment_1.24.0 apeglm_1.24.0
[17] DESeq2_1.42.0 SummarizedExperiment_1.32.0
[19] Biobase_2.62.0 MatrixGenerics_1.14.0
[21] matrixStats_1.2.0 GenomicRanges_1.54.1
[23] GenomeInfoDb_1.38.1 IRanges_2.36.0
[25] S4Vectors_0.40.2 BiocGenerics_0.48.1
[27] edgeR_4.0.3 limma_3.58.1
[29] cowplot_1.1.2 data.table_1.14.10
[31] RColorBrewer_1.1-3 pheatmap_1.0.12
[33] ggthemes_5.0.0 ggsci_3.0.0
[35] ggpubr_0.6.0 reshape2_1.4.4
[37] Matrix.utils_0.9.7 Matrix_1.6-4
[39] ggrepel_0.9.4 viridis_0.6.4
[41] viridisLite_0.4.2 readxl_1.4.3
[43] patchwork_1.1.3 lubridate_1.9.3
[45] forcats_1.0.0 stringr_1.5.1
[47] dplyr_1.1.4 purrr_1.0.2
[49] readr_2.1.4 tidyr_1.3.0
[51] tibble_3.2.1 ggplot2_3.4.4
[53] tidyverse_2.0.0 Seurat_5.0.1
[55] SeuratObject_5.0.1 sp_2.1-2

loaded via a namespace (and not attached):
[1] ProtGenerics_1.34.0 spatstat.sparse_3.0-3 bitops_1.0-7
[4] httr_1.4.7 numDeriv_2016.8-1.1 tools_4.3.1
[7] sctransform_0.4.1 backports_1.4.1 utf8_1.2.4
[10] R6_2.5.1 lazyeval_0.2.2 uwot_0.1.16
[13] withr_2.5.2 prettyunits_1.2.0 gridExtra_2.3
[16] progressr_0.14.0 cli_3.6.2 spatstat.explore_3.2-5
[19] fastDummies_1.7.3 mvtnorm_1.2-4 spatstat.data_3.0-3
[22] ggridges_0.5.5 pbapply_1.7-2 Rsamtools_2.18.0
[25] parallelly_1.36.0 bbmle_1.0.25.1 RSQLite_2.3.4
[28] rstudioapi_0.15.0 generics_0.1.3 shape_1.4.6
[31] ica_1.0-3 spatstat.random_3.2-2 car_3.1-2
[34] ggbeeswarm_0.7.2 fansi_1.0.6 abind_1.4-5
[37] lifecycle_1.0.4 yaml_2.3.8 snakecase_0.11.1
[40] carData_3.0-5 BiocFileCache_2.10.1 SparseArray_1.2.2
[43] Rtsne_0.17 blob_1.2.4 paletteer_1.5.0
[46] grid_4.3.1 promises_1.2.1 crayon_1.5.2
[49] bdsmatrix_1.3-6 miniUI_0.1.1.1 lattice_0.22-5
[52] KEGGREST_1.42.0 pillar_1.9.0 knitr_1.45
[55] rjson_0.2.21 future.apply_1.11.0 codetools_0.2-19
[58] fastmatch_1.1-4 leiden_0.4.3.1 glue_1.6.2
[61] vctrs_0.6.5 spam_2.10-0 cellranger_1.1.0
[64] gtable_0.3.4 rematch2_2.1.2 cachem_1.0.8
[67] emdbook_1.3.13 xfun_0.41 S4Arrays_1.2.0
[70] mime_0.12 coda_0.19-4 survival_3.5-7
[73] RcppRoll_0.3.0 statmod_1.5.0 ellipsis_0.3.2
[76] fitdistrplus_1.1-11 ROCR_1.0-11 nlme_3.1-164
[79] bit64_4.0.5 filelock_1.0.3 progress_1.2.3
[82] RcppAnnoy_0.0.21 irlba_2.3.5.1 vipor_0.4.5
[85] KernSmooth_2.23-22 colorspace_2.1-0 DBI_1.1.3
[88] ggrastr_1.0.2 tidyselect_1.2.0 curl_5.2.0
[91] bit_4.0.5 compiler_4.3.1 xml2_1.3.6
[94] DelayedArray_0.28.0 plotly_4.10.3 scales_1.3.0
[97] lmtest_0.9-40 rappdirs_0.3.3 digest_0.6.33
[100] goftest_1.2-3 spatstat.utils_3.0-4 rmarkdown_2.25
[103] htmltools_0.5.7 pkgconfig_2.0.3 dbplyr_2.4.0
[106] fastmap_1.1.1 rlang_1.1.2 GlobalOptions_0.1.2
[109] htmlwidgets_1.6.4 shiny_1.8.0 zoo_1.8-12
[112] jsonlite_1.8.8 BiocParallel_1.36.0 RCurl_1.98-1.13
[115] magrittr_2.0.3 GenomeInfoDbData_1.2.11 dotCall64_1.1-1
[118] munsell_0.5.0 Rcpp_1.0.11 reticulate_1.34.0
[121] stringi_1.8.3 zlibbioc_1.48.0 MASS_7.3-60
[124] plyr_1.8.9 parallel_4.3.1 listenv_0.9.0
[127] deldir_2.0-2 splines_4.3.1 tensor_1.5
[130] hms_1.1.3 circlize_0.4.16 locfit_1.5-9.8
[133] igraph_1.6.0 spatstat.geom_3.2-7 ggsignif_0.6.4
[136] RcppHNSW_0.5.0 biomaRt_2.58.0 XML_3.99-0.16
[139] evaluate_0.23 ggprism_1.0.4 tzdb_0.4.0
[142] httpuv_1.6.13 grr_0.9.5 RANN_2.6.1
[145] polyclip_1.10-6 future_1.33.0 scattermore_1.2
[148] janitor_2.2.0 broom_1.0.5 xtable_1.8-4
[151] restfulr_0.0.15 RSpectra_0.16-1 rstatix_0.7.2
[154] later_1.3.2 GenomicAlignments_1.38.0 memoise_2.0.1.9000
[157] beeswarm_0.4.0 cluster_2.1.6 timechange_0.2.0
[160] globals_0.16.2 `

Best regard.

[timoast]

I think this is related to some issues with the latest SeuratObject and Matrix release, please see the comment here satijalab/seurat#8089 (comment) and check if that would solve this problem

You can also try installing the latest Matrix release and then re-installing SeuratObject

[ykugo95]

Thank you so much for your quick and kindfull replay.
However I still have the same difficulty even after re-installation of all related packages including Seurat, Signac, Matrix, irlba, and Seuratwrapper to be updated with latest versions.

I can share my seurat object if necessary.
Are there any other possible ways to solve this?

> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.2

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: Asia/Tokyo
tzcode source: internal

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

other attached packages:
 [1] irlba_2.3.5.1                     BSgenome.Hsapiens.UCSC.hg38_1.4.5 BSgenome_1.70.1                  
 [4] rtracklayer_1.62.0                BiocIO_1.12.0                     Biostrings_2.70.1                
 [7] XVector_0.42.0                    EnsDb.Hsapiens.v86_2.99.0         ensembldb_2.26.0                 
[10] AnnotationFilter_1.26.0           GenomicFeatures_1.54.1            AnnotationDbi_1.64.1             
[13] Signac_1.12.0                     scCustomize_2.0.1                 png_0.1-8                        
[16] SingleCellExperiment_1.24.0       apeglm_1.24.0                     DESeq2_1.42.0                    
[19] SummarizedExperiment_1.32.0       Biobase_2.62.0                    MatrixGenerics_1.14.0            
[22] matrixStats_1.2.0                 GenomicRanges_1.54.1              GenomeInfoDb_1.38.2              
[25] IRanges_2.36.0                    S4Vectors_0.40.2                  BiocGenerics_0.48.1              
[28] edgeR_4.0.3                       limma_3.58.1                      cowplot_1.1.2                    
[31] data.table_1.14.10                RColorBrewer_1.1-3                pheatmap_1.0.12                  
[34] ggthemes_5.0.0                    ggsci_3.0.0                       ggpubr_0.6.0                     
[37] reshape2_1.4.4                    Matrix.utils_0.9.7                Matrix_1.6-4                     
[40] ggrepel_0.9.4                     viridis_0.6.4                     viridisLite_0.4.2                
[43] readxl_1.4.3                      patchwork_1.1.3                   lubridate_1.9.3                  
[46] forcats_1.0.0                     stringr_1.5.1                     dplyr_1.1.4                      
[49] purrr_1.0.2                       readr_2.1.4                       tidyr_1.3.0                      
[52] tibble_3.2.1                      ggplot2_3.4.4                     tidyverse_2.0.0                  
[55] Seurat_5.0.1                      SeuratObject_5.0.1                sp_2.1-2                         

loaded via a namespace (and not attached):
  [1] dichromat_2.0-0.1         progress_1.2.3            nnet_7.3-19               goftest_1.2-3            
  [5] vctrs_0.6.5               spatstat.random_3.2-2     digest_0.6.33             shape_1.4.6              
  [9] deldir_2.0-2              parallelly_1.36.0         MASS_7.3-60               httpuv_1.6.13            
 [13] withr_2.5.2               ggrastr_1.0.2             xfun_0.41                 ellipsis_0.3.2           
 [17] survival_3.5-7            memoise_2.0.1.9000        ggbeeswarm_0.7.2          janitor_2.2.0            
 [21] zoo_1.8-12                GlobalOptions_0.1.2       pbapply_1.7-2             Formula_1.2-5            
 [25] prettyunits_1.2.0         rematch2_2.1.2            KEGGREST_1.42.0           promises_1.2.1           
 [29] httr_1.4.7                rstatix_0.7.2             restfulr_0.0.15           globals_0.16.2           
 [33] fitdistrplus_1.1-11       rstudioapi_0.15.0         miniUI_0.1.1.1            generics_0.1.3           
 [37] base64enc_0.1-3           curl_5.2.0                zlibbioc_1.48.0           polyclip_1.10-6          
 [41] GenomeInfoDbData_1.2.11   SparseArray_1.2.2         xtable_1.8-4              evaluate_0.23            
 [45] S4Arrays_1.2.0            BiocFileCache_2.10.1      hms_1.1.3                 colorspace_2.1-0         
 [49] filelock_1.0.3            hdf5r_1.3.8               ROCR_1.0-11               reticulate_1.34.0        
 [53] spatstat.data_3.0-3       magrittr_2.0.3            lmtest_0.9-40             snakecase_0.11.1         
 [57] later_1.3.2               lattice_0.22-5            glmGamPoi_1.14.0          spatstat.geom_3.2-7      
 [61] future.apply_1.11.0       scattermore_1.2           XML_3.99-0.16             RcppAnnoy_0.0.21         
 [65] Hmisc_5.1-1               pillar_1.9.0              nlme_3.1-164              compiler_4.3.1           
 [69] RSpectra_0.16-1           stringi_1.8.3             tensor_1.5                GenomicAlignments_1.38.0 
 [73] plyr_1.8.9                crayon_1.5.2              abind_1.4-5               emdbook_1.3.13           
 [77] locfit_1.5-9.8            bit_4.0.5                 fastmatch_1.1-4           codetools_0.2-19         
 [81] paletteer_1.5.0           biovizBase_1.50.0         plotly_4.10.3             mime_0.12                
 [85] splines_4.3.1             circlize_0.4.16           Rcpp_1.0.11               fastDummies_1.7.3        
 [89] dbplyr_2.4.0              sparseMatrixStats_1.14.0  cellranger_1.1.0          grr_0.9.5                
 [93] knitr_1.45                blob_1.2.4                utf8_1.2.4                listenv_0.9.0            
 [97] checkmate_2.3.1           DelayedMatrixStats_1.24.0 ggsignif_0.6.4            statmod_1.5.0            
[101] tzdb_0.4.0                pkgconfig_2.0.3           tools_4.3.1               cachem_1.0.8             
[105] RSQLite_2.3.4             DBI_1.1.3                 numDeriv_2016.8-1.1       fastmap_1.1.1            
[109] rmarkdown_2.25            scales_1.3.0              grid_4.3.1                ica_1.0-3                
[113] Rsamtools_2.18.0          broom_1.0.5               coda_0.19-4               ggprism_1.0.4            
[117] dotCall64_1.1-1           VariantAnnotation_1.48.1  carData_3.0-5             RANN_2.6.1               
[121] rpart_4.1.23              farver_2.1.1              yaml_2.3.8                foreign_0.8-86           
[125] cli_3.6.2                 leiden_0.4.3.1            lifecycle_1.0.4           uwot_0.1.16              
[129] mvtnorm_1.2-4             backports_1.4.1           BiocParallel_1.36.0       timechange_0.2.0         
[133] gtable_0.3.4              rjson_0.2.21              ggridges_0.5.5            progressr_0.14.0         
[137] parallel_4.3.1            jsonlite_1.8.8            RcppHNSW_0.5.0            bitops_1.0-7             
[141] bit64_4.0.5               Rtsne_0.17                spatstat.utils_3.0-4      bdsmatrix_1.3-6          
[145] lazyeval_0.2.2            shiny_1.8.0               htmltools_0.5.7           sctransform_0.4.1        
[149] rappdirs_0.3.3            glue_1.6.2                spam_2.10-0               RCurl_1.98-1.13          
[153] gridExtra_2.3             igraph_1.6.0              R6_2.5.1                  RcppRoll_0.3.0           
[157] labeling_0.4.3            cluster_2.1.6             bbmle_1.0.25.1            DelayedArray_0.28.0      
[161] tidyselect_1.2.0          vipor_0.4.5               ProtGenerics_1.34.0       htmlTable_2.4.2          
[165] xml2_1.3.6                car_3.1-2                 future_1.33.0             munsell_0.5.0            
[169] KernSmooth_2.23-22        htmlwidgets_1.6.4         biomaRt_2.58.0            rlang_1.1.2              
[173] spatstat.sparse_3.0-3     spatstat.explore_3.2-5    fansi_1.0.6               beeswarm_0.4.0           
> 

Best regard.

[timoast]

Can you try reinstalling SeuratObject (not Seurat)? install.packages("SeuratObject")

[ykugo95]

Thank you, the problem was solved.

I reinstalled SeuratObject as well, but is was not the culprit.
I reinstalled irlba from source file instead of binary; https://cran.r-project.org/src/contrib/irlba_2.3.5.1.tar.gz.
Considering the timeline, I think this worked.

However, I am encountering another problem of LinkPeak(), which I should consult in another thread.
Again, thank you for your kindful support.

[kdzimm]

@timoast and @yosuke1012

I have this same exact issue popping up and I am at my wits' end. I have tried all different variations based on the variety of threads that report this issue and I have had no luck. I have even painfully uninstalled and reinstalled various older versions (particularly Matrix 1.6-1) each of the following packages in a variety of combinations with no luck: Seurat, Signac, Matrix, irlba, and SeuratObject. I have also installed irlba and Matrix both from source like above and it still is not working.

This is the error I get when running RunSVD:

> DefaultAssay(mousebrain) <- "ATAC"
> mousebrain <- RunTFIDF(mousebrain)
Performing TF-IDF normalization
> mousebrain <- FindTopFeatures(mousebrain, min.cutoff = 'q0')
> mousebrain <- RunSVD(mousebrain)
Running SVD
Error in irlba(A = t(x = object), nv = n, work = irlba.work, tol = tol) :
  function 'as_cholmod_sparse' not provided by package 'Matrix'

Full output is attached in the following text file:
Output_irlba_error.txt

Session Info is below (I am working in a high performance computing cluster environment):

R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux 9.2 (Plow)

Matrix products: default
BLAS:   /usr/share/Modules/apps/R/4.3.1/lib64/R/lib/libRblas.so
LAPACK: /usr/share/Modules/apps/R/4.3.1/lib64/R/lib/libRlapack.so;  LAPACK version 3.11.0

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

time zone: America/New_York
tzcode source: system (glibc)

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

other attached packages:
 [1] GenomicRanges_1.54.1 GenomeInfoDb_1.38.1  IRanges_2.36.0
 [4] S4Vectors_0.40.2     BiocGenerics_0.48.1  biovizBase_1.50.0
 [7] ggplot2_3.4.4        dplyr_1.1.4          Signac_1.12.0
[10] Seurat_5.0.1         SeuratObject_5.0.1   sp_2.1-2

loaded via a namespace (and not attached):
  [1] RcppAnnoy_0.0.21            splines_4.3.1
  [3] later_1.3.1                 BiocIO_1.12.0
  [5] filelock_1.0.3              bitops_1.0-7
  [7] tibble_3.2.1                polyclip_1.10-6
  [9] XML_3.99-0.16               rpart_4.1.23
 [11] fastDummies_1.7.3           lifecycle_1.0.4
 [13] ensembldb_2.26.0            globals_0.16.2
 [15] lattice_0.22-5              MASS_7.3-60
 [17] backports_1.4.1             magrittr_2.0.3
 [19] Hmisc_5.1-1                 plotly_4.10.3
 [21] rmarkdown_2.25              yaml_2.3.7
 [23] httpuv_1.6.12               sctransform_0.4.1
 [25] spam_2.10-0                 spatstat.sparse_3.0-3
 [27] reticulate_1.34.0           cowplot_1.1.1
 [29] pbapply_1.7-2               DBI_1.1.3
 [31] RColorBrewer_1.1-3          abind_1.4-5
 [33] zlibbioc_1.48.0             Rtsne_0.16
 [35] purrr_1.0.2                 AnnotationFilter_1.26.0
 [37] RCurl_1.98-1.13             nnet_7.3-19
 [39] VariantAnnotation_1.48.1    rappdirs_0.3.3
 [41] GenomeInfoDbData_1.2.11     ggrepel_0.9.4
 [43] irlba_2.3.5.1               listenv_0.9.0
 [45] spatstat.utils_3.0-4        goftest_1.2-3
 [47] RSpectra_0.16-1             spatstat.random_3.2-2
 [49] fitdistrplus_1.1-11         parallelly_1.36.0
 [51] leiden_0.4.3.1              codetools_0.2-19
 [53] DelayedArray_0.28.0         RcppRoll_0.3.0
 [55] xml2_1.3.5                  tidyselect_1.2.0
 [57] BiocFileCache_2.10.1        matrixStats_1.1.0
 [59] base64enc_0.1-3             spatstat.explore_3.2-5
 [61] GenomicAlignments_1.38.0    jsonlite_1.8.7
 [63] ellipsis_0.3.2              progressr_0.14.0
 [65] Formula_1.2-5               ggridges_0.5.4
 [67] survival_3.5-7              progress_1.2.3
 [69] tools_4.3.1                 ica_1.0-3
 [71] Rcpp_1.0.11                 glue_1.6.2
 [73] gridExtra_2.3               SparseArray_1.2.2
 [75] xfun_0.41                   MatrixGenerics_1.14.0
 [77] withr_2.5.2                 fastmap_1.1.1
 [79] fansi_1.0.5                 digest_0.6.33
 [81] R6_2.5.1                    mime_0.12
 [83] colorspace_2.1-0            scattermore_1.2
 [85] tensor_1.5                  biomaRt_2.58.0
 [87] RSQLite_2.3.3               dichromat_2.0-0.1
 [89] spatstat.data_3.0-3         utf8_1.2.4
 [91] tidyr_1.3.0                 generics_0.1.3
 [93] data.table_1.14.8           rtracklayer_1.62.0
 [95] prettyunits_1.2.0           httr_1.4.7
 [97] htmlwidgets_1.6.3           S4Arrays_1.2.0
 [99] uwot_0.1.16                 pkgconfig_2.0.3
[101] gtable_0.3.4                blob_1.2.4
[103] lmtest_0.9-40               XVector_0.42.0
[105] htmltools_0.5.7             dotCall64_1.1-1
[107] ProtGenerics_1.34.0         scales_1.3.0
[109] Biobase_2.62.0              png_0.1-8
[111] knitr_1.45                  rstudioapi_0.15.0
[113] rjson_0.2.21                reshape2_1.4.4
[115] curl_5.1.0                  checkmate_2.3.0
[117] nlme_3.1-164                cachem_1.0.8
[119] zoo_1.8-12                  stringr_1.5.1
[121] KernSmooth_2.23-22          parallel_4.3.1
[123] miniUI_0.1.1.1              foreign_0.8-86
[125] AnnotationDbi_1.64.1        restfulr_0.0.15
[127] pillar_1.9.0                grid_4.3.1
[129] vctrs_0.6.4                 RANN_2.6.1
[131] promises_1.2.1              dbplyr_2.4.0
[133] xtable_1.8-4                cluster_2.1.6
[135] htmlTable_2.4.2             evaluate_0.23
[137] GenomicFeatures_1.54.1      cli_3.6.1
[139] compiler_4.3.1              Rsamtools_2.18.0
[141] rlang_1.1.2                 crayon_1.5.2
[143] future.apply_1.11.0         plyr_1.8.9
[145] stringi_1.8.2               viridisLite_0.4.2
[147] deldir_2.0-2                BiocParallel_1.36.0
[149] munsell_0.5.0               Biostrings_2.70.1
[151] lazyeval_0.2.2              spatstat.geom_3.2-7
[153] Matrix_1.6-4                BSgenome_1.70.1
[155] RcppHNSW_0.5.0              hms_1.1.3
[157] patchwork_1.1.3             bit64_4.0.5
[159] future_1.33.0               KEGGREST_1.42.0
[161] shiny_1.8.0                 SummarizedExperiment_1.32.0
[163] ROCR_1.0-11                 memoise_2.0.1
[165] igraph_1.6.0                fastmatch_1.1-4
[167] bit_4.0.5

Any help you can provide me with would be very much appreciated!

[ykugo95]

Comparing with your code and my code,
It seems the Matrix package is not attached.
Matrix.utils package is not installed.

I am not sure those two are necessary to run the function, but it would be worth to try it.

Some thread implies those dependency will be corrected after reinstalling Seurat or Signac on the bare (Neither Matrix nor irlba) environment.
https://stackoverflow.com/questions/77442906/runumap-code-error-after-merged-spatial-transcriptomic-objects

I had struggled as well uninstalling and installing some packages, that made it difficult to catch those dependency.

Here is my suggestion:
remove Matrix
remove.packages("Matrix")
remove irbla
remove.packages("irlba")

reinstall them as source file

install.packages("Matrix", type = "source")
install.packages("irlba", type = "source")

We don't need to downgrade all those packages.
Here is my session info() with successful execution.

sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.2.1

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: Asia/Tokyo
tzcode source: internal

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

other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg38_1.4.5 BSgenome_1.70.1
[3] rtracklayer_1.62.0 BiocIO_1.12.0
[5] Biostrings_2.70.1 XVector_0.42.0
[7] EnsDb.Hsapiens.v86_2.99.0 ensembldb_2.26.0
[9] AnnotationFilter_1.26.0 GenomicFeatures_1.54.1
[11] AnnotationDbi_1.64.1 future_1.33.0
[13] Signac_1.12.0 scCustomize_2.0.1
[15] png_0.1-8 SingleCellExperiment_1.24.0
[17] apeglm_1.24.0 DESeq2_1.42.0
[19] SummarizedExperiment_1.32.0 Biobase_2.62.0
[21] MatrixGenerics_1.14.0 matrixStats_1.2.0
[23] GenomicRanges_1.54.1 GenomeInfoDb_1.38.2
[25] IRanges_2.36.0 S4Vectors_0.40.2
[27] BiocGenerics_0.48.1 edgeR_4.0.3
[29] limma_3.58.1 cowplot_1.1.2
[31] data.table_1.14.10 RColorBrewer_1.1-3
[33] pheatmap_1.0.12 ggthemes_5.0.0
[35] ggsci_3.0.0 ggpubr_0.6.0
[37] reshape2_1.4.4 Matrix.utils_0.9.7
[39] Matrix_1.6-4 ggrepel_0.9.4
[41] viridis_0.6.4 viridisLite_0.4.2
[43] readxl_1.4.3 patchwork_1.1.3
[45] lubridate_1.9.3 forcats_1.0.0
[47] stringr_1.5.1 dplyr_1.1.4
[49] purrr_1.0.2 readr_2.1.4
[51] tidyr_1.3.0 tibble_3.2.1
[53] ggplot2_3.4.4 tidyverse_2.0.0
[55] Seurat_5.0.1 SeuratObject_5.0.1
[57] sp_2.1-2

loaded via a namespace (and not attached):
[1] ProtGenerics_1.34.0 spatstat.sparse_3.0-3 bitops_1.0-7
[4] httr_1.4.7 numDeriv_2016.8-1.1 tools_4.3.1
[7] sctransform_0.4.1 backports_1.4.1 utf8_1.2.4
[10] R6_2.5.1 lazyeval_0.2.2 uwot_0.1.16
[13] withr_2.5.2 prettyunits_1.2.0 gridExtra_2.3
[16] progressr_0.14.0 cli_3.6.2 spatstat.explore_3.2-5
[19] fastDummies_1.7.3 mvtnorm_1.2-4 spatstat.data_3.0-3
[22] ggridges_0.5.5 pbapply_1.7-2 Rsamtools_2.18.0
[25] parallelly_1.36.0 bbmle_1.0.25.1 rstudioapi_0.15.0
[28] RSQLite_2.3.4 generics_0.1.3 shape_1.4.6
[31] ica_1.0-3 spatstat.random_3.2-2 car_3.1-2
[34] ggbeeswarm_0.7.2 fansi_1.0.6 abind_1.4-5
[37] lifecycle_1.0.4 yaml_2.3.8 snakecase_0.11.1
[40] carData_3.0-5 BiocFileCache_2.10.1 SparseArray_1.2.2
[43] Rtsne_0.17 paletteer_1.5.0 grid_4.3.1
[46] blob_1.2.4 promises_1.2.1 crayon_1.5.2
[49] bdsmatrix_1.3-6 miniUI_0.1.1.1 lattice_0.22-5
[52] KEGGREST_1.42.0 pillar_1.9.0 knitr_1.45
[55] rjson_0.2.21 future.apply_1.11.0 codetools_0.2-19
[58] fastmatch_1.1-4 leiden_0.4.3.1 glue_1.6.2
[61] vctrs_0.6.5 spam_2.10-0 cellranger_1.1.0
[64] gtable_0.3.4 rematch2_2.1.2 cachem_1.0.8
[67] emdbook_1.3.13 xfun_0.41 S4Arrays_1.2.0
[70] mime_0.12 coda_0.19-4 survival_3.5-7
[73] RcppRoll_0.3.0 statmod_1.5.0 ellipsis_0.3.2
[76] fitdistrplus_1.1-11 ROCR_1.0-11 nlme_3.1-164
[79] bit64_4.0.5 filelock_1.0.3 progress_1.2.3
[82] RcppAnnoy_0.0.21 irlba_2.3.5.1 vipor_0.4.5
[85] KernSmooth_2.23-22 colorspace_2.1-0 DBI_1.1.3
[88] ggrastr_1.0.2 tidyselect_1.2.0 curl_5.2.0
[91] bit_4.0.5 compiler_4.3.1 xml2_1.3.6
[94] DelayedArray_0.28.0 plotly_4.10.3 scales_1.3.0
[97] lmtest_0.9-40 rappdirs_0.3.3 digest_0.6.33
[100] goftest_1.2-3 spatstat.utils_3.0-4 rmarkdown_2.25
[103] htmltools_0.5.7 pkgconfig_2.0.3 dbplyr_2.4.0
[106] fastmap_1.1.1 rlang_1.1.2 GlobalOptions_0.1.2
[109] htmlwidgets_1.6.4 shiny_1.8.0 zoo_1.8-12
[112] jsonlite_1.8.8 BiocParallel_1.36.0 RCurl_1.98-1.13
[115] magrittr_2.0.3 GenomeInfoDbData_1.2.11 dotCall64_1.1-1
[118] munsell_0.5.0 Rcpp_1.0.11 reticulate_1.34.0
[121] stringi_1.8.3 zlibbioc_1.48.0 MASS_7.3-60
[124] plyr_1.8.9 parallel_4.3.1 listenv_0.9.0
[127] deldir_2.0-2 splines_4.3.1 tensor_1.5
[130] hms_1.1.3 circlize_0.4.16 locfit_1.5-9.8
[133] igraph_1.6.0 spatstat.geom_3.2-7 ggsignif_0.6.4
[136] RcppHNSW_0.5.0 biomaRt_2.58.0 XML_3.99-0.16
[139] evaluate_0.23 BiocManager_1.30.22 ggprism_1.0.4
[142] tzdb_0.4.0 httpuv_1.6.13 grr_0.9.5
[145] RANN_2.6.1 polyclip_1.10-6 scattermore_1.2
[148] janitor_2.2.0 broom_1.0.5 xtable_1.8-4
[151] restfulr_0.0.15 RSpectra_0.16-1 rstatix_0.7.2
[154] later_1.3.2 GenomicAlignments_1.38.0 memoise_2.0.1.9000
[157] beeswarm_0.4.0 cluster_2.1.6 timechange_0.2.0
[160] globals_0.16.2

I hope all goes well for you.

[kdzimm]

Thank you - I really appreciate the reply. I tried again to remove and install Matrix and irlba from source as you suggested and I loaded Matrix and Matrix.utils. I am not sure what did it, but everything seems to be working now. Thanks again!