Error running "RunSVD" function

[myaqubi]

Hi

I am trying to run the RunSVD function on my scATACseq dataset, however I am getting the following error:

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'

After searching online, I found posts suggesting it could be a compatibility issue with the 'Matrix' package. The suggestion was to install version 1.6-1 of the 'Matrix' package. However, upon installing this version, I encountered a new error when running the 'RunTFIDF' function. It seems this error might be due to the updated 'Matrix' package. Any assistance on resolving this would be greatly appreciated.

[timoast]

What is the error in RunTFIDF? It does sound like this is due to some updates in Matrix/SeuratObject

[Sun-storm]

Hi! I have the exact same issue. I also found that, even though I have Signac 1.12.0, which supposedly supports SeuratObject v5, I get a warning when I install the package saying:

Signac built for for SeuratObject v4 was just loaded with SeuratObject v5;
disabling v5 assays and validation routines, and ensuring assays work in strict
v3/v4 compatibility mode

Could that be the issue?

Edit: As a side note, I run RunTFIDF() as part of my process before trying to run RunSVD() and didn't have any issues.

[myaqubi]

Hi Tim, Thanks for your answer. This is what I get upon running this function: Performing TF-IDF normalization Error in tcrossprod(x, y) : requires numeric/complex matrix/vector arguments

…

________________________________ From: Tim Stuart ***@***.***> Sent: Thursday, November 16, 2023 10:13 PM To: stuart-lab/signac ***@***.***> Cc: Moein Yaqubi ***@***.***>; Author ***@***.***> Subject: Re: [stuart-lab/signac] Error running "RunSVD" function (Issue #1532) What is the error in RunTFIDF? It does sound like this is due to some updates in Matrix/SeuratObject — Reply to this email directly, view it on GitHub<#1532 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AJVFRBOLTFDPXJU4QDICGQLYE3P73AVCNFSM6AAAAAA7OWG2OOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMJVG4ZDCNJYGM>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[timoast]

Try updating Matrix and re-installing SeuratObject, it seems like this issues could be related to the discussion here: satijalab/seurat-object@d567ec8

[myaqubi]

Hi Tim, The problem is now solved, thanks. I made a new R environment and installed all the required packages in that environment using renv::install function.

…

________________________________ From: Tim Stuart ***@***.***> Sent: Sunday, November 19, 2023 7:57 PM To: stuart-lab/signac ***@***.***> Cc: Moein Yaqubi ***@***.***>; Author ***@***.***> Subject: Re: [stuart-lab/signac] Error running "RunSVD" function (Issue #1532) Try updating Matrix and re-installing SeuratObject, it seems like this issues could be related to the discussion here: ***@***.***<satijalab/seurat-object@d567ec8> — Reply to this email directly, view it on GitHub<#1532 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AJVFRBOZ4WTNP54GNCBIQO3YFK2JPAVCNFSM6AAAAAA7OWG2OOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMJYGA4TGMBXGU>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[Usamahussein551980]

Hi Tim,
Thanks for your great tools.
I have got a problem in my analysis of multiome dataset during RNA and ATAC analysis:

############## SCTransform #############
combined_6 <- SCTransform(combined_6, verbose = FALSE) %>%
RunPCA() %>%
RunUMAP(dims = 1:50,reduction.name = 'umap.rna', reduction.key = 'rnaUMAP_')

The ERROR:
Error in irlba::irlba(L, nv = n, nu = 0, maxit = iters) :
function 'as_cholmod_sparse' not provided by package 'Matrix'

Although I updated the Matrix and SeuratObject according to your instruction, but still have the same issue. Even though restarting the R session and installing the updates of Matrix and last version of Signac and reinstalling the SeuratObject, but still return the same issue.

############ ATAC analysis ###############

combined_6 <- RunSVD(combined_6)
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'

Could you please provide some help in this issue??

sessionInfo()

R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

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

time zone: America/Chicago
tzcode source: internal

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

other attached packages:
[1] Matrix_1.6-3 igraph_1.5.1 tidygraph_1.2.3
[4] ggraph_2.1.0 doParallel_1.0.17 iterators_1.0.14
[7] foreach_1.5.2 Pando_1.0.5 BSgenome.Hsapiens.UCSC.hg38_1.4.5
[10] BSgenome.Hsapiens.NCBI.GRCh38_1.3.1000 BSgenome_1.70.1 rtracklayer_1.62.0
[13] BiocIO_1.12.0 Biostrings_2.70.1 XVector_0.42.0
[16] EnsDb.Hsapiens.v86_2.99.0 ensembldb_2.26.0 AnnotationFilter_1.26.0
[19] GenomicFeatures_1.54.1 AnnotationDbi_1.64.1 Biobase_2.62.0
[22] GenomicRanges_1.54.1 GenomeInfoDb_1.38.0 IRanges_2.36.0
[25] S4Vectors_0.40.1 BiocGenerics_0.48.1 dplyr_1.1.4
[28] ggplot2_3.4.4 Signac_1.12.9000 hdf5r_1.3.8
[31] SeuratDisk_0.0.0.9021 SeuratObject_5.0.1 Seurat_4.4.0

loaded via a namespace (and not attached):
[1] fs_1.6.3 ProtGenerics_1.34.0 matrixStats_1.0.0 spatstat.sparse_3.0-3
[5] bitops_1.0-7 devtools_2.4.5 httr_1.4.7 RColorBrewer_1.1-3
[9] profvis_0.3.8 tools_4.3.1 sctransform_0.4.1 utf8_1.2.4
[13] R6_2.5.1 lazyeval_0.2.2 uwot_0.1.16 urlchecker_1.0.1
[17] withr_2.5.2 sp_2.1-1 prettyunits_1.2.0 gridExtra_2.3
[21] progressr_0.14.0 cli_3.6.1 spatstat.explore_3.2-5 spatstat.data_3.0-3
[25] ggridges_0.5.4 pbapply_1.7-2 Rsamtools_2.18.0 dichromat_2.0-0.1
[29] parallelly_1.36.0 sessioninfo_1.2.2 maps_3.4.1.1 pals_1.8
[33] rstudioapi_0.15.0 RSQLite_2.3.3 generics_0.1.3 ica_1.0-3
[37] spatstat.random_3.2-1 fansi_1.0.5 clipr_0.8.0 abind_1.4-5
[41] lifecycle_1.0.4 yaml_2.3.7 SummarizedExperiment_1.32.0 SparseArray_1.2.0
[45] BiocFileCache_2.10.1 Rtsne_0.16 grid_4.3.1 blob_1.2.4
[49] promises_1.2.1 ExperimentHub_2.10.0 crayon_1.5.2 miniUI_0.1.1.1
[53] lattice_0.22-5 cowplot_1.1.1 mapproj_1.2.11 KEGGREST_1.42.0
[57] pillar_1.9.0 rjson_0.2.21 future.apply_1.11.0 codetools_0.2-19
[61] fastmatch_1.1-4 leiden_0.4.3 glue_1.6.2 data.table_1.14.8
[65] remotes_2.4.2.1 vctrs_0.6.4 png_0.1-8 spam_2.10-0
[69] gtable_0.3.4 cachem_1.0.8 S4Arrays_1.2.0 mime_0.12
[73] survival_3.5-7 RcppRoll_0.3.0 interactiveDisplayBase_1.40.0 ellipsis_0.3.2
[77] fitdistrplus_1.1-11 ROCR_1.0-11 nlme_3.1-163 usethis_2.2.2
[81] bit64_4.0.5 progress_1.2.2 filelock_1.0.2 RcppAnnoy_0.0.21
[85] irlba_2.3.5.1 KernSmooth_2.23-22 colorspace_2.1-0 DBI_1.1.3
[89] celldex_1.12.0 tidyselect_1.2.0 processx_3.8.2 bit_4.0.5
[93] compiler_4.3.1 curl_5.1.0 xml2_1.3.5 DelayedArray_0.28.0
[97] plotly_4.10.3 scales_1.2.1 lmtest_0.9-40 callr_3.7.3
[101] rappdirs_0.3.3 stringr_1.5.1 digest_0.6.33 goftest_1.2-3
[105] spatstat.utils_3.0-4 presto_1.0.0 htmltools_0.5.6.1 pkgconfig_2.0.3
[109] sparseMatrixStats_1.14.0 MatrixGenerics_1.14.0 dbplyr_2.4.0 fastmap_1.1.1
[113] rlang_1.1.1 htmlwidgets_1.6.2 shiny_1.7.5.1 DelayedMatrixStats_1.24.0
[117] farver_2.1.1 zoo_1.8-12 jsonlite_1.8.7 BiocParallel_1.36.0
[121] RCurl_1.98-1.13 magrittr_2.0.3 GenomeInfoDbData_1.2.11 dotCall64_1.1-0
[125] patchwork_1.1.3.9000 munsell_0.5.0 Rcpp_1.0.11 viridis_0.6.4
[129] reticulate_1.34.0 stringi_1.7.12 zlibbioc_1.48.0 MASS_7.3-60
[133] AnnotationHub_3.10.0 plyr_1.8.9 pkgbuild_1.4.2 listenv_0.9.0
[137] ggrepel_0.9.4 deldir_1.0-9 graphlayouts_1.0.2 splines_4.3.1
[141] tensor_1.5 hms_1.1.3 ps_1.7.5 spatstat.geom_3.2-7
[145] reshape2_1.4.4 biomaRt_2.58.0 pkgload_1.3.3 BiocVersion_3.18.0
[149] XML_3.99-0.15 BiocManager_1.30.22 tweenr_2.0.2 httpuv_1.6.12
[153] RANN_2.6.1 tidyr_1.3.0 purrr_1.0.2 polyclip_1.10-6
[157] future_1.33.0 scattermore_1.2 ggforce_0.4.1 xtable_1.8-4
[161] restfulr_0.0.15 later_1.3.1 viridisLite_0.4.2 ggpointdensity_0.1.0
[165] tibble_3.2.1 memoise_2.0.1 GenomicAlignments_1.38.0 cluster_2.1.4
[169] globals_0.16.2

[timoast]

@Usamahussein551980 please see #1530