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[chsnys]

Hi i am getting this error for the same code and same versions of packages i used earlier where i did not got any errors.
archr error.docx

archr error.docx

Can you please provide support. I am attaching session info below:

sessionInfo()
R version 4.2.3 (2023-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
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

Random number generation:
RNG: L'Ecuyer-CMRG
Normal: Inversion
Sample: Rejection

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

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

other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg38_1.4.5 BSgenome_1.66.3
[3] rtracklayer_1.58.0 Biostrings_2.66.0
[5] XVector_0.38.0 Seurat_5.1.0
[7] SeuratObject_5.0.2 sp_2.1-4
[9] rhdf5_2.42.1 SummarizedExperiment_1.28.0
[11] Biobase_2.58.0 MatrixGenerics_1.10.0
[13] Rcpp_1.0.12 Matrix_1.6-5
[15] GenomicRanges_1.50.2 GenomeInfoDb_1.34.9
[17] IRanges_2.32.0 S4Vectors_0.36.2
[19] BiocGenerics_0.44.0 matrixStats_1.3.0
[21] data.table_1.15.4 stringr_1.5.1
[23] plyr_1.8.9 magrittr_2.0.3
[25] ggplot2_3.5.1 gtable_0.3.5
[27] gtools_3.9.5 gridExtra_2.3
[29] ArchR_1.0.2

loaded via a namespace (and not attached):
[1] spam_2.10-0 igraph_2.0.3
[3] lazyeval_0.2.2 splines_4.2.3
[5] RcppHNSW_0.6.0 BiocParallel_1.32.6
[7] listenv_0.9.1 scattermore_1.2
[9] digest_0.6.35 htmltools_0.5.8.1
[11] fansi_1.0.6 tensor_1.5
[13] cluster_2.1.6 ROCR_1.0-11
[15] globals_0.16.3 spatstat.sparse_3.0-3
[17] colorspace_2.1-0 ggrepel_0.9.5
[19] xfun_0.44 dplyr_1.1.4
[21] crayon_1.5.2 RCurl_1.98-1.14
[23] jsonlite_1.8.8 progressr_0.14.0
[25] spatstat.data_3.0-4 survival_3.6-4
[27] zoo_1.8-12 glue_1.7.0
[29] polyclip_1.10-6 zlibbioc_1.44.0
[31] leiden_0.4.3.1 DelayedArray_0.24.0
[33] Rhdf5lib_1.20.0 future.apply_1.11.2
[35] abind_1.4-5 scales_1.3.0
[37] spatstat.random_3.2-3 miniUI_0.1.1.1
[39] viridisLite_0.4.2 xtable_1.8-4
[41] reticulate_1.36.1 dotCall64_1.1-1
[43] htmlwidgets_1.6.4 httr_1.4.7
[45] RColorBrewer_1.1-3 ica_1.0-3
[47] XML_3.99-0.16.1 pkgconfig_2.0.3
[49] uwot_0.2.2 deldir_2.0-4
[51] utf8_1.2.4 tidyselect_1.2.1
[53] rlang_1.1.3 reshape2_1.4.4
[55] later_1.3.2 munsell_0.5.1
[57] tools_4.2.3 cli_3.6.2
[59] generics_0.1.3 ggridges_0.5.6
[61] fastmap_1.2.0 yaml_2.3.8
[63] goftest_1.2-3 knitr_1.47
[65] fitdistrplus_1.1-11 purrr_1.0.2
[67] RANN_2.6.1 pbapply_1.7-2
[69] future_1.33.2 nlme_3.1-164
[71] mime_0.12 compiler_4.2.3
[73] rstudioapi_0.16.0 plotly_4.10.4
[75] png_0.1-8 spatstat.utils_3.0-4
[77] tibble_3.2.1 stringi_1.8.4
[79] RSpectra_0.16-1 lattice_0.22-6
[81] vctrs_0.6.5 pillar_1.9.0
[83] lifecycle_1.0.4 rhdf5filters_1.10.1
[85] spatstat.geom_3.2-9 lmtest_0.9-40
[87] RcppAnnoy_0.0.22 cowplot_1.1.3
[89] bitops_1.0-7 irlba_2.3.5.1
[91] httpuv_1.6.15 patchwork_1.2.0
[93] BiocIO_1.8.0 R6_2.5.1
[95] promises_1.3.0 KernSmooth_2.23-22
[97] parallelly_1.37.1 codetools_0.2-20
[99] fastDummies_1.7.3 MASS_7.3-60.0.1
[101] rjson_0.2.21 rprojroot_2.0.4
[103] withr_3.0.0 GenomicAlignments_1.34.1
[105] sctransform_0.4.1 Rsamtools_2.14.0
[107] GenomeInfoDbData_1.2.9 tidyr_1.3.1
[109] Rtsne_0.17 spatstat.explore_3.2-7
[111] shiny_1.8.1.1 restfulr_0.0.15

[rcorces]

Hi @chsnys! Thanks for using ArchR! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other
responsibilities as a PI. I have not been responding to issue posts and I have not been pushing updates to the software. We are actively searching to hire
a computational biologist to continue to develop and maintain ArchR and related tools. If you know someone who might be a good fit, please let us know!
In the meantime, your issue will likely go without a reply. Most issues with ArchR right not relate to compatibility. Try reverting to R 4.1 and Bioconductor 3.15.
Newer versions of Seurat and Matrix also are causing issues. Sorry for not being able to provide active support for this package at this time.