Error when loading an SRA project - "'NA' indices are not (yet?) supported for sparse Matrices"

[aobermayer4]

I was trying to load in the junction data for project "SRP187599" and after regular loading prompt through all of the files I received the error below. I know there is a Matrix Market format through the Recount3 Study Explorer I could download, but I was hoping to use the R function. I am not sure if this is something on my end or has to do with this projects data. I made a temp cache just to see if something in the original cache was an issue, but had the same error both times. if I do not specify "jxn" the other count data loads just fine.

"Error in intI(j, n = x@Dim[2], dn[[2]], give.dn = FALSE) :
'NA' indices are not (yet?) supported for sparse Matrices"

Please see my code and session info below.

Please let me know if anymore information is needed. Thank you!

Code:

library(recount3)

options("recount3_organism_human_project_homes_URL_http://duffel.rail.bio/recount3" = c("data_sources/sra", "data_sources/gtex", "data_sources/tcga"))

rse_jxn <- recount3::create_rse_manual(
  project = "SRP187599",
  project_home = "data_sources/sra",
  organism = "human",
  type = "jxn",
  bfc = recount3_cache("~/R/Recount3_Temp_Cache/")
)

Output in R Studio console:

2023-07-21 17:18:34 downloading and reading the metadata.
2023-07-21 17:18:34 caching file sra.sra.SRP187599.MD.gz.
adding rname 'http://duffel.rail.bio/recount3/human/data_sources/sra/metadata/99/SRP187599/sra.sra.SRP187599.MD.gz'
  |========================================================================================================================================================================| 100%

2023-07-21 17:18:35 caching file sra.recount_project.SRP187599.MD.gz.
adding rname 'http://duffel.rail.bio/recount3/human/data_sources/sra/metadata/99/SRP187599/sra.recount_project.SRP187599.MD.gz'
  |========================================================================================================================================================================| 100%

2023-07-21 17:18:36 caching file sra.recount_qc.SRP187599.MD.gz.
adding rname 'http://duffel.rail.bio/recount3/human/data_sources/sra/metadata/99/SRP187599/sra.recount_qc.SRP187599.MD.gz'
  |========================================================================================================================================================================| 100%

2023-07-21 17:18:37 caching file sra.recount_seq_qc.SRP187599.MD.gz.
adding rname 'http://duffel.rail.bio/recount3/human/data_sources/sra/metadata/99/SRP187599/sra.recount_seq_qc.SRP187599.MD.gz'
  |========================================================================================================================================================================| 100%

2023-07-21 17:18:38 caching file sra.recount_pred.SRP187599.MD.gz.
adding rname 'http://duffel.rail.bio/recount3/human/data_sources/sra/metadata/99/SRP187599/sra.recount_pred.SRP187599.MD.gz'
  |========================================================================================================================================================================| 100%

2023-07-21 17:18:38 downloading and reading the feature information.
2023-07-21 17:18:39 caching file sra.junctions.SRP187599.ALL.RR.gz.
adding rname 'http://duffel.rail.bio/recount3/human/data_sources/sra/junctions/99/SRP187599/sra.junctions.SRP187599.ALL.RR.gz'
  |========================================================================================================================================================================| 100%

2023-07-21 17:18:40 downloading and reading the counts: 119 samples across 118579 features.
2023-07-21 17:18:40 caching file sra.junctions.SRP187599.ALL.MM.gz.
adding rname 'http://duffel.rail.bio/recount3/human/data_sources/sra/junctions/99/SRP187599/sra.junctions.SRP187599.ALL.MM.gz'
  |========================================================================================================================================================================| 100%

2023-07-21 17:18:41 matching exon-exon junction counts with the metadata.
2023-07-21 17:18:41 caching file sra.junctions.SRP187599.ALL.ID.gz.
adding rname 'http://duffel.rail.bio/recount3/human/data_sources/sra/junctions/99/SRP187599/sra.junctions.SRP187599.ALL.ID.gz'
  |========================================================================================================================================================================| 100%

Error in intI(j, n = x@Dim[2], dn[[2]], give.dn = FALSE) : 
  'NA' indices are not (yet?) supported for sparse Matrices

Session Info:

R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

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

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

other attached packages:
 [1] recount3_1.10.2             SummarizedExperiment_1.28.0 Biobase_2.58.0              GenomicRanges_1.50.2        GenomeInfoDb_1.34.9         IRanges_2.32.0             
 [7] S4Vectors_0.36.2            BiocGenerics_0.44.0         MatrixGenerics_1.10.0       matrixStats_0.63.0         

loaded via a namespace (and not attached):
  [1] BiocFileCache_2.6.1      plyr_1.8.8               igraph_1.4.2             lazyeval_0.2.2           sp_1.6-0                 splines_4.2.2           
  [7] BiocParallel_1.32.6      listenv_0.9.0            scattermore_1.1          ggplot2_3.4.2            digest_0.6.31            htmltools_0.5.5         
 [13] fansi_1.0.3              magrittr_2.0.3           memoise_2.0.1            tensor_1.5               cluster_2.1.4            ROCR_1.0-11             
 [19] globals_0.16.2           Biostrings_2.66.0        R.utils_2.12.2           spatstat.sparse_3.0-1    colorspace_2.1-0         blob_1.2.4              
 [25] rappdirs_0.3.3           ggrepel_0.9.3            dplyr_1.1.2              crayon_1.5.2             RCurl_1.98-1.12          jsonlite_1.8.4          
 [31] progressr_0.13.0         spatstat.data_3.0-1      survival_3.4-0           zoo_1.8-12               glue_1.6.2               polyclip_1.10-4         
 [37] gtable_0.3.3             zlibbioc_1.44.0          XVector_0.38.0           leiden_0.4.3             DelayedArray_0.24.0      future.apply_1.10.0     
 [43] abind_1.4-5              scales_1.2.1             DBI_1.1.3                spatstat.random_3.1-5    miniUI_0.1.1.1           Rcpp_1.0.10             
 [49] viridisLite_0.4.2        xtable_1.8-4             reticulate_1.28          bit_4.0.5                htmlwidgets_1.6.2        httr_1.4.6              
 [55] RColorBrewer_1.1-3       ellipsis_0.3.2           Seurat_4.3.0             ica_1.0-3                pkgconfig_2.0.3          XML_3.99-0.14           
 [61] R.methodsS3_1.8.2        deldir_1.0-9             uwot_0.1.14              dbplyr_2.3.2.9000        utf8_1.2.2               tidyselect_1.2.0        
 [67] rlang_1.1.1              reshape2_1.4.4           later_1.3.1              munsell_0.5.0            tools_4.2.2              cachem_1.0.7            
 [73] cli_3.4.1                generics_0.1.3           RSQLite_2.3.1            ggridges_0.5.4           stringr_1.5.0            fastmap_1.1.1           
 [79] goftest_1.2-3            yaml_2.3.7               bit64_4.0.5              fitdistrplus_1.1-11      purrr_1.0.1              RANN_2.6.1              
 [85] nlme_3.1-160             pbapply_1.7-0            future_1.32.0            mime_0.12                R.oo_1.25.0              hdf5r_1.3.8             
 [91] compiler_4.2.2           rstudioapi_0.14          plotly_4.10.1            filelock_1.0.2           curl_5.0.0               png_0.1-8               
 [97] spatstat.utils_3.0-3     tibble_3.2.1             stringi_1.7.8            lattice_0.20-45          Matrix_1.5-4.1           SeuratDisk_0.0.0.9020   
[103] vctrs_0.6.2              pillar_1.9.0             lifecycle_1.0.3          spatstat.geom_3.2-1      lmtest_0.9-40            RcppAnnoy_0.0.20        
[109] data.table_1.14.8        cowplot_1.1.1            bitops_1.0-7             irlba_2.3.5.1            httpuv_1.6.11            patchwork_1.1.2         
[115] rtracklayer_1.58.0       R6_2.5.1                 BiocIO_1.8.0             promises_1.2.0.1         KernSmooth_2.23-20       gridExtra_2.3           
[121] parallelly_1.35.0        sessioninfo_1.2.2        codetools_0.2-18         MASS_7.3-58.1            rjson_0.2.21             withr_2.5.0             
[127] SeuratObject_4.1.3       GenomicAlignments_1.34.1 sctransform_0.3.5        Rsamtools_2.14.0         GenomeInfoDbData_1.2.9   parallel_4.2.2          
[133] grid_4.2.2               tidyr_1.3.0              Rtsne_0.16               spatstat.explore_3.2-1   shiny_1.7.4              restfulr_0.0.15