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preprocess_cds Error in function 'as_cholmod_sparse' not provided by package 'Matrix' #690

Open weiyouzi321 opened 1 year ago

weiyouzi321 commented 1 year ago

Describe the bug Error in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth = TRUE, : function 'as_cholmod_sparse' not provided by package 'Matrix'

To Reproduce cds<-preprocess_cds(cds, num_dim = 30,norm_method = "none")

traceback() 4: (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth = TRUE, tol = 1e-05, v = NULL, right_only = FALSE, verbose = FALSE, scale = NULL, center = NULL, shift = NULL, mult = NULL, fastpath = TRUE, svtol = tol, smallest = FALSE, ...) { ropts <- options(warn = 1) mflag <- new.env() mflag$flag <- FALSE on.exit(options(ropts)) interchange <- FALSE eps <- .Machine$double.eps mcall <- as.list(match.call()) random <- eval(mcall[["rng"]]) if (is.null(random)) random <- rnorm maxritz <- eval(mcall[["maxritz"]]) if (is.null(maxritz)) maxritz <- 3 eps2 <- eval(mcall[["invariant_subspace_tolerance"]]) if (is.null(eps2)) ... 3: do.call(irlba::irlba, args = args) 2: sparse_prcomp_irlba(Matrix::t(FM), n = min(num_dim, min(dim(FM)) - 1), center = scaling, scale. = scaling) 1: preprocess_cds(cds, num_dim = 30, norm_method = "none")

Expected behavior A clear and concise description of what you expected to happen.

Screenshots 1699791798943

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=Chinese (Simplified)_China.utf8 [2] LC_CTYPE=Chinese (Simplified)_China.utf8
[3] LC_MONETARY=Chinese (Simplified)_China.utf8 [4] LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.utf8

time zone: Asia/Shanghai tzcode source: internal

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

other attached packages: [1] Seurat_4.3.0.1 SeuratObject_5.0.0 sp_2.1-1
[4] monocle3_1.3.4 SingleCellExperiment_1.24.0 SummarizedExperiment_1.32.0 [7] GenomicRanges_1.54.1 GenomeInfoDb_1.38.1 IRanges_2.36.0
[10] S4Vectors_0.40.1 MatrixGenerics_1.14.0 matrixStats_1.1.0
[13] Biobase_2.62.0 BiocGenerics_0.48.1

loaded via a namespace (and not attached): [1] RcppAnnoy_0.0.21 splines_4.3.1 later_1.3.0
[4] bitops_1.0-7 tibble_3.2.1 polyclip_1.10-4
[7] lifecycle_1.0.4 globals_0.16.2 processx_3.8.2
[10] lattice_0.21-8 MASS_7.3-60 magrittr_2.0.3
[13] plotly_4.10.2 remotes_2.4.2.1 httpuv_1.6.9
[16] sctransform_0.3.5 spam_2.9-1 sessioninfo_1.2.2
[19] pkgbuild_1.4.2 spatstat.sparse_3.0-2 reticulate_1.30
[22] cowplot_1.1.1 pbapply_1.7-2 DBI_1.1.3
[25] minqa_1.2.6 RColorBrewer_1.1-3 abind_1.4-5
[28] pkgload_1.3.3 zlibbioc_1.48.0 Rtsne_0.16
[31] purrr_1.0.1 RCurl_1.98-1.13 GenomeInfoDbData_1.2.11
[34] ggrepel_0.9.3 irlba_2.3.5.1 listenv_0.9.0
[37] spatstat.utils_3.0-3 terra_1.7-55 pheatmap_1.0.12
[40] goftest_1.2-3 spatstat.random_3.1-5 fitdistrplus_1.1-11
[43] parallelly_1.36.0 DelayedMatrixStats_1.24.0 leiden_0.4.3
[46] codetools_0.2-19 DelayedArray_0.28.0 tidyselect_1.2.0
[49] lme4_1.1-35.1 spatstat.explore_3.2-1 jsonlite_1.8.7
[52] ellipsis_0.3.2 progressr_0.14.0 ggridges_0.5.4
[55] survival_3.5-5 tools_4.3.1 ica_1.0-3
[58] Rcpp_1.0.10 glue_1.6.2 gridExtra_2.3
[61] SparseArray_1.2.2 usethis_2.2.2 dplyr_1.1.3
[64] fastmap_1.1.1 boot_1.3-28.1 fansi_1.0.5
[67] callr_3.7.3 digest_0.6.31 R6_2.5.1
[70] mime_0.12 colorspace_2.1-0 scattermore_1.2
[73] tensor_1.5 spatstat.data_3.0-1 RSQLite_2.3.1
[76] utf8_1.2.4 tidyr_1.3.0 generics_0.1.3
[79] data.table_1.14.8 prettyunits_1.2.0 httr_1.4.7
[82] htmlwidgets_1.6.2 S4Arrays_1.2.0 uwot_0.1.16
[85] pkgconfig_2.0.3 gtable_0.3.4 blob_1.2.4
[88] lmtest_0.9-40 XVector_0.42.0 htmltools_0.5.5
[91] profvis_0.3.8 dotCall64_1.0-2 scales_1.2.1
[94] png_0.1-8 rstudioapi_0.15.0 reshape2_1.4.4
[97] nlme_3.1-162 nloptr_2.0.3 cachem_1.0.7
[100] zoo_1.8-12 stringr_1.5.0 KernSmooth_2.23-22
[103] parallel_4.3.1 miniUI_0.1.1.1 AnnotationDbi_1.62.2
[106] pillar_1.9.0 grid_4.3.1 vctrs_0.6.1
[109] RANN_2.6.1 urlchecker_1.0.1 promises_1.2.0.1
[112] xtable_1.8-4 cluster_2.1.4 cli_3.4.0
[115] compiler_4.3.1 rlang_1.1.2 crayon_1.5.2
[118] future.apply_1.11.0 ps_1.7.5 plyr_1.8.9
[121] fs_1.6.3 stringi_1.7.12 deldir_1.0-9
[124] viridisLite_0.4.2 assertthat_0.2.1 munsell_0.5.0
[127] Biostrings_2.68.1 lazyeval_0.2.2 spatstat.geom_3.2-4
[130] devtools_2.4.5 Matrix_1.6-2 patchwork_1.1.2
[133] sparseMatrixStats_1.14.0 bit64_4.0.5 future_1.33.0
[136] ggplot2_3.4.4 KEGGREST_1.40.0 shiny_1.7.5.1
[139] ROCR_1.0-11 igraph_1.5.1 memoise_2.0.1
[142] bit_4.0.5

Additional context Add any other context about the problem here.

ZayaAyush commented 1 year ago

I have the same issue. I couldn't resolve this problem! If someone fixed this problem, how did you figure out this problem? Please share

cyang-2014 commented 1 year ago

I have the same issue. But I found a solution here https://stackoverflow.com/questions/77442906/runumap-code-error-after-merged-spatial-transcriptomic-objects, mentioning the irlba package issue: https://github.com/bwlewis/irlba/issues/70. So I used the commands below in R:

remove.packages('irlba')

install.packages('irlba')

ZayaAyush commented 12 months ago

Thank you, After restarting R Studio, I uninstalled the latest version of Matrix and installed a previous version (1.6-1.1), which resolved the issue. remotes::install_version("Matrix", version = "1.6-1.1")

pronoymondal commented 11 months ago

I had the same issue. Reinstalling "monocle3" package worked for me.

njumedw commented 10 months ago

Thank you, After restarting R Studio, I uninstalled the latest version of Matrix and installed a previous version (1.6-1.1), which resolved the issue. remotes::install_version("Matrix", version = "1.6-1.1")

I've removed the Matrix and installed the version (1.6-1.1). However, several packages, including Seuratobject, reported error ">=1.6-3 is required". I also removed the monocle3 and reinstalled it, and it did not work too.

njumedw commented 10 months ago

Problem solved after reinstalled package "irlba", as I run the traceback and found the error actually happened on the irlba. Seems that the "Matrix" package treats the sparse matrix dependent on several packages, and update these packages may work for dealing with the issue.

greengarden0925 commented 9 months ago

I follow the instruction to install "irlba"(latest version: 2.3.5.1) and "Matrix"(version 1.6-1.1). When I ran the following codes, the same error happened. big_cds <- monocle3::preprocess_cds(big_cds, num_dim = 50,method = "PCA") Error in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth = TRUE, : function 'as_cholmod_sparse' not provided by package 'Matrix'

The following is my session info `> sessionInfo() R version 4.3.2 (2023-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.6 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3; LAPACK version 3.9.0

locale: [1] LC_CTYPE=en_US.UTF-8
[2] LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8
[8] LC_NAME=C
[9] LC_ADDRESS=C
[10] LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 [12] LC_IDENTIFICATION=C

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

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

other attached packages: [1] metap_1.9
[2] multtest_2.58.0
[3] dittoSeq_1.14.0
[4] monocle3_1.3.4
[5] SeuratWrappers_0.3.3
[6] pcaMethods_1.94.0
[7] DESeq2_1.42.0
[8] clustree_0.5.1
[9] ggraph_2.1.0
[10] harmony_1.2.0
[11] Rcpp_1.0.12
[12] DoubletFinder_2.0.4
[13] forcats_1.0.0
[14] stringr_1.5.1
[15] dplyr_1.1.4
[16] purrr_1.0.2
[17] readr_2.1.5
[18] tidyr_1.3.1
[19] tibble_3.2.1
[20] ggplot2_3.4.4
[21] tidyverse_2.0.0
[22] scCustomize_2.0.1
[23] celldex_1.12.0
[24] RColorBrewer_1.1-3
[25] glmGamPoi_1.14.0
[26] hdf5r_1.3.9
[27] batchelor_1.18.1
[28] SingleCellExperiment_1.24.0 [29] limma_3.58.1
[30] SingleR_2.4.1
[31] SummarizedExperiment_1.32.0 [32] Biobase_2.62.0
[33] GenomicRanges_1.54.1
[34] GenomeInfoDb_1.38.5
[35] IRanges_2.36.0
[36] S4Vectors_0.40.2
[37] MatrixGenerics_1.14.0
[38] matrixStats_1.2.0
[39] terra_1.7-65
[40] Seurat_5.0.1
[41] SeuratObject_5.0.1
[42] sp_2.1-2
[43] ggrastr_1.0.2
[44] devtools_2.4.5
[45] usethis_2.2.2
[46] pdfCluster_1.0-4
[47] BiocGenerics_0.48.1
[48] data.table_1.14.10
[49] lubridate_1.9.3
[50] BiocManager_1.30.22

loaded via a namespace (and not attached): [1] R.methodsS3_1.8.2
[2] urlchecker_1.0.1
[3] goftest_1.2-3
[4] Biostrings_2.70.2
[5] TH.data_1.1-2
[6] vctrs_0.6.5
[7] spatstat.random_3.2-2
[8] digest_0.6.34
[9] png_0.1-8
[10] shape_1.4.6
[11] ggrepel_0.9.5
[12] deldir_2.0-2
[13] parallelly_1.36.0
[14] MASS_7.3-60.0.1
[15] reshape2_1.4.4
[16] httpuv_1.6.14
[17] withr_3.0.0
[18] ellipsis_0.3.2
[19] survival_3.5-7
[20] memoise_2.0.1
[21] ggbeeswarm_0.7.2
[22] janitor_2.2.0
[23] profvis_0.3.8
[24] zoo_1.8-12
[25] GlobalOptions_0.1.2
[26] pbapply_1.7-2
[27] R.oo_1.26.0
[28] rematch2_2.1.2
[29] KEGGREST_1.42.0
[30] promises_1.2.1
[31] httr_1.4.7
[32] globals_0.16.2
[33] fitdistrplus_1.1-11
[34] ps_1.7.6
[35] rstudioapi_0.15.0
[36] miniUI_0.1.1.1
[37] generics_0.1.3
[38] processx_3.8.3
[39] curl_5.2.0
[40] zlibbioc_1.48.0
[41] ScaledMatrix_1.10.0
[42] polyclip_1.10-6
[43] TFisher_0.2.0
[44] GenomeInfoDbData_1.2.11
[45] ExperimentHub_2.10.0
[46] SparseArray_1.2.3
[47] interactiveDisplayBase_1.40.0 [48] desc_1.4.3
[49] xtable_1.8-4
[50] S4Arrays_1.2.0
[51] BiocFileCache_2.10.1
[52] hms_1.1.3
[53] irlba_2.3.5.1
[54] colorspace_2.1-0
[55] filelock_1.0.3
[56] ROCR_1.0-11
[57] reticulate_1.34.0
[58] spatstat.data_3.0-4
[59] magrittr_2.0.3
[60] lmtest_0.9-40
[61] snakecase_0.11.1
[62] later_1.3.2
[63] viridis_0.6.4
[64] lattice_0.22-5
[65] spatstat.geom_3.2-8
[66] future.apply_1.11.1
[67] scattermore_1.2
[68] scuttle_1.12.0
[69] cowplot_1.1.3
[70] RcppAnnoy_0.0.22
[71] pillar_1.9.0
[72] nlme_3.1-164
[73] compiler_4.3.2
[74] beachmat_2.18.0
[75] RSpectra_0.16-1
[76] stringi_1.8.3
[77] tensor_1.5
[78] minqa_1.2.6
[79] plyr_1.8.9
[80] crayon_1.5.2
[81] abind_1.4-5
[82] sn_2.1.1
[83] locfit_1.5-9.8
[84] mathjaxr_1.6-0
[85] graphlayouts_1.1.0
[86] bit_4.0.5
[87] sandwich_3.1-0
[88] multcomp_1.4-25
[89] codetools_0.2-19
[90] BiocSingular_1.18.0
[91] paletteer_1.6.0
[92] plotly_4.10.4
[93] mime_0.12
[94] splines_4.3.2
[95] circlize_0.4.15
[96] fastDummies_1.7.3
[97] dbplyr_2.4.0
[98] sparseMatrixStats_1.14.0
[99] magic_1.6-1
[100] blob_1.2.4
[101] utf8_1.2.4
[102] BiocVersion_3.18.1
[103] lme4_1.1-35.1
[104] fs_1.6.3
[105] listenv_0.9.0
[106] DelayedMatrixStats_1.24.0
[107] Rdpack_2.6
[108] pkgbuild_1.4.3
[109] Matrix_1.6-1.1
[110] callr_3.7.3
[111] statmod_1.5.0
[112] tzdb_0.4.0
[113] tweenr_2.0.2
[114] pkgconfig_2.0.3
[115] pheatmap_1.0.12
[116] tools_4.3.2
[117] cachem_1.0.8
[118] rbibutils_2.2.16
[119] RSQLite_2.3.5
[120] viridisLite_0.4.2
[121] DBI_1.2.1
[122] numDeriv_2016.8-1.1
[123] fastmap_1.1.1
[124] scales_1.3.0
[125] grid_4.3.2
[126] ica_1.0-3
[127] AnnotationHub_3.10.0
[128] patchwork_1.2.0
[129] ggprism_1.0.4
[130] dotCall64_1.1-1
[131] RANN_2.6.1
[132] farver_2.1.1
[133] tidygraph_1.3.0
[134] yaml_2.3.8
[135] cli_3.6.2
[136] leiden_0.4.3.1
[137] lifecycle_1.0.4
[138] uwot_0.1.16
[139] mvtnorm_1.2-4
[140] sessioninfo_1.2.2
[141] BiocParallel_1.36.0
[142] timechange_0.3.0
[143] gtable_0.3.4
[144] ggridges_0.5.6
[145] progressr_0.14.0
[146] parallel_4.3.2
[147] jsonlite_1.8.8
[148] RcppHNSW_0.5.0
[149] bitops_1.0-7
[150] assertthat_0.2.1
[151] bit64_4.0.5
[152] qqconf_1.3.2
[153] Rtsne_0.17
[154] spatstat.utils_3.0-4
[155] BiocNeighbors_1.20.2
[156] mutoss_0.1-13
[157] R.utils_2.12.3
[158] lazyeval_0.2.2
[159] shiny_1.8.0
[160] htmltools_0.5.7
[161] sctransform_0.4.1
[162] rappdirs_0.3.3
[163] glue_1.7.0
[164] spam_2.10-0
[165] ResidualMatrix_1.12.0
[166] XVector_0.42.0
[167] RCurl_1.98-1.14
[168] mnormt_2.1.1
[169] gridExtra_2.3
[170] boot_1.3-28.1
[171] igraph_1.6.0
[172] R6_2.5.1
[173] cluster_2.1.6
[174] pkgload_1.3.4
[175] nloptr_2.0.3
[176] plotrix_3.8-4
[177] DelayedArray_0.28.0
[178] tidyselect_1.2.0
[179] vipor_0.4.7
[180] ggforce_0.4.1
[181] AnnotationDbi_1.64.1
[182] future_1.33.1
[183] rsvd_1.0.5
[184] munsell_0.5.0
[185] KernSmooth_2.23-22
[186] geometry_0.4.7
[187] htmlwidgets_1.6.4
[188] rlang_1.1.3
[189] spatstat.sparse_3.0-3
[190] spatstat.explore_3.2-5
[191] remotes_2.4.2.1
[192] fansi_1.0.6
[193] beeswarm_0.4.0 `

greengarden0925 commented 9 months ago

I follow the instruction to install "irlba"(latest version: 2.3.5.1) and "Matrix"(version 1.6-1.1). When I ran the following codes, the same error happened. big_cds <- monocle3::preprocess_cds(big_cds, num_dim = 50,method = "PCA") Error in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth = TRUE, : function 'as_cholmod_sparse' not provided by package 'Matrix'

The following is my session info `> sessionInfo() R version 4.3.2 (2023-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.6 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3; LAPACK version 3.9.0

locale: [1] LC_CTYPE=en_US.UTF-8 [2] LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 [6] LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 [8] LC_NAME=C [9] LC_ADDRESS=C [10] LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 [12] LC_IDENTIFICATION=C

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

attached base packages: [1] stats4 stats graphics grDevices utils [6] datasets methods base

other attached packages: [1] metap_1.9 [2] multtest_2.58.0 [3] dittoSeq_1.14.0 [4] monocle3_1.3.4 [5] SeuratWrappers_0.3.3 [6] pcaMethods_1.94.0 [7] DESeq2_1.42.0 [8] clustree_0.5.1 [9] ggraph_2.1.0 [10] harmony_1.2.0 [11] Rcpp_1.0.12 [12] DoubletFinder_2.0.4 [13] forcats_1.0.0 [14] stringr_1.5.1 [15] dplyr_1.1.4 [16] purrr_1.0.2 [17] readr_2.1.5 [18] tidyr_1.3.1 [19] tibble_3.2.1 [20] ggplot2_3.4.4 [21] tidyverse_2.0.0 [22] scCustomize_2.0.1 [23] celldex_1.12.0 [24] RColorBrewer_1.1-3 [25] glmGamPoi_1.14.0 [26] hdf5r_1.3.9 [27] batchelor_1.18.1 [28] SingleCellExperiment_1.24.0 [29] limma_3.58.1 [30] SingleR_2.4.1 [31] SummarizedExperiment_1.32.0 [32] Biobase_2.62.0 [33] GenomicRanges_1.54.1 [34] GenomeInfoDb_1.38.5 [35] IRanges_2.36.0 [36] S4Vectors_0.40.2 [37] MatrixGenerics_1.14.0 [38] matrixStats_1.2.0 [39] terra_1.7-65 [40] Seurat_5.0.1 [41] SeuratObject_5.0.1 [42] sp_2.1-2 [43] ggrastr_1.0.2 [44] devtools_2.4.5 [45] usethis_2.2.2 [46] pdfCluster_1.0-4 [47] BiocGenerics_0.48.1 [48] data.table_1.14.10 [49] lubridate_1.9.3 [50] BiocManager_1.30.22

loaded via a namespace (and not attached): [1] R.methodsS3_1.8.2 [2] urlchecker_1.0.1 [3] goftest_1.2-3 [4] Biostrings_2.70.2 [5] TH.data_1.1-2 [6] vctrs_0.6.5 [7] spatstat.random_3.2-2 [8] digest_0.6.34 [9] png_0.1-8 [10] shape_1.4.6 [11] ggrepel_0.9.5 [12] deldir_2.0-2 [13] parallelly_1.36.0 [14] MASS_7.3-60.0.1 [15] reshape2_1.4.4 [16] httpuv_1.6.14 [17] withr_3.0.0 [18] ellipsis_0.3.2 [19] survival_3.5-7 [20] memoise_2.0.1 [21] ggbeeswarm_0.7.2 [22] janitor_2.2.0 [23] profvis_0.3.8 [24] zoo_1.8-12 [25] GlobalOptions_0.1.2 [26] pbapply_1.7-2 [27] R.oo_1.26.0 [28] rematch2_2.1.2 [29] KEGGREST_1.42.0 [30] promises_1.2.1 [31] httr_1.4.7 [32] globals_0.16.2 [33] fitdistrplus_1.1-11 [34] ps_1.7.6 [35] rstudioapi_0.15.0 [36] miniUI_0.1.1.1 [37] generics_0.1.3 [38] processx_3.8.3 [39] curl_5.2.0 [40] zlibbioc_1.48.0 [41] ScaledMatrix_1.10.0 [42] polyclip_1.10-6 [43] TFisher_0.2.0 [44] GenomeInfoDbData_1.2.11 [45] ExperimentHub_2.10.0 [46] SparseArray_1.2.3 [47] interactiveDisplayBase_1.40.0 [48] desc_1.4.3 [49] xtable_1.8-4 [50] S4Arrays_1.2.0 [51] BiocFileCache_2.10.1 [52] hms_1.1.3 [53] irlba_2.3.5.1 [54] colorspace_2.1-0 [55] filelock_1.0.3 [56] ROCR_1.0-11 [57] reticulate_1.34.0 [58] spatstat.data_3.0-4 [59] magrittr_2.0.3 [60] lmtest_0.9-40 [61] snakecase_0.11.1 [62] later_1.3.2 [63] viridis_0.6.4 [64] lattice_0.22-5 [65] spatstat.geom_3.2-8 [66] future.apply_1.11.1 [67] scattermore_1.2 [68] scuttle_1.12.0 [69] cowplot_1.1.3 [70] RcppAnnoy_0.0.22 [71] pillar_1.9.0 [72] nlme_3.1-164 [73] compiler_4.3.2 [74] beachmat_2.18.0 [75] RSpectra_0.16-1 [76] stringi_1.8.3 [77] tensor_1.5 [78] minqa_1.2.6 [79] plyr_1.8.9 [80] crayon_1.5.2 [81] abind_1.4-5 [82] sn_2.1.1 [83] locfit_1.5-9.8 [84] mathjaxr_1.6-0 [85] graphlayouts_1.1.0 [86] bit_4.0.5 [87] sandwich_3.1-0 [88] multcomp_1.4-25 [89] codetools_0.2-19 [90] BiocSingular_1.18.0 [91] paletteer_1.6.0 [92] plotly_4.10.4 [93] mime_0.12 [94] splines_4.3.2 [95] circlize_0.4.15 [96] fastDummies_1.7.3 [97] dbplyr_2.4.0 [98] sparseMatrixStats_1.14.0 [99] magic_1.6-1 [100] blob_1.2.4 [101] utf8_1.2.4 [102] BiocVersion_3.18.1 [103] lme4_1.1-35.1 [104] fs_1.6.3 [105] listenv_0.9.0 [106] DelayedMatrixStats_1.24.0 [107] Rdpack_2.6 [108] pkgbuild_1.4.3 [109] Matrix_1.6-1.1 [110] callr_3.7.3 [111] statmod_1.5.0 [112] tzdb_0.4.0 [113] tweenr_2.0.2 [114] pkgconfig_2.0.3 [115] pheatmap_1.0.12 [116] tools_4.3.2 [117] cachem_1.0.8 [118] rbibutils_2.2.16 [119] RSQLite_2.3.5 [120] viridisLite_0.4.2 [121] DBI_1.2.1 [122] numDeriv_2016.8-1.1 [123] fastmap_1.1.1 [124] scales_1.3.0 [125] grid_4.3.2 [126] ica_1.0-3 [127] AnnotationHub_3.10.0 [128] patchwork_1.2.0 [129] ggprism_1.0.4 [130] dotCall64_1.1-1 [131] RANN_2.6.1 [132] farver_2.1.1 [133] tidygraph_1.3.0 [134] yaml_2.3.8 [135] cli_3.6.2 [136] leiden_0.4.3.1 [137] lifecycle_1.0.4 [138] uwot_0.1.16 [139] mvtnorm_1.2-4 [140] sessioninfo_1.2.2 [141] BiocParallel_1.36.0 [142] timechange_0.3.0 [143] gtable_0.3.4 [144] ggridges_0.5.6 [145] progressr_0.14.0 [146] parallel_4.3.2 [147] jsonlite_1.8.8 [148] RcppHNSW_0.5.0 [149] bitops_1.0-7 [150] assertthat_0.2.1 [151] bit64_4.0.5 [152] qqconf_1.3.2 [153] Rtsne_0.17 [154] spatstat.utils_3.0-4 [155] BiocNeighbors_1.20.2 [156] mutoss_0.1-13 [157] R.utils_2.12.3 [158] lazyeval_0.2.2 [159] shiny_1.8.0 [160] htmltools_0.5.7 [161] sctransform_0.4.1 [162] rappdirs_0.3.3 [163] glue_1.7.0 [164] spam_2.10-0 [165] ResidualMatrix_1.12.0 [166] XVector_0.42.0 [167] RCurl_1.98-1.14 [168] mnormt_2.1.1 [169] gridExtra_2.3 [170] boot_1.3-28.1 [171] igraph_1.6.0 [172] R6_2.5.1 [173] cluster_2.1.6 [174] pkgload_1.3.4 [175] nloptr_2.0.3 [176] plotrix_3.8-4 [177] DelayedArray_0.28.0 [178] tidyselect_1.2.0 [179] vipor_0.4.7 [180] ggforce_0.4.1 [181] AnnotationDbi_1.64.1 [182] future_1.33.1 [183] rsvd_1.0.5 [184] munsell_0.5.0 [185] KernSmooth_2.23-22 [186] geometry_0.4.7 [187] htmlwidgets_1.6.4 [188] rlang_1.1.3 [189] spatstat.sparse_3.0-3 [190] spatstat.explore_3.2-5 [191] remotes_2.4.2.1 [192] fansi_1.0.6 [193] beeswarm_0.4.0 `

I found the workaround. Restart R studio and following the codes. Restart R studio is the key point. remove.packages("Matrix") remove.packages("irlba") install.packages("Matrix",type="source", dependencies=T) install.packages("irlba",type="source", dependencies=T)

fjh1997 commented 8 months ago

I follow the instruction to install "irlba"(latest version: 2.3.5.1) and "Matrix"(version 1.6-1.1). When I ran the following codes, the same error happened. big_cds <- monocle3::preprocess_cds(big_cds, num_dim = 50,method = "PCA") Error in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth = TRUE, : function 'as_cholmod_sparse' not provided by package 'Matrix' The following is my session info > sessionInfo() R version 4.3.2 (2023-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.6 LTS Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3; LAPACK version 3.9.0 locale: [1] LC_CTYPE=en_US.UTF-8 [2] LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 [6] LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 [8] LC_NAME=C [9] LC_ADDRESS=C [10] LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 [12] LC_IDENTIFICATION=C time zone: America/New_York tzcode source: system (glibc) attached base packages: [1] stats4 stats graphics grDevices utils [6] datasets methods base other attached packages: [1] metap_1.9 [2] multtest_2.58.0 [3] dittoSeq_1.14.0 [4] monocle3_1.3.4 [5] SeuratWrappers_0.3.3 [6] pcaMethods_1.94.0 [7] DESeq2_1.42.0 [8] clustree_0.5.1 [9] ggraph_2.1.0 [10] harmony_1.2.0 [11] Rcpp_1.0.12 [12] DoubletFinder_2.0.4 [13] forcats_1.0.0 [14] stringr_1.5.1 [15] dplyr_1.1.4 [16] purrr_1.0.2 [17] readr_2.1.5 [18] tidyr_1.3.1 [19] tibble_3.2.1 [20] ggplot2_3.4.4 [21] tidyverse_2.0.0 [22] scCustomize_2.0.1 [23] celldex_1.12.0 [24] RColorBrewer_1.1-3 [25] glmGamPoi_1.14.0 [26] hdf5r_1.3.9 [27] batchelor_1.18.1 [28] SingleCellExperiment_1.24.0 [29] limma_3.58.1 [30] SingleR_2.4.1 [31] SummarizedExperiment_1.32.0 [32] Biobase_2.62.0 [33] GenomicRanges_1.54.1 [34] GenomeInfoDb_1.38.5 [35] IRanges_2.36.0 [36] S4Vectors_0.40.2 [37] MatrixGenerics_1.14.0 [38] matrixStats_1.2.0 [39] terra_1.7-65 [40] Seurat_5.0.1 [41] SeuratObject_5.0.1 [42] sp_2.1-2 [43] ggrastr_1.0.2 [44] devtools_2.4.5 [45] usethis_2.2.2 [46] pdfCluster_1.0-4 [47] BiocGenerics_0.48.1 [48] data.table_1.14.10 [49] lubridate_1.9.3 [50] BiocManager_1.30.22 loaded via a namespace (and not attached): [1] R.methodsS3_1.8.2 [2] urlchecker_1.0.1 [3] goftest_1.2-3 [4] Biostrings_2.70.2 [5] TH.data_1.1-2 [6] vctrs_0.6.5 [7] spatstat.random_3.2-2 [8] digest_0.6.34 [9] png_0.1-8 [10] shape_1.4.6 [11] ggrepel_0.9.5 [12] deldir_2.0-2 [13] parallelly_1.36.0 [14] MASS_7.3-60.0.1 [15] reshape2_1.4.4 [16] httpuv_1.6.14 [17] withr_3.0.0 [18] ellipsis_0.3.2 [19] survival_3.5-7 [20] memoise_2.0.1 [21] ggbeeswarm_0.7.2 [22] janitor_2.2.0 [23] profvis_0.3.8 [24] zoo_1.8-12 [25] GlobalOptions_0.1.2 [26] pbapply_1.7-2 [27] R.oo_1.26.0 [28] rematch2_2.1.2 [29] KEGGREST_1.42.0 [30] promises_1.2.1 [31] httr_1.4.7 [32] globals_0.16.2 [33] fitdistrplus_1.1-11 [34] ps_1.7.6 [35] rstudioapi_0.15.0 [36] miniUI_0.1.1.1 [37] generics_0.1.3 [38] processx_3.8.3 [39] curl_5.2.0 [40] zlibbioc_1.48.0 [41] ScaledMatrix_1.10.0 [42] polyclip_1.10-6 [43] TFisher_0.2.0 [44] GenomeInfoDbData_1.2.11 [45] ExperimentHub_2.10.0 [46] SparseArray_1.2.3 [47] interactiveDisplayBase_1.40.0 [48] desc_1.4.3 [49] xtable_1.8-4 [50] S4Arrays_1.2.0 [51] BiocFileCache_2.10.1 [52] hms_1.1.3 [53] irlba_2.3.5.1 [54] colorspace_2.1-0 [55] filelock_1.0.3 [56] ROCR_1.0-11 [57] reticulate_1.34.0 [58] spatstat.data_3.0-4 [59] magrittr_2.0.3 [60] lmtest_0.9-40 [61] snakecase_0.11.1 [62] later_1.3.2 [63] viridis_0.6.4 [64] lattice_0.22-5 [65] spatstat.geom_3.2-8 [66] future.apply_1.11.1 [67] scattermore_1.2 [68] scuttle_1.12.0 [69] cowplot_1.1.3 [70] RcppAnnoy_0.0.22 [71] pillar_1.9.0 [72] nlme_3.1-164 [73] compiler_4.3.2 [74] beachmat_2.18.0 [75] RSpectra_0.16-1 [76] stringi_1.8.3 [77] tensor_1.5 [78] minqa_1.2.6 [79] plyr_1.8.9 [80] crayon_1.5.2 [81] abind_1.4-5 [82] sn_2.1.1 [83] locfit_1.5-9.8 [84] mathjaxr_1.6-0 [85] graphlayouts_1.1.0 [86] bit_4.0.5 [87] sandwich_3.1-0 [88] multcomp_1.4-25 [89] codetools_0.2-19 [90] BiocSingular_1.18.0 [91] paletteer_1.6.0 [92] plotly_4.10.4 [93] mime_0.12 [94] splines_4.3.2 [95] circlize_0.4.15 [96] fastDummies_1.7.3 [97] dbplyr_2.4.0 [98] sparseMatrixStats_1.14.0 [99] magic_1.6-1 [100] blob_1.2.4 [101] utf8_1.2.4 [102] BiocVersion_3.18.1 [103] lme4_1.1-35.1 [104] fs_1.6.3 [105] listenv_0.9.0 [106] DelayedMatrixStats_1.24.0 [107] Rdpack_2.6 [108] pkgbuild_1.4.3 [109] Matrix_1.6-1.1 [110] callr_3.7.3 [111] statmod_1.5.0 [112] tzdb_0.4.0 [113] tweenr_2.0.2 [114] pkgconfig_2.0.3 [115] pheatmap_1.0.12 [116] tools_4.3.2 [117] cachem_1.0.8 [118] rbibutils_2.2.16 [119] RSQLite_2.3.5 [120] viridisLite_0.4.2 [121] DBI_1.2.1 [122] numDeriv_2016.8-1.1 [123] fastmap_1.1.1 [124] scales_1.3.0 [125] grid_4.3.2 [126] ica_1.0-3 [127] AnnotationHub_3.10.0 [128] patchwork_1.2.0 [129] ggprism_1.0.4 [130] dotCall64_1.1-1 [131] RANN_2.6.1 [132] farver_2.1.1 [133] tidygraph_1.3.0 [134] yaml_2.3.8 [135] cli_3.6.2 [136] leiden_0.4.3.1 [137] lifecycle_1.0.4 [138] uwot_0.1.16 [139] mvtnorm_1.2-4 [140] sessioninfo_1.2.2 [141] BiocParallel_1.36.0 [142] timechange_0.3.0 [143] gtable_0.3.4 [144] ggridges_0.5.6 [145] progressr_0.14.0 [146] parallel_4.3.2 [147] jsonlite_1.8.8 [148] RcppHNSW_0.5.0 [149] bitops_1.0-7 [150] assertthat_0.2.1 [151] bit64_4.0.5 [152] qqconf_1.3.2 [153] Rtsne_0.17 [154] spatstat.utils_3.0-4 [155] BiocNeighbors_1.20.2 [156] mutoss_0.1-13 [157] R.utils_2.12.3 [158] lazyeval_0.2.2 [159] shiny_1.8.0 [160] htmltools_0.5.7 [161] sctransform_0.4.1 [162] rappdirs_0.3.3 [163] glue_1.7.0 [164] spam_2.10-0 [165] ResidualMatrix_1.12.0 [166] XVector_0.42.0 [167] RCurl_1.98-1.14 [168] mnormt_2.1.1 [169] gridExtra_2.3 [170] boot_1.3-28.1 [171] igraph_1.6.0 [172] R6_2.5.1 [173] cluster_2.1.6 [174] pkgload_1.3.4 [175] nloptr_2.0.3 [176] plotrix_3.8-4 [177] DelayedArray_0.28.0 [178] tidyselect_1.2.0 [179] vipor_0.4.7 [180] ggforce_0.4.1 [181] AnnotationDbi_1.64.1 [182] future_1.33.1 [183] rsvd_1.0.5 [184] munsell_0.5.0 [185] KernSmooth_2.23-22 [186] geometry_0.4.7 [187] htmlwidgets_1.6.4 [188] rlang_1.1.3 [189] spatstat.sparse_3.0-3 [190] spatstat.explore_3.2-5 [191] remotes_2.4.2.1 [192] fansi_1.0.6 [193] beeswarm_0.4.0

I found the workaround. Restart R studio and following the codes. Restart R studio is the key point. remove.packages("Matrix") remove.packages("irlba") install.packages("Matrix",type="source", dependencies=T) install.packages("irlba",type="source", dependencies=T)

Thank you! However ,I met the gfortran link error when compiling in MACOS sonoma

library not found for lgfortran

And I install gfortrain manually from github and set the linker flag to correspond path such as below in ~/.R/Makevar as doc said. also you can make a soft link 

ln -s /usr/local/gfortran /opt/gfortran
FLIBS = -L/opt/gfortran/lib/gcc/aarch64-apple-darwin23/13.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmat

Then compile again to to solve it! 

remove.packages("Matrix")
remove.packages("irlba")
install.packages("Matrix",type="source", dependencies=T)
install.packages("irlba",type="source", dependencies=T)
lijxug commented 7 months ago

Downgrading Matrix to 1.5-1 works for me

adho13396 commented 7 months ago

I have tried all the above in the last 6 days and all measures have failed (removing and reinstalling Matrix, irlba, R, R-Studio, and even Monocle 3. I need a solution. Downgrading of package "Matrix" also did not work for me.

DayuGuo commented 7 months ago

I have tried all the above in the last 6 days and all measures have failed (removing and reinstalling Matrix, irlba, R, R-Studio, and even Monocle 3. I need a solution. Downgrading of package "Matrix" also did not work for me.

I have the same issue.

Additionally, when I downgrade to 'Matrix' 1.5-1, SeuratObject no longer functions properly, requiring Matrix >= 1.6.3. When I downgrade SeuratObject to an older version that supports 'Matrix' 1.5-1, Seurat fails to function properly. I suspect this might be due to the update in Seurat 5. It's like the butterfly effect.

adho13396 commented 7 months ago

Can you provide me with an advice how to solve this problem?

I have been using Monocle 3 successfully until last week. When I tried to preprocess the uploaded data the above error message kept coming up. It has not happened before I followed the instruction to update some of the packages necessary for running Monocle3. How can I get the Monocle 3 functional again?

Von: Zhaoyu Guo @.> Antworten an: cole-trapnell-lab/monocle3 @.> Datum: Sonntag, 31. März 2024 um 06:10 An: cole-trapnell-lab/monocle3 @.> Cc: @." @.>, Comment @.> Betreff: Re: [cole-trapnell-lab/monocle3] preprocess_cds Error in function 'as_cholmod_sparse' not provided by package 'Matrix' (Issue #690)

I have tried all the above in the last 6 days and all measures have failed (removing and reinstalling Matrix, irlba, R, R-Studio, and even Monocle 3. I need a solution. Downgrading of package "Matrix" also did not work for me.

I have the same issue.

Additionally, when I downgrade to 'Matrix' 1.5-1, SeuratObject no longer functions properly, requiring Matrix >= 1.6.3. When I downgrade SeuratObject to an older version that supports 'Matrix' 1.5-1, Seurat fails to function properly. I suspect this might be due to the update in Seurat 5. It's like the butterfly effect.

— Reply to this email directly, view it on GitHubhttps://github.com/cole-trapnell-lab/monocle3/issues/690#issuecomment-2028547189, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ARO4SQGOC457O67AJPS4Z73Y26ECHAVCNFSM6AAAAAA7H7JELWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMRYGU2DOMJYHE. You are receiving this because you commented.Message ID: @.***>

apal6 commented 7 months ago

Hi,

I tried to install the packages and still the error occurs. Any follow-ups?

Thank you, Aastha

Anan2024Huang commented 7 months ago

I have the same issue. I used Macbook with M1 chip currently. When I degrade my Matrix package, it always showed the gfortran problem. how to solve it?

adho13396 commented 7 months ago

I have not been able to solve the challenge yet.

Von: Anan2024Huang @.> Antworten an: cole-trapnell-lab/monocle3 @.> Datum: Sonntag, 7. April 2024 um 03:15 An: cole-trapnell-lab/monocle3 @.> Cc: @." @.>, Comment @.> Betreff: Re: [cole-trapnell-lab/monocle3] preprocess_cds Error in function 'as_cholmod_sparse' not provided by package 'Matrix' (Issue #690)

I have the same issue. I used Macbook with M1 chip currently. When I degrade my Matrix package, it always showed the gfortran problem. how to solve it?

— Reply to this email directly, view it on GitHubhttps://github.com/cole-trapnell-lab/monocle3/issues/690#issuecomment-2041261588, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ARO4SQHIBACDA73OGRSQZZDY4CM3XAVCNFSM6AAAAAA7H7JELWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANBRGI3DCNJYHA. You are receiving this because you commented.Message ID: @.***>

DayuGuo commented 7 months ago

I have not been able to solve the challenge yet. Von: Anan2024Huang @.> Antworten an: cole-trapnell-lab/monocle3 @.> Datum: Sonntag, 7. April 2024 um 03:15 An: cole-trapnell-lab/monocle3 @.> Cc: @." @.>, Comment @.> Betreff: Re: [cole-trapnell-lab/monocle3] preprocess_cds Error in function 'as_cholmod_sparse' not provided by package 'Matrix' (Issue #690) I have the same issue. I used Macbook with M1 chip currently. When I degrade my Matrix package, it always showed the gfortran problem. how to solve it? — Reply to this email directly, view it on GitHub<#690 (comment)>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ARO4SQHIBACDA73OGRSQZZDY4CM3XAVCNFSM6AAAAAA7H7JELWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANBRGI3DCNJYHA. You are receiving this because you commented.Message ID: @.***>

Try add the following information in .R/Makevars. (.R is a hidden folder, if there is no Makevars inside, you need to create one.)

FC = /opt/homebrew/bin/gfortran 
F77 = /opt/homebrew/bin/gfortran  
FLIBS = -L/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/13 -lgfortran -lquadmath -lm
Anan2024Huang commented 7 months ago

Does anyone post the tutorial for the Mac. How to set up the gfortran when installing Matrix.

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发件人: Zhaoyu Guo @.> 发送时间: Sunday, April 7, 2024 1:55:51 PM 收件人: cole-trapnell-lab/monocle3 @.> 抄送: Anan2024Huang @.>; Comment @.> 主题: Re: [cole-trapnell-lab/monocle3] preprocess_cds Error in function 'as_cholmod_sparse' not provided by package 'Matrix' (Issue #690)

I have not been able to solve the challenge yet. Von: Anan2024Huang @.> Antworten an: cole-trapnell-lab/monocle3 @.> Datum: Sonntag, 7. April 2024 um 03:15 An: cole-trapnell-lab/monocle3 @.> Cc: @." @.>, Comment @.> Betreff: Re: [cole-trapnell-lab/monocle3] preprocess_cds Error in function 'as_cholmod_sparse' not provided by package 'Matrix' (Issue #690https://github.com/cole-trapnell-lab/monocle3/issues/690) I have the same issue. I used Macbook with M1 chip currently. When I degrade my Matrix package, it always showed the gfortran problem. how to solve it? ― Reply to this email directly, view it on GitHub<#690 (comment)https://github.com/cole-trapnell-lab/monocle3/issues/690#issuecomment-2041261588>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ARO4SQHIBACDA73OGRSQZZDY4CM3XAVCNFSM6AAAAAA7H7JELWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANBRGI3DCNJYHA. You are receiving this because you commented.Message ID: @.***>

Try add the following information in .R/Makevars. (.R is a hidden folder, if there is no Makevars inside, you need to create one.)

FC = /opt/homebrew/bin/gfortran F77 = /opt/homebrew/bin/gfortran FLIBS = -L/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/13 -lgfortran -lquadmath -lm

― Reply to this email directly, view it on GitHubhttps://github.com/cole-trapnell-lab/monocle3/issues/690#issuecomment-2041325441, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BHGD3KJZVYKF7742EFVWTUTY4DNWPAVCNFSM6AAAAAA7H7JELWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANBRGMZDKNBUGE. You are receiving this because you commented.Message ID: @.***>

martuskaR commented 7 months ago

Same problem here, using Mac with M1 chip. Looking forward to a solution!

gucascau commented 6 months ago

I also use Mac with M1 chip. I tried everything mentioned above and faced with similar problem.

For those of you who using the Seurat V5, I would suggest to degrade the Matrix version to 1.6.3, which works for me now.

remove.packages("Matrix")
remotes::install_version("Matrix", version = "1.6-3"))
apal6 commented 6 months ago

Hi,

I tried all the suggested methods above and still no luck. Any further update?

Thank you!

reinertanalytics commented 6 months ago

I am also experiencing the same issue. I cannot use the older version of Matrix because as others have said, I then run into issues with Seurat.

gucascau commented 6 months ago

I also think you guys probably need to consider the Rstudio version. I faced with installing the old version of Matrix in the Rstudio, which I ended up installing it in R console. Then it works very well.

adho13396 commented 6 months ago

Converting back to the R version 4.3.2. (2023-10-31) – “Eye Holes” seems to have worked for me. The “Matrix” file has remained 1.6-5

Von: Xin Wang @.> Antworten an: cole-trapnell-lab/monocle3 @.> Datum: Mittwoch, 1. Mai 2024 um 22:46 An: cole-trapnell-lab/monocle3 @.> Cc: @." @.>, Comment @.> Betreff: Re: [cole-trapnell-lab/monocle3] preprocess_cds Error in function 'as_cholmod_sparse' not provided by package 'Matrix' (Issue #690)

I also think you guys probably need to consider the Rstudio version. I faced with installing the old version of Matrix in the Rstudio, which I ended up installing it in R console. Then it works very well.

— Reply to this email directly, view it on GitHubhttps://github.com/cole-trapnell-lab/monocle3/issues/690#issuecomment-2089114270, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ARO4SQB6XAA4VUPA3DBRVQTZAFICHAVCNFSM6AAAAAA7H7JELWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBZGEYTIMRXGA. You are receiving this because you commented.Message ID: @.***>

Franklin593 commented 6 months ago

I encountered the same situation, and upgrading/downgrading versions of matrix, irlba, or monocle3 didn't help. However, I eventually found a solution. As an rstudio-server user, even though installation was successful under a regular user, it seems that both old and new versions of the package were present, with the old version of Matrix being called first. By deleting all versions of the Matrix package under root and then reinstalling the latest version, I was able to resolve it. I hope my experience can help others.

Grace1206 commented 6 months ago

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

This solved this problem! You can have a try

51432 commented 4 months ago

I follow the instruction to install "irlba"(latest version: 2.3.5.1) and "Matrix"(version 1.6-1.1). When I ran the following codes, the same error happened. big_cds <- monocle3::preprocess_cds(big_cds, num_dim = 50,method = "PCA") Error in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth = TRUE, : function 'as_cholmod_sparse' not provided by package 'Matrix' The following is my session info > sessionInfo() R version 4.3.2 (2023-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.6 LTS Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3; LAPACK version 3.9.0 locale: [1] LC_CTYPE=en_US.UTF-8 [2] LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 [6] LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 [8] LC_NAME=C [9] LC_ADDRESS=C [10] LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 [12] LC_IDENTIFICATION=C time zone: America/New_York tzcode source: system (glibc) attached base packages: [1] stats4 stats graphics grDevices utils [6] datasets methods base other attached packages: [1] metap_1.9 [2] multtest_2.58.0 [3] dittoSeq_1.14.0 [4] monocle3_1.3.4 [5] SeuratWrappers_0.3.3 [6] pcaMethods_1.94.0 [7] DESeq2_1.42.0 [8] clustree_0.5.1 [9] ggraph_2.1.0 [10] harmony_1.2.0 [11] Rcpp_1.0.12 [12] DoubletFinder_2.0.4 [13] forcats_1.0.0 [14] stringr_1.5.1 [15] dplyr_1.1.4 [16] purrr_1.0.2 [17] readr_2.1.5 [18] tidyr_1.3.1 [19] tibble_3.2.1 [20] ggplot2_3.4.4 [21] tidyverse_2.0.0 [22] scCustomize_2.0.1 [23] celldex_1.12.0 [24] RColorBrewer_1.1-3 [25] glmGamPoi_1.14.0 [26] hdf5r_1.3.9 [27] batchelor_1.18.1 [28] SingleCellExperiment_1.24.0 [29] limma_3.58.1 [30] SingleR_2.4.1 [31] SummarizedExperiment_1.32.0 [32] Biobase_2.62.0 [33] GenomicRanges_1.54.1 [34] GenomeInfoDb_1.38.5 [35] IRanges_2.36.0 [36] S4Vectors_0.40.2 [37] MatrixGenerics_1.14.0 [38] matrixStats_1.2.0 [39] terra_1.7-65 [40] Seurat_5.0.1 [41] SeuratObject_5.0.1 [42] sp_2.1-2 [43] ggrastr_1.0.2 [44] devtools_2.4.5 [45] usethis_2.2.2 [46] pdfCluster_1.0-4 [47] BiocGenerics_0.48.1 [48] data.table_1.14.10 [49] lubridate_1.9.3 [50] BiocManager_1.30.22 loaded via a namespace (and not attached): [1] R.methodsS3_1.8.2 [2] urlchecker_1.0.1 [3] goftest_1.2-3 [4] Biostrings_2.70.2 [5] TH.data_1.1-2 [6] vctrs_0.6.5 [7] spatstat.random_3.2-2 [8] digest_0.6.34 [9] png_0.1-8 [10] shape_1.4.6 [11] ggrepel_0.9.5 [12] deldir_2.0-2 [13] parallelly_1.36.0 [14] MASS_7.3-60.0.1 [15] reshape2_1.4.4 [16] httpuv_1.6.14 [17] withr_3.0.0 [18] ellipsis_0.3.2 [19] survival_3.5-7 [20] memoise_2.0.1 [21] ggbeeswarm_0.7.2 [22] janitor_2.2.0 [23] profvis_0.3.8 [24] zoo_1.8-12 [25] GlobalOptions_0.1.2 [26] pbapply_1.7-2 [27] R.oo_1.26.0 [28] rematch2_2.1.2 [29] KEGGREST_1.42.0 [30] promises_1.2.1 [31] httr_1.4.7 [32] globals_0.16.2 [33] fitdistrplus_1.1-11 [34] ps_1.7.6 [35] rstudioapi_0.15.0 [36] miniUI_0.1.1.1 [37] generics_0.1.3 [38] processx_3.8.3 [39] curl_5.2.0 [40] zlibbioc_1.48.0 [41] ScaledMatrix_1.10.0 [42] polyclip_1.10-6 [43] TFisher_0.2.0 [44] GenomeInfoDbData_1.2.11 [45] ExperimentHub_2.10.0 [46] SparseArray_1.2.3 [47] interactiveDisplayBase_1.40.0 [48] desc_1.4.3 [49] xtable_1.8-4 [50] S4Arrays_1.2.0 [51] BiocFileCache_2.10.1 [52] hms_1.1.3 [53] irlba_2.3.5.1 [54] colorspace_2.1-0 [55] filelock_1.0.3 [56] ROCR_1.0-11 [57] reticulate_1.34.0 [58] spatstat.data_3.0-4 [59] magrittr_2.0.3 [60] lmtest_0.9-40 [61] snakecase_0.11.1 [62] later_1.3.2 [63] viridis_0.6.4 [64] lattice_0.22-5 [65] spatstat.geom_3.2-8 [66] future.apply_1.11.1 [67] scattermore_1.2 [68] scuttle_1.12.0 [69] cowplot_1.1.3 [70] RcppAnnoy_0.0.22 [71] pillar_1.9.0 [72] nlme_3.1-164 [73] compiler_4.3.2 [74] beachmat_2.18.0 [75] RSpectra_0.16-1 [76] stringi_1.8.3 [77] tensor_1.5 [78] minqa_1.2.6 [79] plyr_1.8.9 [80] crayon_1.5.2 [81] abind_1.4-5 [82] sn_2.1.1 [83] locfit_1.5-9.8 [84] mathjaxr_1.6-0 [85] graphlayouts_1.1.0 [86] bit_4.0.5 [87] sandwich_3.1-0 [88] multcomp_1.4-25 [89] codetools_0.2-19 [90] BiocSingular_1.18.0 [91] paletteer_1.6.0 [92] plotly_4.10.4 [93] mime_0.12 [94] splines_4.3.2 [95] circlize_0.4.15 [96] fastDummies_1.7.3 [97] dbplyr_2.4.0 [98] sparseMatrixStats_1.14.0 [99] magic_1.6-1 [100] blob_1.2.4 [101] utf8_1.2.4 [102] BiocVersion_3.18.1 [103] lme4_1.1-35.1 [104] fs_1.6.3 [105] listenv_0.9.0 [106] DelayedMatrixStats_1.24.0 [107] Rdpack_2.6 [108] pkgbuild_1.4.3 [109] Matrix_1.6-1.1 [110] callr_3.7.3 [111] statmod_1.5.0 [112] tzdb_0.4.0 [113] tweenr_2.0.2 [114] pkgconfig_2.0.3 [115] pheatmap_1.0.12 [116] tools_4.3.2 [117] cachem_1.0.8 [118] rbibutils_2.2.16 [119] RSQLite_2.3.5 [120] viridisLite_0.4.2 [121] DBI_1.2.1 [122] numDeriv_2016.8-1.1 [123] fastmap_1.1.1 [124] scales_1.3.0 [125] grid_4.3.2 [126] ica_1.0-3 [127] AnnotationHub_3.10.0 [128] patchwork_1.2.0 [129] ggprism_1.0.4 [130] dotCall64_1.1-1 [131] RANN_2.6.1 [132] farver_2.1.1 [133] tidygraph_1.3.0 [134] yaml_2.3.8 [135] cli_3.6.2 [136] leiden_0.4.3.1 [137] lifecycle_1.0.4 [138] uwot_0.1.16 [139] mvtnorm_1.2-4 [140] sessioninfo_1.2.2 [141] BiocParallel_1.36.0 [142] timechange_0.3.0 [143] gtable_0.3.4 [144] ggridges_0.5.6 [145] progressr_0.14.0 [146] parallel_4.3.2 [147] jsonlite_1.8.8 [148] RcppHNSW_0.5.0 [149] bitops_1.0-7 [150] assertthat_0.2.1 [151] bit64_4.0.5 [152] qqconf_1.3.2 [153] Rtsne_0.17 [154] spatstat.utils_3.0-4 [155] BiocNeighbors_1.20.2 [156] mutoss_0.1-13 [157] R.utils_2.12.3 [158] lazyeval_0.2.2 [159] shiny_1.8.0 [160] htmltools_0.5.7 [161] sctransform_0.4.1 [162] rappdirs_0.3.3 [163] glue_1.7.0 [164] spam_2.10-0 [165] ResidualMatrix_1.12.0 [166] XVector_0.42.0 [167] RCurl_1.98-1.14 [168] mnormt_2.1.1 [169] gridExtra_2.3 [170] boot_1.3-28.1 [171] igraph_1.6.0 [172] R6_2.5.1 [173] cluster_2.1.6 [174] pkgload_1.3.4 [175] nloptr_2.0.3 [176] plotrix_3.8-4 [177] DelayedArray_0.28.0 [178] tidyselect_1.2.0 [179] vipor_0.4.7 [180] ggforce_0.4.1 [181] AnnotationDbi_1.64.1 [182] future_1.33.1 [183] rsvd_1.0.5 [184] munsell_0.5.0 [185] KernSmooth_2.23-22 [186] geometry_0.4.7 [187] htmlwidgets_1.6.4 [188] rlang_1.1.3 [189] spatstat.sparse_3.0-3 [190] spatstat.explore_3.2-5 [191] remotes_2.4.2.1 [192] fansi_1.0.6 [193] beeswarm_0.4.0

I found the workaround. Restart R studio and following the codes. Restart R studio is the key point. remove.packages("Matrix") remove.packages("irlba") install.packages("Matrix",type="source", dependencies=T) install.packages("irlba",type="source", dependencies=T)

That is very useful! thank U!

JosieCen commented 3 months ago

I follow the instruction to install "irlba"(latest version: 2.3.5.1) and "Matrix"(version 1.6-1.1). When I ran the following codes, the same error happened. big_cds <- monocle3::preprocess_cds(big_cds, num_dim = 50,method = "PCA") Error in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth = TRUE, : function 'as_cholmod_sparse' not provided by package 'Matrix' The following is my session info > sessionInfo() R version 4.3.2 (2023-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.6 LTS Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3; LAPACK version 3.9.0 locale: [1] LC_CTYPE=en_US.UTF-8 [2] LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 [6] LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 [8] LC_NAME=C [9] LC_ADDRESS=C [10] LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 [12] LC_IDENTIFICATION=C time zone: America/New_York tzcode source: system (glibc) attached base packages: [1] stats4 stats graphics grDevices utils [6] datasets methods base other attached packages: [1] metap_1.9 [2] multtest_2.58.0 [3] dittoSeq_1.14.0 [4] monocle3_1.3.4 [5] SeuratWrappers_0.3.3 [6] pcaMethods_1.94.0 [7] DESeq2_1.42.0 [8] clustree_0.5.1 [9] ggraph_2.1.0 [10] harmony_1.2.0 [11] Rcpp_1.0.12 [12] DoubletFinder_2.0.4 [13] forcats_1.0.0 [14] stringr_1.5.1 [15] dplyr_1.1.4 [16] purrr_1.0.2 [17] readr_2.1.5 [18] tidyr_1.3.1 [19] tibble_3.2.1 [20] ggplot2_3.4.4 [21] tidyverse_2.0.0 [22] scCustomize_2.0.1 [23] celldex_1.12.0 [24] RColorBrewer_1.1-3 [25] glmGamPoi_1.14.0 [26] hdf5r_1.3.9 [27] batchelor_1.18.1 [28] SingleCellExperiment_1.24.0 [29] limma_3.58.1 [30] SingleR_2.4.1 [31] SummarizedExperiment_1.32.0 [32] Biobase_2.62.0 [33] GenomicRanges_1.54.1 [34] GenomeInfoDb_1.38.5 [35] IRanges_2.36.0 [36] S4Vectors_0.40.2 [37] MatrixGenerics_1.14.0 [38] matrixStats_1.2.0 [39] terra_1.7-65 [40] Seurat_5.0.1 [41] SeuratObject_5.0.1 [42] sp_2.1-2 [43] ggrastr_1.0.2 [44] devtools_2.4.5 [45] usethis_2.2.2 [46] pdfCluster_1.0-4 [47] BiocGenerics_0.48.1 [48] data.table_1.14.10 [49] lubridate_1.9.3 [50] BiocManager_1.30.22 loaded via a namespace (and not attached): [1] R.methodsS3_1.8.2 [2] urlchecker_1.0.1 [3] goftest_1.2-3 [4] Biostrings_2.70.2 [5] TH.data_1.1-2 [6] vctrs_0.6.5 [7] spatstat.random_3.2-2 [8] digest_0.6.34 [9] png_0.1-8 [10] shape_1.4.6 [11] ggrepel_0.9.5 [12] deldir_2.0-2 [13] parallelly_1.36.0 [14] MASS_7.3-60.0.1 [15] reshape2_1.4.4 [16] httpuv_1.6.14 [17] withr_3.0.0 [18] ellipsis_0.3.2 [19] survival_3.5-7 [20] memoise_2.0.1 [21] ggbeeswarm_0.7.2 [22] janitor_2.2.0 [23] profvis_0.3.8 [24] zoo_1.8-12 [25] GlobalOptions_0.1.2 [26] pbapply_1.7-2 [27] R.oo_1.26.0 [28] rematch2_2.1.2 [29] KEGGREST_1.42.0 [30] promises_1.2.1 [31] httr_1.4.7 [32] globals_0.16.2 [33] fitdistrplus_1.1-11 [34] ps_1.7.6 [35] rstudioapi_0.15.0 [36] miniUI_0.1.1.1 [37] generics_0.1.3 [38] processx_3.8.3 [39] curl_5.2.0 [40] zlibbioc_1.48.0 [41] ScaledMatrix_1.10.0 [42] polyclip_1.10-6 [43] TFisher_0.2.0 [44] GenomeInfoDbData_1.2.11 [45] ExperimentHub_2.10.0 [46] SparseArray_1.2.3 [47] interactiveDisplayBase_1.40.0 [48] desc_1.4.3 [49] xtable_1.8-4 [50] S4Arrays_1.2.0 [51] BiocFileCache_2.10.1 [52] hms_1.1.3 [53] irlba_2.3.5.1 [54] colorspace_2.1-0 [55] filelock_1.0.3 [56] ROCR_1.0-11 [57] reticulate_1.34.0 [58] spatstat.data_3.0-4 [59] magrittr_2.0.3 [60] lmtest_0.9-40 [61] snakecase_0.11.1 [62] later_1.3.2 [63] viridis_0.6.4 [64] lattice_0.22-5 [65] spatstat.geom_3.2-8 [66] future.apply_1.11.1 [67] scattermore_1.2 [68] scuttle_1.12.0 [69] cowplot_1.1.3 [70] RcppAnnoy_0.0.22 [71] pillar_1.9.0 [72] nlme_3.1-164 [73] compiler_4.3.2 [74] beachmat_2.18.0 [75] RSpectra_0.16-1 [76] stringi_1.8.3 [77] tensor_1.5 [78] minqa_1.2.6 [79] plyr_1.8.9 [80] crayon_1.5.2 [81] abind_1.4-5 [82] sn_2.1.1 [83] locfit_1.5-9.8 [84] mathjaxr_1.6-0 [85] graphlayouts_1.1.0 [86] bit_4.0.5 [87] sandwich_3.1-0 [88] multcomp_1.4-25 [89] codetools_0.2-19 [90] BiocSingular_1.18.0 [91] paletteer_1.6.0 [92] plotly_4.10.4 [93] mime_0.12 [94] splines_4.3.2 [95] circlize_0.4.15 [96] fastDummies_1.7.3 [97] dbplyr_2.4.0 [98] sparseMatrixStats_1.14.0 [99] magic_1.6-1 [100] blob_1.2.4 [101] utf8_1.2.4 [102] BiocVersion_3.18.1 [103] lme4_1.1-35.1 [104] fs_1.6.3 [105] listenv_0.9.0 [106] DelayedMatrixStats_1.24.0 [107] Rdpack_2.6 [108] pkgbuild_1.4.3 [109] Matrix_1.6-1.1 [110] callr_3.7.3 [111] statmod_1.5.0 [112] tzdb_0.4.0 [113] tweenr_2.0.2 [114] pkgconfig_2.0.3 [115] pheatmap_1.0.12 [116] tools_4.3.2 [117] cachem_1.0.8 [118] rbibutils_2.2.16 [119] RSQLite_2.3.5 [120] viridisLite_0.4.2 [121] DBI_1.2.1 [122] numDeriv_2016.8-1.1 [123] fastmap_1.1.1 [124] scales_1.3.0 [125] grid_4.3.2 [126] ica_1.0-3 [127] AnnotationHub_3.10.0 [128] patchwork_1.2.0 [129] ggprism_1.0.4 [130] dotCall64_1.1-1 [131] RANN_2.6.1 [132] farver_2.1.1 [133] tidygraph_1.3.0 [134] yaml_2.3.8 [135] cli_3.6.2 [136] leiden_0.4.3.1 [137] lifecycle_1.0.4 [138] uwot_0.1.16 [139] mvtnorm_1.2-4 [140] sessioninfo_1.2.2 [141] BiocParallel_1.36.0 [142] timechange_0.3.0 [143] gtable_0.3.4 [144] ggridges_0.5.6 [145] progressr_0.14.0 [146] parallel_4.3.2 [147] jsonlite_1.8.8 [148] RcppHNSW_0.5.0 [149] bitops_1.0-7 [150] assertthat_0.2.1 [151] bit64_4.0.5 [152] qqconf_1.3.2 [153] Rtsne_0.17 [154] spatstat.utils_3.0-4 [155] BiocNeighbors_1.20.2 [156] mutoss_0.1-13 [157] R.utils_2.12.3 [158] lazyeval_0.2.2 [159] shiny_1.8.0 [160] htmltools_0.5.7 [161] sctransform_0.4.1 [162] rappdirs_0.3.3 [163] glue_1.7.0 [164] spam_2.10-0 [165] ResidualMatrix_1.12.0 [166] XVector_0.42.0 [167] RCurl_1.98-1.14 [168] mnormt_2.1.1 [169] gridExtra_2.3 [170] boot_1.3-28.1 [171] igraph_1.6.0 [172] R6_2.5.1 [173] cluster_2.1.6 [174] pkgload_1.3.4 [175] nloptr_2.0.3 [176] plotrix_3.8-4 [177] DelayedArray_0.28.0 [178] tidyselect_1.2.0 [179] vipor_0.4.7 [180] ggforce_0.4.1 [181] AnnotationDbi_1.64.1 [182] future_1.33.1 [183] rsvd_1.0.5 [184] munsell_0.5.0 [185] KernSmooth_2.23-22 [186] geometry_0.4.7 [187] htmlwidgets_1.6.4 [188] rlang_1.1.3 [189] spatstat.sparse_3.0-3 [190] spatstat.explore_3.2-5 [191] remotes_2.4.2.1 [192] fansi_1.0.6 [193] beeswarm_0.4.0

I found the workaround. Restart R studio and following the codes. Restart R studio is the key point. remove.packages("Matrix") remove.packages("irlba") install.packages("Matrix",type="source", dependencies=T) install.packages("irlba",type="source", dependencies=T)

Can you tell me the versions of your Matrix and irlba packages? I'm using version 4.2.2 of R, version 1.6.4 of Matrix and version 2.3.5.1 of irlba , but I'm still getting this error.

pnolabs commented 3 months ago

...

I found the workaround. Restart R studio and following the codes. Restart R studio is the key point. remove.packages("Matrix") remove.packages("irlba") install.packages("Matrix",type="source", dependencies=T) install.packages("irlba",type="source", dependencies=T)

Can you tell me the versions of your Matrix and irlba packages? I'm using version 4.2.2 of R, version 1.6.4 of Matrix and version 2.3.5.1 of irlba , but I'm still getting this error.

Hallo everyone! I am also facing the same issue. After updating all the R packages, deleting 'Matrix' and 'irlba', restarting R, re-installing 'Matrix' and 'irlba' I still get the following error:

cds_subset class: cell_data_set dim: 29567 17976 metadata(1): citations assays(3): counts logcounts scaledata rownames(29567): OR4F5 AL627309.1 ... AC004556.1 AC240274.1 rowData names(1): gene_short_name colnames(17976): NF_14_AAACGAAAGCAACAGC-1 NF_14_AAACGAAAGCGACTAG-1 ... NF_32_TTGATGGAGACCAAAT-1 NF_32_TTGTTTGGTTCTAAGC-1 colData names(36): orig.ident nCount_RNA ... monocle3_cell_type garnett_cluster reducedDimNames(13): PCA UMAP ... TSNE.CCA TSNE.HARMONY mainExpName: RNA altExpNames(0):

garnett_markers A tibble: 34 × 10 Groups: gene_short_name [34] gene_id gene_short_name cell_group marker_score mean_expression fraction_expressing specificity

1 SLC19A2 SLC19A2 7 0.629 0.00164 0.894 0.704 2 BRINP3 BRINP3 6 0.386 0.000499 0.557 0.692 3 PTPRC PTPRC 2 0.548 0.000862 0.790 0.693 4 PTPRG PTPRG 7 0.534 0.0106 0.988 0.540 5 AC0263… AC026316.5 4 0.440 0.000793 0.684 0.643 6 LINC00… LINC00578 6 0.431 0.000912 0.608 0.708 7 UNC5C UNC5C 1 0.370 0.000632 0.673 0.550 8 FSTL5 FSTL5 5 0.483 0.000771 0.633 0.763 9 SORBS2 SORBS2 8 0.531 0.00171 0.891 0.596 10 ELL2 ELL2 7 0.530 0.00248 0.841 0.629 i 24 more rows i 3 more variables: pseudo_R2 , marker_test_p_value , marker_test_q_value i Use `print(n = ...)` to see more rows classifier <- train_cell_classifier(cds_subset, marker_file = here::here(datadir, paste(accession, "Garnett_marker_file.txt", sep = "_")), db=org.Hs.eg.db::org.Hs.eg.db, cds_gene_id_type = "SYMBOL", num_unknown = 50, marker_file_gene_id_type = "SYMBOL", cores=8) There are 8 cell type definitions Warnung: 2 genes could not be converted from SYMBOL to ENSEMBL These genes are listed below: Warnung: The following genes from the cell type definition file are notpresent in the cell dataset. Please check these genes forerrors. Cell type determination will continue, ignoring thesegenes. AC026316.5 AC002066.1Error in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth = TRUE, : function 'as_cholmod_sparse' not provided by package 'Matrix' sessionInfo() R version 4.4.1 (2024-06-14) Platform: x86_64-pc-linux-gnu Running under: Ubuntu 22.04.4 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0

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

time zone: Etc/UTC tzcode source: system (glibc)

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

other attached packages: [1] monocle3_1.3.7 SingleCellExperiment_1.26.0 SummarizedExperiment_1.34.0 [4] GenomicRanges_1.56.0 GenomeInfoDb_1.40.0 IRanges_2.38.0
[7] S4Vectors_0.42.0 MatrixGenerics_1.16.0 matrixStats_1.3.0
[10] Biobase_2.64.0 BiocGenerics_0.50.0

loaded via a namespace (and not attached): [1] RColorBrewer_1.1-3 rstudioapi_0.16.0 jsonlite_1.8.8
[4] magrittr_2.0.3 spatstat.utils_3.0-5 nloptr_2.1.1
[7] zlibbioc_1.50.0 vctrs_0.6.5 ROCR_1.0-11
[10] minqa_1.2.7 spatstat.explore_3.3-1 htmltools_0.5.8.1
[13] S4Arrays_1.4.0 SparseArray_1.4.3 sctransform_0.4.1
[16] parallelly_1.38.0 KernSmooth_2.23-24 htmlwidgets_1.6.4
[19] ica_1.0-3 plyr_1.8.9 plotly_4.10.4.9000
[22] zoo_1.8-12 igraph_2.0.3 mime_0.12
[25] lifecycle_1.0.4 pkgconfig_2.0.3 Matrix_1.6-4
[28] R6_2.5.1 fastmap_1.2.0 GenomeInfoDbData_1.2.12 [31] fitdistrplus_1.2-1 future_1.34.0 shiny_1.9.1
[34] digest_0.6.36 colorspace_2.1-1 patchwork_1.2.0
[37] Seurat_5.1.0 tensor_1.5 RSpectra_0.16-2
[40] irlba_2.3.5.1 progressr_0.14.0 fansi_1.0.6
[43] spatstat.sparse_3.1-0 httr_1.4.7 polyclip_1.10-7
[46] abind_1.4-5 compiler_4.4.1 fastDummies_1.7.3
[49] MASS_7.3-61 DelayedArray_0.30.1 tools_4.4.1
[52] lmtest_0.9-40 httpuv_1.6.15 future.apply_1.11.2
[55] goftest_1.2-3 glue_1.7.0 nlme_3.1-165
[58] promises_1.3.0 grid_4.4.1 Rtsne_0.17
[61] cluster_2.1.6 reshape2_1.4.4 generics_0.1.3
[64] gtable_0.3.5 spatstat.data_3.1-2 tidyr_1.3.1
[67] data.table_1.15.4 sp_2.1-4 utf8_1.2.4
[70] XVector_0.44.0 spatstat.geom_3.3-2 RcppAnnoy_0.0.22
[73] ggrepel_0.9.5 RANN_2.6.1 pillar_1.9.0
[76] stringr_1.5.1 spam_2.10-0 RcppHNSW_0.6.0
[79] later_1.3.2 splines_4.4.1 dplyr_1.1.4
[82] lattice_0.22-6 survival_3.7-0 deldir_2.0-4
[85] tidyselect_1.2.1 miniUI_0.1.1.1 pbapply_1.7-2
[88] gridExtra_2.3 scattermore_1.2 stringi_1.8.4
[91] UCSC.utils_1.0.0 boot_1.3-30 lazyeval_0.2.2
[94] codetools_0.2-20 tibble_3.2.1 cli_3.6.3
[97] uwot_0.2.2 xtable_1.8-4 reticulate_1.38.0
[100] munsell_0.5.1 Rcpp_1.0.13 globals_0.16.3
[103] spatstat.random_3.3-1 png_0.1-8 spatstat.univar_3.0-0
[106] parallel_4.4.1 ggplot2_3.5.1 dotCall64_1.1-1
[109] lme4_1.1-35.5 listenv_0.9.1 viridisLite_0.4.2
[112] scales_1.3.0 ggridges_0.5.6 SeuratObject_5.0.2
[115] leiden_0.4.3.1 purrr_1.0.2 crayon_1.5.3
[118] rlang_1.1.4 cowplot_1.1.3

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

packageVersion(c("irlba")) [1] ‘2.3.5.1’ packageVersion(c("Matrix")) [1] ‘1.6.4’

Any ideas what i could check next? I appreciate your time and help :)

JosieCen commented 3 months ago

...

I found the workaround. Restart R studio and following the codes. Restart R studio is the key point. remove.packages("Matrix") remove.packages("irlba") install.packages("Matrix",type="source", dependencies=T) install.packages("irlba",type="source", dependencies=T)

Can you tell me the versions of your Matrix and irlba packages? I'm using version 4.2.2 of R, version 1.6.4 of Matrix and version 2.3.5.1 of irlba , but I'm still getting this error.

Hallo everyone! I am also facing the same issue. After updating all the R packages, deleting 'Matrix' and 'irlba', restarting R, re-installing 'Matrix' and 'irlba' I still get the following error:

cds_subset class: cell_data_set dim: 29567 17976 metadata(1): citations assays(3): counts logcounts scaledata rownames(29567): OR4F5 AL627309.1 ... AC004556.1 AC240274.1 rowData names(1): gene_short_name colnames(17976): NF_14_AAACGAAAGCAACAGC-1 NF_14_AAACGAAAGCGACTAG-1 ... NF_32_TTGATGGAGACCAAAT-1 NF_32_TTGTTTGGTTCTAAGC-1 colData names(36): orig.ident nCount_RNA ... monocle3_cell_type garnett_cluster reducedDimNames(13): PCA UMAP ... TSNE.CCA TSNE.HARMONY mainExpName: RNA altExpNames(0):

garnett_markers A tibble: 34 × 10 Groups: gene_short_name [34] gene_id gene_short_name cell_group marker_score mean_expression fraction_expressing specificity

1 SLC19A2 SLC19A2 7 0.629 0.00164 0.894 0.704 2 BRINP3 BRINP3 6 0.386 0.000499 0.557 0.692 3 PTPRC PTPRC 2 0.548 0.000862 0.790 0.693 4 PTPRG PTPRG 7 0.534 0.0106 0.988 0.540 5 AC0263… AC026316.5 4 0.440 0.000793 0.684 0.643 6 LINC00… LINC00578 6 0.431 0.000912 0.608 0.708 7 UNC5C UNC5C 1 0.370 0.000632 0.673 0.550 8 FSTL5 FSTL5 5 0.483 0.000771 0.633 0.763 9 SORBS2 SORBS2 8 0.531 0.00171 0.891 0.596 10 ELL2 ELL2 7 0.530 0.00248 0.841 0.629 i 24 more rows i 3 more variables: pseudo_R2 , marker_test_p_value , marker_test_q_value i Use print(n = ...) to see more rows

classifier <- train_cell_classifier(cds_subset, marker_file = here::here(datadir, paste(accession, "Garnett_markerfile.txt", sep = "")), db=org.Hs.eg.db::org.Hs.eg.db, cds_gene_id_type = "SYMBOL", num_unknown = 50, marker_file_gene_id_type = "SYMBOL", cores=8) There are 8 cell type definitions Warnung: 2 genes could not be converted from SYMBOL to ENSEMBL These genes are listed below: Warnung: The following genes from the cell type definition file are notpresent in the cell dataset. Please check these genes forerrors. Cell type determination will continue, ignoring thesegenes. AC026316.5 AC002066.1Error in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth = TRUE, : function 'as_cholmod_sparse' not provided by package 'Matrix'

sessionInfo() R version 4.4.1 (2024-06-14) Platform: x86_64-pc-linux-gnu Running under: Ubuntu 22.04.4 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0

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

time zone: Etc/UTC tzcode source: system (glibc)

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

other attached packages: [1] monocle3_1.3.7 SingleCellExperiment_1.26.0 SummarizedExperiment_1.34.0 [4] GenomicRanges_1.56.0 GenomeInfoDb_1.40.0 IRanges_2.38.0 [7] S4Vectors_0.42.0 MatrixGenerics_1.16.0 matrixStats_1.3.0 [10] Biobase_2.64.0 BiocGenerics_0.50.0

loaded via a namespace (and not attached): [1] RColorBrewer_1.1-3 rstudioapi_0.16.0 jsonlite_1.8.8 [4] magrittr_2.0.3 spatstat.utils_3.0-5 nloptr_2.1.1 [7] zlibbioc_1.50.0 vctrs_0.6.5 ROCR_1.0-11 [10] minqa_1.2.7 spatstat.explore_3.3-1 htmltools_0.5.8.1 [13] S4Arrays_1.4.0 SparseArray_1.4.3 sctransform_0.4.1 [16] parallelly_1.38.0 KernSmooth_2.23-24 htmlwidgets_1.6.4 [19] ica_1.0-3 plyr_1.8.9 plotly_4.10.4.9000 [22] zoo_1.8-12 igraph_2.0.3 mime_0.12 [25] lifecycle_1.0.4 pkgconfig_2.0.3 Matrix_1.6-4 [28] R6_2.5.1 fastmap_1.2.0 GenomeInfoDbData_1.2.12 [31] fitdistrplus_1.2-1 future_1.34.0 shiny_1.9.1 [34] digest_0.6.36 colorspace_2.1-1 patchwork_1.2.0 [37] Seurat_5.1.0 tensor_1.5 RSpectra_0.16-2 [40] irlba_2.3.5.1 progressr_0.14.0 fansi_1.0.6 [43] spatstat.sparse_3.1-0 httr_1.4.7 polyclip_1.10-7 [46] abind_1.4-5 compiler_4.4.1 fastDummies_1.7.3 [49] MASS_7.3-61 DelayedArray_0.30.1 tools_4.4.1 [52] lmtest_0.9-40 httpuv_1.6.15 future.apply_1.11.2 [55] goftest_1.2-3 glue_1.7.0 nlme_3.1-165 [58] promises_1.3.0 grid_4.4.1 Rtsne_0.17 [61] cluster_2.1.6 reshape2_1.4.4 generics_0.1.3 [64] gtable_0.3.5 spatstat.data_3.1-2 tidyr_1.3.1 [67] data.table_1.15.4 sp_2.1-4 utf8_1.2.4 [70] XVector_0.44.0 spatstat.geom_3.3-2 RcppAnnoy_0.0.22 [73] ggrepel_0.9.5 RANN_2.6.1 pillar_1.9.0 [76] stringr_1.5.1 spam_2.10-0 RcppHNSW_0.6.0 [79] later_1.3.2 splines_4.4.1 dplyr_1.1.4 [82] lattice_0.22-6 survival_3.7-0 deldir_2.0-4 [85] tidyselect_1.2.1 miniUI_0.1.1.1 pbapply_1.7-2 [88] gridExtra_2.3 scattermore_1.2 stringi_1.8.4 [91] UCSC.utils_1.0.0 boot_1.3-30 lazyeval_0.2.2 [94] codetools_0.2-20 tibble_3.2.1 cli_3.6.3 [97] uwot_0.2.2 xtable_1.8-4 reticulate_1.38.0 [100] munsell_0.5.1 Rcpp_1.0.13 globals_0.16.3 [103] spatstat.random_3.3-1 png_0.1-8 spatstat.univar_3.0-0 [106] parallel_4.4.1 ggplot2_3.5.1 dotCall64_1.1-1 [109] lme4_1.1-35.5 listenv_0.9.1 viridisLite_0.4.2 [112] scales_1.3.0 ggridges_0.5.6 SeuratObject_5.0.2 [115] leiden_0.4.3.1 purrr_1.0.2 crayon_1.5.3 [118] rlang_1.1.4 cowplot_1.1.3

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

packageVersion(c("irlba")) [1] ‘2.3.5.1’ packageVersion(c("Matrix")) [1] ‘1.6.4’

Any ideas what i could check next? I appreciate your time and help :)

I have solved this problem, the key is that after installing the 1.6.4 version of the Matrix package, you need to uninstall the existing irlba package and then reinstall the latest version of the irlba package. The problem appears to be a problem with the function in the dependency irlba package installed with the 1.6.4 version of the Matrix package. You can try the above methods.

Rajnikantraut007 commented 1 week ago

I was able to solve this issue with these simple steps:

restart R Studio

remove.packages("Matrix") remove.packages("irlba")

restart R Studio

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

remove.packages("monocle3")

restart R Studio

devtools::install_github('cole-trapnell-lab/monocle3', force = T)

restart R Studio

library(monocle3) . . .