azzurradep commented on issue #48066: URL: https://github.com/apache/arrow/issues/48066#issuecomment-3927858148
> [@azzurradep](https://github.com/azzurradep) Thanks for reporting; are you able to provide sessionInfo information similar to above, with more info on your operating system, Arrow version etc? Thank you so much for your reply. Here are the information from both when I use the xenium file that works and when I use the other one which gives me the error. I am struggling to understand why is working with one but not the other. Xenium file 1- working > library(future) > options(future.seed = TRUE) > RNGkind("L'Ecuyer-CMRG") > set.seed(1234) > plan("multisession", workers = 6) > options(future.globals.maxSize = 8 * 1024^3) > > library(ggplot2) > library(arrow) Attaching package: ‘arrow’ The following object is masked from ‘package:utils’: timestamp > library(Seurat) Loading required package: SeuratObject Loading required package: sp Attaching package: ‘SeuratObject’ The following objects are masked from ‘package:base’: intersect, t > path <- "/Users/azzurradepace/Desktop/Xenium/output-XETG00160__0032909__Region_1__20240911__163848/output-XETG00160__0032909__Region_1__20240911__163848" > # Load the Xenium data > xenium.obj <- LoadXenium(path, fov = "fov", segmentations = "cell") Cell_seg columns: cell_id, segmentation_method Genome matrix has multiple modalities, returning a list of matrices for this genome Warning: Feature names cannot have underscores ('_'), replacing with dashes ('-') Warning: Feature names cannot have underscores ('_'), replacing with dashes ('-') Warning: Feature names cannot have underscores ('_'), replacing with dashes ('-') Warning: Feature names cannot have underscores ('_'), replacing with dashes ('-') Warning: Feature names cannot have underscores ('_'), replacing with dashes ('-') Warning: Feature names cannot have underscores ('_'), replacing with dashes ('-') > packageVersion("arrow") [1] ‘22.0.0.1’ > R.version.string [1] "R version 4.5.2 (2025-10-31)" Xenium file 2- not working > library(future) > options(future.seed = TRUE) > RNGkind("L'Ecuyer-CMRG") > set.seed(1234) > plan("multisession", workers = 6) > options(future.globals.maxSize = 8 * 1024^3) > library(ggplot2) > library(arrow) Attaching package: ‘arrow’ The following object is masked from ‘package:utils’: timestamp > library(Seurat) Loading required package: SeuratObject Loading required package: sp Attaching package: ‘SeuratObject’ The following objects are masked from ‘package:base’: intersect, t > path <- "/Users/azzurradepace/Desktop/Xenium/output-XETG00160__0061567__CTS__20250919__114240/output-XETG00160__0061567__CTS__20250919__114240" > # Load the Xenium data > xenium.obj <- LoadXenium(path, fov = "fov", segmentations = "cell") Cell_seg columns: cell_id, segmentation_method Genome matrix has multiple modalities, returning a list of matrices for this genome Error : Invalid: Invalid number of indices: 0 Error in file(file, "rt") : cannot open the connection Error in FUN(X[[i]], ...) : Xenium outputs were incomplete: missing transcripts. Xenium outputs no longer include `transcripts.csv.gz`. Instead, please install `arrow` to read transcripts.parquet > packageVersion("arrow") [1] ‘22.0.0.1’ > R.version.string [1] "R version 4.5.2 (2025-10-31)" > > sessionInfo() R version 4.5.2 (2025-10-31) Platform: aarch64-apple-darwin20 Running under: macOS Sequoia 15.6.1 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1 Random number generation: RNG: L'Ecuyer-CMRG Normal: Inversion Sample: Rejection 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: Europe/London tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Seurat_5.4.0 SeuratObject_5.3.0 sp_2.2-1 arrow_22.0.0.1 ggplot2_4.0.2 future_1.69.0 loaded via a namespace (and not attached): [1] deldir_2.0-4 pbapply_1.7-4 gridExtra_2.3 rlang_1.1.7 magrittr_2.0.4 RcppAnnoy_0.0.23 [7] otel_0.2.0 matrixStats_1.5.0 ggridges_0.5.7 compiler_4.5.2 spatstat.geom_3.7-0 png_0.1-8 [13] vctrs_0.7.1 reshape2_1.4.5 hdf5r_1.3.12 stringr_1.6.0 pkgconfig_2.0.3 fastmap_1.2.0 [19] promises_1.5.0 purrr_1.2.1 bit_4.6.0 jsonlite_2.0.0 goftest_1.2-3 later_1.4.6 [25] spatstat.utils_3.2-1 irlba_2.3.7 parallel_4.5.2 cluster_2.1.8.2 R6_2.6.1 ica_1.0-3 [31] stringi_1.8.7 RColorBrewer_1.1-3 spatstat.data_3.1-9 reticulate_1.45.0 parallelly_1.46.1 spatstat.univar_3.1-6 [37] lmtest_0.9-40 scattermore_1.2 Rcpp_1.1.1 assertthat_0.2.1 tensor_1.5.1 future.apply_1.20.1 [43] zoo_1.8-15 sctransform_0.4.3 httpuv_1.6.16 Matrix_1.7-4 splines_4.5.2 igraph_2.2.2 [49] tidyselect_1.2.1 rstudioapi_0.18.0 abind_1.4-8 spatstat.random_3.4-4 codetools_0.2-20 miniUI_0.1.2 [55] spatstat.explore_3.7-0 listenv_0.10.0 lattice_0.22-9 tibble_3.3.1 plyr_1.8.9 shiny_1.12.1 [61] withr_3.0.2 S7_0.2.1 ROCR_1.0-12 Rtsne_0.17 fastDummies_1.7.5 survival_3.8-6 [67] polyclip_1.10-7 fitdistrplus_1.2-6 pillar_1.11.1 KernSmooth_2.23-26 plotly_4.12.0 generics_0.1.4 [73] RcppHNSW_0.6.0 scales_1.4.0 globals_0.19.0 xtable_1.8-4 glue_1.8.0 lazyeval_0.2.2 [79] tools_4.5.2 data.table_1.18.2.1 RSpectra_0.16-2 RANN_2.6.2 dotCall64_1.2 cowplot_1.2.0 [85] grid_4.5.2 tidyr_1.3.2 nlme_3.1-168 patchwork_1.3.2 cli_3.6.5 spatstat.sparse_3.1-0 [91] spam_2.11-3 viridisLite_0.4.3 dplyr_1.2.0 uwot_0.2.4 gtable_0.3.6 digest_0.6.39 [97] progressr_0.18.0 ggrepel_0.9.6 htmlwidgets_1.6.4 farver_2.1.2 htmltools_0.5.9 lifecycle_1.0.5 [103] httr_1.4.8 mime_0.13 bit64_4.6.0-1 MASS_7.3-65 > -- This is an automated message from the Apache Git Service. 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