rcorces
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millerkaplanlab
Attach your log file ArchR-plotEmbedding-47a31fbbb49d-Date-2022-12-23_Time-15-04-58.log
Describe the bug Each time I run the code for plotEmbedding, I get the following error: Error in h5checktypeOrOpenLoc(file, readonly = TRUE, fapl = NULL, native = native) : Error in h5checktypeOrOpenLoc(). Cannot open file. File '/Users/Dina/Desktop/E17_ARCHR_DEC21/ArchROutput/ArrowFiles/E17_SVZ.arrow' does not exist.
To Reproduce
Expected behavior Expected to generate a plot
Screenshots
Session Info R version 4.2.1 (2022-06-23) Platform: x86_64-apple-darwin17.0 (64-bit)
Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
Random number generation: RNG: L'Ecuyer-CMRG Normal: Inversion Sample: Rejection
locale: [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
attached base packages: [1] grid stats4 stats graphics grDevices utils datasets methods
[9] base
other attached packages: [1] SeuratObject_4.1.3 Seurat_4.3.0
[3] rhdf5_2.42.0 Rcpp_1.0.9
[5] Matrix_1.5-3 data.table_1.14.6
[7] stringr_1.5.0 plyr_1.8.8
[9] magrittr_2.0.3 ggplot2_3.4.0
[11] gtable_0.3.1 gtools_3.9.4
[13] gridExtra_2.3 ArchR_1.0.2
[15] SummarizedExperiment_1.28.0 Biobase_2.58.0
[17] GenomicRanges_1.50.2 GenomeInfoDb_1.34.4
[19] IRanges_2.32.0 S4Vectors_0.36.1
[21] BiocGenerics_0.44.0 MatrixGenerics_1.10.0
[23] matrixStats_0.63.0
loaded via a namespace (and not attached): [1] igraph_1.3.5 lazyeval_0.2.2 sp_1.5-1
[4] splines_4.2.1 listenv_0.9.0 scattermore_0.8
[7] usethis_2.1.6 digest_0.6.31 htmltools_0.5.4
[10] fansi_1.0.3 memoise_2.0.1 tensor_1.5
[13] cluster_2.1.4 ROCR_1.0-11 remotes_2.4.2
[16] globals_0.16.2 spatstat.sparse_3.0-0 prettyunits_1.1.1
[19] colorspace_2.0-3 ggrepel_0.9.2 dplyr_1.0.10
[22] callr_3.7.3 crayon_1.5.2 RCurl_1.98-1.9
[25] jsonlite_1.8.4 progressr_0.12.0 spatstat.data_3.0-0
[28] survival_3.4-0 zoo_1.8-11 glue_1.6.2
[31] polyclip_1.10-4 zlibbioc_1.44.0 XVector_0.38.0
[34] leiden_0.4.3 DelayedArray_0.24.0 pkgbuild_1.4.0
[37] Rhdf5lib_1.20.0 future.apply_1.10.0 abind_1.4-5
[40] scales_1.2.1 DBI_1.1.3 spatstat.random_3.0-1 [43] miniUI_0.1.1.1 viridisLite_0.4.1 xtable_1.8-4
[46] reticulate_1.26 profvis_0.3.7 htmlwidgets_1.6.0
[49] httr_1.4.4 RColorBrewer_1.1-3 ellipsis_0.3.2
[52] ica_1.0-3 urlchecker_1.0.1 pkgconfig_2.0.3
[55] uwot_0.1.14.9000 deldir_1.0-6 utf8_1.2.2
[58] tidyselect_1.2.0 rlang_1.0.6 reshape2_1.4.4
[61] later_1.3.0 munsell_0.5.0 tools_4.2.1
[64] cachem_1.0.6 cli_3.4.1 generics_0.1.3
[67] devtools_2.4.5 ggridges_0.5.4 fastmap_1.1.0
[70] goftest_1.2-3 processx_3.8.0 fs_1.5.2
[73] fitdistrplus_1.1-8 purrr_0.3.5 RANN_2.6.1
[76] nlme_3.1-161 pbapply_1.6-0 future_1.30.0
[79] mime_0.12 compiler_4.2.1 rstudioapi_0.14
[82] plotly_4.10.1 png_0.1-8 spatstat.utils_3.0-1
[85] tibble_3.1.8 stringi_1.7.8 ps_1.7.2
[88] lattice_0.20-45 vctrs_0.5.1 pillar_1.8.1
[91] lifecycle_1.0.3 rhdf5filters_1.10.0 BiocManager_1.30.19
[94] spatstat.geom_3.0-3 lmtest_0.9-40 RcppAnnoy_0.0.20
[97] cowplot_1.1.1 bitops_1.0-7 irlba_2.3.5.1
[100] httpuv_1.6.7 patchwork_1.1.2 R6_2.5.1
[103] promises_1.2.0.1 KernSmooth_2.23-20 parallelly_1.33.0
[106] sessioninfo_1.2.2 codetools_0.2-18 MASS_7.3-58.1
[109] assertthat_0.2.1 pkgload_1.3.2 withr_2.5.0
[112] sctransform_0.3.5 GenomeInfoDbData_1.2.9 parallel_4.2.1
[115] tidyr_1.2.1 Cairo_1.6-0 Rtsne_0.16
[118] spatstat.explore_3.0-5 shiny_1.7.4
Additional context Add any other context about the problem here.