Issue with Rsamtools reading a remote file on Windows
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cthangav • 0
@71327c7c
Last seen 23 months ago
United States

Hello, there appears to be an issue when I use Rsamtools to read a remote file on Windows. Is this a bug?

> tbx <- TabixFile(file = "https://cf.10xgenomics.com/samples/cell-arc/1.0.0/pbmc_granulocyte_sorted_10k/pbmc_granulocyte_sorted_10k_atac_fragments.tsv.gz", yieldSize = 10)
> scanTabix(file = tbx)
Error: scanTabix: failed to open file: https://cf.10xgenomics.com/samples/cell-arc/1.0.0/pbmc_granulocyte_sorted_10k/pbmc_granulocyte_sorted_10k_atac_fragments.tsv.gz
 path: https://cf.10xgenomics.com/samples/cell-arc/1.0.0/pbmc_granulocyte_sorted_10k/pbmc_granulocyte_sorted_10k_atac_fragments.tsv.gz
 index: https://cf.10xgenomics.com/samples/cell-arc/1.0.0/pbmc_granulocyte_sorted_10k/pbmc_granulocyte_sorted_10k_atac_fragments.tsv.gz.tbi

> sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
 [1] cowplot_1.1.1                 ggplot2_3.3.3                 EnsDb.Hsapiens.v86_2.99.0     ensembldb_2.14.0             
 [5] AnnotationFilter_1.14.0       GenomicFeatures_1.42.3        AnnotationDbi_1.52.0          Biobase_2.50.0               
 [9] Signac_1.1.1                  SeuratObject_4.0.0            Seurat_4.0.1                  pbmcMultiome.SeuratData_0.1.0
[13] SeuratData_0.2.1              githubinstall_0.2.2           devtools_2.4.0                usethis_2.0.1                
[17] Rsamtools_2.6.0               Biostrings_2.58.0             XVector_0.30.0                GenomicRanges_1.42.0         
[21] GenomeInfoDb_1.26.7           IRanges_2.24.1                S4Vectors_0.28.1              BiocGenerics_0.36.0          

loaded via a namespace (and not attached):
  [1] rappdirs_0.3.3              SnowballC_0.7.0             rtracklayer_1.49.5          scattermore_0.7            
  [5] GGally_2.1.1                tidyr_1.1.3                 bit64_4.0.5                 knitr_1.31                 
  [9] irlba_2.3.3                 DelayedArray_0.16.3         data.table_1.14.0           rpart_4.1-15               
 [13] RCurl_1.98-1.3              generics_0.1.0              callr_3.7.0                 RSQLite_2.2.5              
 [17] RANN_2.6.1                  future_1.21.0               bit_4.0.4                   spatstat.data_2.1-0        
 [21] xml2_1.3.2                  httpuv_1.5.5                SummarizedExperiment_1.20.0 assertthat_0.2.1           
 [25] xfun_0.22                   hms_1.0.0                   promises_1.2.0.1            fansi_0.4.2                
 [29] progress_1.2.2              dbplyr_2.1.1                igraph_1.2.6                DBI_1.1.1                  
 [33] htmlwidgets_1.5.3           reshape_0.8.8               spatstat.geom_2.0-1         purrr_0.3.4                
 [37] ellipsis_0.3.1              RSpectra_0.16-0             dplyr_1.0.5                 backports_1.2.1            
 [41] biomaRt_2.46.3              deldir_0.2-10               MatrixGenerics_1.2.1        vctrs_0.3.7                
 [45] remotes_2.3.0               ROCR_1.0-11                 abind_1.4-5                 cachem_1.0.4               
 [49] withr_2.4.1                 ggforce_0.3.3               BSgenome_1.58.0             checkmate_2.0.0            
 [53] sctransform_0.3.2           GenomicAlignments_1.26.0    prettyunits_1.1.1           goftest_1.2-2              
 [57] cluster_2.1.1               lazyeval_0.2.2              crayon_1.4.1                pkgconfig_2.0.3            
 [61] labeling_0.4.2              tweenr_1.0.2                nlme_3.1-152                pkgload_1.2.1              
 [65] ProtGenerics_1.22.0         nnet_7.3-15                 rlang_0.4.10                globals_0.14.0             
 [69] lifecycle_1.0.0             miniUI_0.1.1.1              BiocFileCache_1.14.0        dichromat_2.0-0            
 [73] rprojroot_2.0.2             polyclip_1.10-0             matrixStats_0.58.0          lmtest_0.9-38              
 [77] graph_1.68.0                Matrix_1.3-2                ggseqlogo_0.1               zoo_1.8-9                  
 [81] base64enc_0.1-3             ggridges_0.5.3              processx_3.5.1              png_0.1-7                  
 [85] viridisLite_0.3.0           bitops_1.0-6                KernSmooth_2.23-18          blob_1.2.1                 
 [89] stringr_1.4.0               parallelly_1.24.0           jpeg_0.1-8.1                scales_1.1.1               
 [93] memoise_2.0.0               magrittr_2.0.1              plyr_1.8.6                  ica_1.0-2                  
 [97] zlibbioc_1.36.0             compiler_4.0.5              RColorBrewer_1.1-2          fitdistrplus_1.1-3         
[101] cli_2.4.0                   listenv_0.8.0               patchwork_1.1.1             pbapply_1.4-3              
[105] ps_1.6.0                    htmlTable_2.1.0             Formula_1.2-4               MASS_7.3-53.1              
[109] mgcv_1.8-34                 tidyselect_1.1.0            stringi_1.5.3               askpass_1.1                
[113] latticeExtra_0.6-29         ggrepel_0.9.1               grid_4.0.5                  VariantAnnotation_1.36.0   
[117] fastmatch_1.1-0             tools_4.0.5                 future.apply_1.7.0          rstudioapi_0.13            
[121] foreign_0.8-81              lsa_0.73.2                  gridExtra_2.3               farver_2.1.0               
[125] Rtsne_0.15                  digest_0.6.27               BiocManager_1.30.12         shiny_1.6.0                
[129] Rcpp_1.0.6                  later_1.1.0.1               RcppAnnoy_0.0.18            OrganismDbi_1.32.0         
[133] httr_1.4.2                  ggbio_1.38.0                biovizBase_1.38.0           colorspace_2.0-0           
[137] XML_3.99-0.6                fs_1.5.0                    tensor_1.5                  reticulate_1.18            
[141] splines_4.0.5               uwot_0.1.10                 RBGL_1.66.0                 RcppRoll_0.3.0             
[145] spatstat.utils_2.1-0        plotly_4.9.3                sessioninfo_1.1.1           xtable_1.8-4               
[149] jsonlite_1.7.2              testthat_3.0.2              R6_2.5.0                    Hmisc_4.5-0                
[153] pillar_1.5.1                htmltools_0.5.1.1           mime_0.10                   glue_1.4.2                 
[157] fastmap_1.1.0               BiocParallel_1.24.1         codetools_0.2-18            pkgbuild_1.2.0             
[161] utf8_1.2.1                  lattice_0.20-41             spatstat.sparse_2.0-0       tibble_3.1.0               
[165] curl_4.3                    leiden_0.3.7                openssl_1.4.3               survival_3.2-10            
[169] desc_1.3.0                  munsell_0.5.0               GenomeInfoDbData_1.2.4      reshape2_1.4.4             
[173] gtable_0.3.0                spatstat.core_2.0-0
Rsamtools • 726 views
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did you find a way around this? i am also having the same issues.

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