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

[weiyouzi321]

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

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]

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]

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: bwlewis/irlba#70. So I used the commands below in R:

remove.packages('irlba')

install.packages('irlba')

[ZayaAyush]

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]

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

[njumedw]

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]

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]

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]

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]

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]

Downgrading Matrix to 1.5-1 works for me

[adho13396]

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]

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]

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 GitHub<#690 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ARO4SQGOC457O67AJPS4Z73Y26ECHAVCNFSM6AAAAAA7H7JELWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMRYGU2DOMJYHE>. You are receiving this because you commented.Message ID: ***@***.***>

[apal6]

Hi,

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

Thank you,
Aastha

[Anan2024Huang]

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]

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 unsubscribe<https://github.com/notifications/unsubscribe-auth/ARO4SQHIBACDA73OGRSQZZDY4CM3XAVCNFSM6AAAAAA7H7JELWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANBRGI3DCNJYHA>. You are receiving this because you commented.Message ID: ***@***.***>

[DayuGuo]

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]

Does anyone post the tutorial for the Mac. How to set up the gfortran when installing Matrix. 发送自 Outlook for iOS<https://aka.ms/o0ukef>

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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 #690<#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)<#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 ― Reply to this email directly, view it on GitHub<#690 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BHGD3KJZVYKF7742EFVWTUTY4DNWPAVCNFSM6AAAAAA7H7JELWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANBRGMZDKNBUGE>. You are receiving this because you commented.Message ID: ***@***.***>

[martuskaR]

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

[gucascau]

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]

Hi,

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

Thank you!

[reinertanalytics]

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]

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]

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 GitHub<#690 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ARO4SQB6XAA4VUPA3DBRVQTZAFICHAVCNFSM6AAAAAA7H7JELWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBZGEYTIMRXGA>. You are receiving this because you commented.Message ID: ***@***.***>

[Franklin593]

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.