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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
did you find a way around this? i am also having the same issues.