rcorces
commented
1 month ago Hi @Aya-Balbaa-72! 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.
leefall
Hi all, I am having an issue with addIterativeLSI , using TileMatrix , I get this error:
ArchR logging to : ArchRLogs/ArchR-addIterativeLSI-34f754ef9709-Date-2024-08-12_Time-22-18-58.603256.log If there is an issue, please report to github with logFile! Error in .availableSeqnames(ArrowFiles, subGroup = useMatrix) : Not All Seqnames Identical!
R version 4.3.1 (2023-06-16) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 22.04.3 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 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 LC_COLLATE=C.UTF-8 [5] LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 LC_PAPER=C.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C time zone: Etc/UTC tzcode source: system (glibc) attached base packages: [1] parallel stats4 grid stats graphics grDevices utils datasets methods base other attached packages: [1] hexbin_1.28.3 harmony_1.2.0 [3] uwot_0.2.2 ggridges_0.5.6 [5] BSgenome.Hsapiens.UCSC.hg38_1.4.5 BSgenome_1.70.2 [7] rtracklayer_1.62.0 BiocIO_1.12.0 [9] Biostrings_2.70.3 XVector_0.42.0 [11] nabor_0.5.0 Seurat_5.0.1 [13] SeuratObject_5.0.0 sp_2.1-4 [15] rhdf5_2.46.1 SummarizedExperiment_1.32.0 [17] Biobase_2.62.0 MatrixGenerics_1.14.0 [19] Rcpp_1.0.12 Matrix_1.6-1 [21] GenomicRanges_1.54.1 GenomeInfoDb_1.38.8 [23] IRanges_2.36.0 S4Vectors_0.40.2 [25] BiocGenerics_0.48.1 matrixStats_1.3.0 [27] data.table_1.15.4 stringr_1.5.1 [29] plyr_1.8.9 magrittr_2.0.3 [31] ggplot2_3.4.0 gtable_0.3.5 [33] gtools_3.9.5 gridExtra_2.3 [35] ArchR_1.0.2 loaded via a namespace (and not attached): [1] RcppAnnoy_0.0.22 splines_4.3.1 later_1.3.2 [4] bitops_1.0-7 tibble_3.2.1 polyclip_1.10-6 [7] XML_3.99-0.16.1 fastDummies_1.7.3 lifecycle_1.0.4 [10] doParallel_1.0.17 globals_0.16.3 lattice_0.21-8 [13] MASS_7.3-60 plotly_4.10.4 yaml_2.3.8 [16] remotes_2.5.0 httpuv_1.6.15 sctransform_0.4.1 [19] spam_2.10-0 sessioninfo_1.2.2 pkgbuild_1.4.4 [22] spatstat.sparse_3.0-3 reticulate_1.37.0 cowplot_1.1.3 [25] pbapply_1.7-2 RColorBrewer_1.1-3 abind_1.4-5 [28] pkgload_1.3.4 zlibbioc_1.48.2 Rtsne_0.17 [31] purrr_1.0.2 RCurl_1.98-1.14 circlize_0.4.16 [34] GenomeInfoDbData_1.2.11 ggrepel_0.9.5 irlba_2.3.5.1 [37] listenv_0.9.1 spatstat.utils_3.0-5 goftest_1.2-3 [40] RSpectra_0.16-1 spatstat.random_3.2-3 fitdistrplus_1.1-11 [43] parallelly_1.37.1 leiden_0.4.3.1 codetools_0.2-19 [46] DelayedArray_0.28.0 shape_1.4.6.1 tidyselect_1.2.1 [49] farver_2.1.2 spatstat.explore_3.2-7 GenomicAlignments_1.38.2 [52] jsonlite_1.8.8 GetoptLong_1.0.5 ellipsis_0.3.2 [55] progressr_0.14.0 iterators_1.0.14 survival_3.5-5 [58] foreach_1.5.2 tools_4.3.1 ica_1.0-3 [61] glue_1.7.0 SparseArray_1.2.4 usethis_2.2.3 [64] dplyr_1.1.4 withr_3.0.0 BiocManager_1.30.23 [67] fastmap_1.2.0 rhdf5filters_1.14.1 fansi_1.0.6 [70] digest_0.6.35 R6_2.5.1 mime_0.12 [73] colorspace_2.1-0 scattermore_1.2 Cairo_1.6-2 [76] tensor_1.5 spatstat.data_3.0-4 utf8_1.2.4 [79] tidyr_1.3.1 generics_0.1.3 httr_1.4.7 [82] htmlwidgets_1.6.4 S4Arrays_1.2.1 pkgconfig_2.0.3 [85] ComplexHeatmap_2.18.0 lmtest_0.9-40 htmltools_0.5.8.1 [88] profvis_0.3.8 dotCall64_1.1-1 clue_0.3-65 [91] scales_1.3.0 png_0.1-8 rstudioapi_0.16.0 [94] reshape2_1.4.4 rjson_0.2.21 nlme_3.1-162 [97] GlobalOptions_0.1.2 zoo_1.8-12 cachem_1.1.0 [100] KernSmooth_2.23-21 miniUI_0.1.1.1 restfulr_0.0.15 [103] pillar_1.9.0 vctrs_0.6.5 RANN_2.6.1 [106] urlchecker_1.0.1 promises_1.3.0 xtable_1.8-4 [109] cluster_2.1.4 cli_3.6.3 compiler_4.3.1 [112] Rsamtools_2.18.0 rlang_1.1.4 crayon_1.5.2 [115] future.apply_1.11.2 labeling_0.4.3 fs_1.6.4 [118] stringi_1.8.4 viridisLite_0.4.2 deldir_2.0-4 [121] BiocParallel_1.36.0 munsell_0.5.1 lazyeval_0.2.2 [124] devtools_2.4.5 spatstat.geom_3.2-9 RcppHNSW_0.6.0 [127] patchwork_1.2.0 future_1.33.2 Rhdf5lib_1.24.2 [130] shiny_1.8.1.1 ROCR_1.0-11 igraph_2.0.3 [133] memoise_2.0.1
Any suggestions please how to fix that? Thank you!