Bdiv ordinal plot Umap

[shwetha141]

Hello , I get this error whenever I run bdiv_ord_plot.

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

I thought it was my data but I get the same error for the example data set hmp. I tried this site-satijalab/seurat#8100

R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.4.1

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

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

time zone: America/Chicago
tzcode source: internal

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

other attached packages:
[1] ape_5.7-1 readxl_1.4.3
[3] data.table_1.15.4 RColorBrewer_1.1-3
[5] heatmaply_1.5.0 Hmisc_5.1-2
[7] DT_0.33 knitr_1.45
[9] tsne_0.1-3.1 GGally_2.2.1
[11] reshape2_1.4.4 robustHD_0.8.0
[13] robustbase_0.99-2 perry_0.3.1
[15] corrplot_0.92 gplots_3.1.3.1
[17] rstatix_0.7.2 ComplexHeatmap_2.18.0
[19] DESeq2_1.42.1 ANCOMBC_2.4.0
[21] phyloseq_1.46.0 glue_1.7.0
[23] viridis_0.6.5 viridisLite_0.4.2
[25] plotly_4.10.4 ggpubr_0.6.0
[27] gridExtra_2.3 hrbrthemes_0.8.7
[29] rbiom_2.0.0.9120 BiocManager_1.30.22
[31] vegan_2.6-4 lattice_0.22-6
[33] permute_0.9-7 lubridate_1.9.3
[35] forcats_1.0.0 stringr_1.5.1
[37] dplyr_1.1.4 purrr_1.0.2
[39] readr_2.1.5 tidyr_1.3.1
[41] tibble_3.2.1 ggplot2_3.5.0
[43] tidyverse_2.0.0 TreeSummarizedExperiment_2.10.0
[45] Biostrings_2.70.3 XVector_0.42.0
[47] SingleCellExperiment_1.24.0 SummarizedExperiment_1.32.0
[49] Biobase_2.62.0 GenomicRanges_1.54.1
[51] GenomeInfoDb_1.38.8 IRanges_2.36.0
[53] MatrixGenerics_1.14.0 matrixStats_1.2.0
[55] S4Vectors_0.40.2 BiocGenerics_0.48.1

loaded via a namespace (and not attached):
[1] R.methodsS3_1.8.2 gld_2.6.6
[3] nnet_7.3-19 TH.data_1.1-2
[5] vctrs_0.6.5 energy_1.7-11
[7] digest_0.6.35 png_0.1-8
[9] shape_1.4.6.1 proxy_0.4-27
[11] Exact_3.2 registry_0.5-1
[13] ggrepel_0.9.5 httpcode_0.3.0
[15] MASS_7.3-60.0.1 fontLiberation_0.1.0
[17] httpuv_1.6.15 foreach_1.5.2
[19] withr_3.0.0 xfun_0.43
[21] survival_3.5-8 doRNG_1.8.6
[23] memoise_2.0.1 crul_1.4.0
[25] ggbeeswarm_0.7.2 emmeans_1.10.1
[27] gmp_0.7-4 systemfonts_1.0.6
[29] ragg_1.3.0 tidytree_0.4.6
[31] zoo_1.8-12 GlobalOptions_0.1.2
[33] gtools_3.9.5 R.oo_1.26.0
[35] DEoptimR_1.1-3 Formula_1.2-5
[37] promises_1.3.0 httr_1.4.7
[39] rhdf5filters_1.14.1 rhdf5_2.46.1
[41] rstudioapi_0.16.0 generics_0.1.3
[43] base64enc_0.1-3 curl_5.2.1
[45] zlibbioc_1.48.2 ScaledMatrix_1.10.0
[47] ca_0.71.1 GenomeInfoDbData_1.2.11
[49] SparseArray_1.2.4 xtable_1.8-4
[51] ade4_1.7-22 doParallel_1.0.17
[53] evaluate_0.23 S4Arrays_1.2.1
[55] hms_1.1.3 irlba_2.3.5.1
[57] colorspace_2.1-0 magrittr_2.0.3
[59] later_1.3.2 DECIPHER_2.30.0
[61] scuttle_1.12.0 class_7.3-22
[63] pillar_1.9.0 nlme_3.1-164
[65] iterators_1.0.14 decontam_1.22.0
[67] caTools_1.18.2 compiler_4.3.2
[69] beachmat_2.18.1 stringi_1.8.3
[71] biomformat_1.30.0 TSP_1.2-4
[73] DescTools_0.99.54 dendextend_1.17.1
[75] minqa_1.2.6 plyr_1.8.9
[77] crayon_1.5.2 abind_1.4-5
[79] scater_1.30.1 ggtext_0.1.2
[81] locfit_1.5-9.9 bit_4.0.5
[83] mia_1.10.0 rootSolve_1.8.2.4
[85] sandwich_3.1-0 codetools_0.2-20
[87] multcomp_1.4-25 textshaping_0.3.7
[89] BiocSingular_1.18.0 slam_0.1-50
[91] e1071_1.7-14 lmom_3.0
[93] GetoptLong_1.0.5 multtest_2.58.0
[95] mime_0.12 MultiAssayExperiment_1.28.0
[97] splines_4.3.2 circlize_0.4.16
[99] Rcpp_1.0.12 sparseMatrixStats_1.14.0
[101] cellranger_1.1.0 Rttf2pt1_1.3.12
[103] gridtext_0.1.5 blob_1.2.4
[105] utf8_1.2.4 clue_0.3-65
[107] lme4_1.1-35.2 fs_1.6.3
[109] checkmate_2.3.1 DelayedMatrixStats_1.24.0
[111] Rdpack_2.6 expm_0.999-9
[113] gsl_2.1-8 ggsignif_0.6.4
[115] estimability_1.5 Matrix_1.6-5
[117] tzdb_0.4.0 pkgconfig_2.0.3
[119] tools_4.3.2 cachem_1.0.8
[121] rbibutils_2.2.16 RSQLite_2.3.6
[123] DBI_1.2.2 numDeriv_2016.8-1.1
[125] fastmap_1.1.1 rmarkdown_2.26
[127] scales_1.3.0 broom_1.0.5
[129] patchwork_1.2.0 coda_0.19-4.1
[131] ggstats_0.6.0 carData_3.0-5
[133] rpart_4.1.23 farver_2.1.1
[135] mgcv_1.9-1 foreign_0.8-86
[137] cli_3.6.2 webshot_0.5.5
[139] lifecycle_1.0.4 uwot_0.1.16
[141] mvtnorm_1.2-4 bluster_1.12.0
[143] backports_1.4.1 BiocParallel_1.36.0
[145] timechange_0.3.0 gtable_0.3.4
[147] rjson_0.2.21 CVXR_1.0-12
[149] jsonlite_1.8.8 seriation_1.5.4
[151] bitops_1.0-7 assertthat_0.2.1
[153] bit64_4.0.5 yulab.utils_0.1.4
[155] BiocNeighbors_1.20.2 RcppParallel_5.1.7
[157] R.utils_2.12.3 lazyeval_0.2.2
[159] shiny_1.8.1.1 htmltools_0.5.8.1
[161] gfonts_0.2.0 gdtools_0.3.7
[163] RCurl_1.98-1.14 treeio_1.26.0
[165] boot_1.3-30 igraph_2.0.3
[167] extrafontdb_1.0 R6_2.5.1
[169] labeling_0.4.3 Rmpfr_0.9-5
[171] ggh4x_0.2.8 cluster_2.1.6
[173] rngtools_1.5.2 Rhdf5lib_1.24.2
[175] nloptr_2.0.3 DirichletMultinomial_1.44.0
[177] DelayedArray_0.28.0 tidyselect_1.2.1
[179] vipor_0.4.7 htmlTable_2.4.2
[181] xml2_1.3.6 fontBitstreamVera_0.1.1
[183] car_3.1-2 rsvd_1.0.5
[185] munsell_0.5.1 KernSmooth_2.23-22
[187] fontquiver_0.2.1 htmlwidgets_1.6.4
[189] rlang_1.1.3 extrafont_0.19
[191] lmerTest_3.1-3 ggnewscale_0.4.10
[193] fansi_1.0.6 beeswarm_0.4.0

[dansmith01]

Hi @shwetha141

Did any of the comments on satijalab/seurat#8100 help to fix this for you?

[shwetha141]

Hi, I tried installing Matrix and irlba from source, it didn't work. It gives me an error. Yet to work on the solution below.

This seems a recent change since I had no issues on 5th of April, when I wrote the code. :(. Another thing (I think this is major), the issue is with MAc since I ran the same code on windows , it works fine. The versions for Matrix and irlba are the same. Sorry for the updates.!
I looked at irlba repo, they seem to have noted the change but I can't understand it . I will try to read it more patiently.
bwlewis/irlba#70

Thank you to both Cinzialo and zhuldyzhanzak! I have now solved the problem. Here is my solution: 1. Go to https://cran.r-project.org/bin/macosx/tools/, download an installer package gfortran-12.2-universal.pkg
2. In R: install.packages("Matrix", type = "source")
3. In R: install.packages("irlba", type = "source")

[shwetha141]

Hi , this issue has been resolved, the following solution worked for me. Thank you.!

Thank you to both Cinzialo and zhuldyzhanzak! I have now solved the problem. Here is my solution: 1. Go to https://cran.r-project.org/bin/macosx/tools/, download an installer package gfortran-12.2-universal.pkg
2. In R: install.packages("Matrix", type = "source")
3. In R: install.packages("irlba", type = "source")

[dansmith01]

Glad to hear it!