Read_Metrics_10X error · Issue #115 · samuel-marsh/scCustomize (original) (raw)

LOVE scCustomize!! However, I found something that doesn't seem to work.

This command:
raw_metrics <- Read_Metrics_10X(base_path = file.path("..","results"), default_10X = T)
Produces this error:
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
cannot open file '../results/C1/outsmetrics_summary.csv': No such file or directory

It looks like the "outs" directory isn't followed by a "/". Note that I'm on Windows so I generally use file.path to avoid issues with directory/file coding. I also tried saying default_10X = F and adding secondary_path = "outs/" or "outs" and I get the same error.

Thanks!

sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C LC_TIME=English_United States.utf8

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] qs_0.25.5 viridis_0.6.3 viridisLite_0.4.2 patchwork_1.1.2 lubridate_1.9.2 forcats_1.0.0 stringr_1.5.0
[8] dplyr_1.1.2 purrr_1.0.1 readr_2.1.4 tidyr_1.3.0 tibble_3.2.1 ggplot2_3.4.2 tidyverse_2.0.0
[15] scCustomize_1.1.1 SeuratObject_4.1.3 Seurat_4.3.0.1

loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 rstudioapi_0.15.0 jsonlite_1.8.7 shape_1.4.6 magrittr_2.0.3
[6] spatstat.utils_3.0-3 ggbeeswarm_0.7.2 farver_2.1.1 GlobalOptions_0.1.2 vctrs_0.6.3
[11] ROCR_1.0-11 spatstat.explore_3.2-1 paletteer_1.5.0 janitor_2.2.0 htmltools_0.5.5
[16] sctransform_0.3.5 parallelly_1.36.0 KernSmooth_2.23-22 htmlwidgets_1.6.2 ica_1.0-3
[21] plyr_1.8.8 plotly_4.10.2 zoo_1.8-12 igraph_1.5.0 mime_0.12
[26] lifecycle_1.0.3 pkgconfig_2.0.3 Matrix_1.6-0 R6_2.5.1 fastmap_1.1.1
[31] fitdistrplus_1.1-11 future_1.33.0 shiny_1.7.4.1 snakecase_0.11.0 digest_0.6.33
[36] colorspace_2.1-0 rematch2_2.1.2 tensor_1.5 prismatic_1.1.1 irlba_2.3.5.1
[41] labeling_0.4.2 progressr_0.13.0 fansi_1.0.4 spatstat.sparse_3.0-2 timechange_0.2.0
[46] httr_1.4.6 polyclip_1.10-4 abind_1.4-5 compiler_4.3.1 withr_2.5.0
[51] MASS_7.3-60 tools_4.3.1 vipor_0.4.5 lmtest_0.9-40 beeswarm_0.4.0
[56] httpuv_1.6.11 future.apply_1.11.0 goftest_1.2-3 glue_1.6.2 nlme_3.1-162
[61] promises_1.2.0.1 grid_4.3.1 Rtsne_0.16 cluster_2.1.4 reshape2_1.4.4
[66] generics_0.1.3 gtable_0.3.3 spatstat.data_3.0-1 tzdb_0.4.0 RApiSerialize_0.1.2
[71] hms_1.1.3 data.table_1.14.8 stringfish_0.15.8 sp_2.0-0 utf8_1.2.3
[76] spatstat.geom_3.2-2 RcppAnnoy_0.0.21 ggrepel_0.9.3 RANN_2.6.1 pillar_1.9.0
[81] ggprism_1.0.4 later_1.3.1 circlize_0.4.15 splines_4.3.1 lattice_0.21-8
[86] survival_3.5-5 deldir_1.0-9 tidyselect_1.2.0 miniUI_0.1.1.1 pbapply_1.7-2
[91] gridExtra_2.3 scattermore_1.2 matrixStats_1.0.0 stringi_1.7.12 lazyeval_0.2.2
[96] codetools_0.2-19 BiocManager_1.30.21 cli_3.6.1 RcppParallel_5.1.7 uwot_0.1.16
[101] xtable_1.8-4 reticulate_1.30 munsell_0.5.0 Rcpp_1.0.11 globals_0.16.2
[106] spatstat.random_3.1-5 png_0.1-8 ggrastr_1.0.2 parallel_4.3.1 ellipsis_0.3.2
[111] listenv_0.9.0 scales_1.2.1 ggridges_0.5.4 leiden_0.4.3 rlang_1.1.1
[116] cowplot_1.1.1

insert reproducible example here

sessionInfo() output

PASTE HERE sessionInfo() output