I'm attempting to download some data from GTEx with recount3 and I'm getting an invalid description error when the download begins, as well as a warning that one of the URLs being referenced is not available.

> library(recount3)
> human_projects <- available_projects()
2020-10-29 09:52:51 caching file sra.recount_project.MD.gz.
2020-10-29 09:52:51 caching file gtex.recount_project.MD.gz.
2020-10-29 09:52:51 caching file tcga.recount_project.MD.gz.
> proj_info <- subset(human_projects,
+                     project == "BLOOD_VESSEL" & project_type == "data_sources"
+                     )
> rse_blood_vessel <- create_rse(proj_info)
2020-10-29 09:52:54 downloading and reading the metadata.
2020-10-29 09:52:54 caching file gtex.gtex.BLOOD_VESSEL.MD.gz.
2020-10-29 09:52:54 caching file gtex.recount_project.BLOOD_VESSEL.MD.gz.
2020-10-29 09:52:55 caching file gtex.recount_qc.BLOOD_VESSEL.MD.gz.
2020-10-29 09:52:55 caching file gtex.recount_seq_qc.BLOOD_VESSEL.MD.gz.
2020-10-29 09:52:55 downloading and reading the feature information.
2020-10-29 09:52:55 caching file human.gene_sums.G026.gtf.gz.
2020-10-29 09:52:56 downloading and reading the counts: 1398 samples across 63856 features.
Error in file(file, "rt") : invalid 'description' argument
In addition: Warning message:
The 'url' <http://idies.jhu.edu/recount3/data/human/data_sources/gtex/gene_sums/EL/BLOOD_VESSEL/gtex.gene_sums.BLOOD_VESSEL.G026.gz> does not exist or is not available. 
> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Pop!_OS 20.04 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8      
 [8] LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] recount3_1.0.0              SummarizedExperiment_1.20.0 Biobase_2.50.0              GenomicRanges_1.42.0        GenomeInfoDb_1.26.0         IRanges_2.24.0              S4Vectors_0.28.0           
 [8] BiocGenerics_0.36.0         MatrixGenerics_1.2.0        matrixStats_0.57.0         

loaded via a namespace (and not attached):
 [1] tidyselect_1.1.0         purrr_0.3.4              lattice_0.20-41          vctrs_0.3.4              generics_0.0.2           BiocFileCache_1.14.0     rtracklayer_1.50.0      
 [8] blob_1.2.1               XML_3.99-0.5             rlang_0.4.8              R.oo_1.24.0              pillar_1.4.6             withr_2.3.0              glue_1.4.2              
[15] DBI_1.1.0                R.utils_2.10.1           BiocParallel_1.24.0      rappdirs_0.3.1           bit64_4.0.5              dbplyr_1.4.4             sessioninfo_1.1.1       
[22] GenomeInfoDbData_1.2.4   lifecycle_0.2.0          zlibbioc_1.36.0          Biostrings_2.58.0        R.methodsS3_1.8.1        memoise_1.1.0            curl_4.3                
[29] fansi_0.4.1              Rcpp_1.0.5               DelayedArray_0.16.0      XVector_0.30.0           bit_4.0.4                Rsamtools_2.6.0          digest_0.6.27           
[36] dplyr_1.0.2              grid_4.0.3               cli_2.1.0                tools_4.0.3              bitops_1.0-6             magrittr_1.5             RCurl_1.98-1.2          
[43] tibble_3.0.4             RSQLite_2.2.1            crayon_1.3.4             pkgconfig_2.0.3          ellipsis_0.3.1           Matrix_1.2-18            data.table_1.13.2       
[50] assertthat_0.2.1         httr_1.4.2               rstudioapi_0.11          R6_2.5.0                 GenomicAlignments_1.26.0 compiler_4.0.3

Hi,

Thanks for reporting this issue! It has been resolved now thanks to speedy work by Christopher Wilks. Thanks Chris!

The root problem was that we had uploaded the GTEx data to the IDIES data server but had not moved it to the paths expected by the recount3 R package. You don't need to update the R package, simply, run the commands again.

Best, Leo

I have the same issue when trying to download "exon" data ("gene" data works ok):

> rse = create_rse(subset(human_projects, project=='UVM'), type = "exon", annotation = "gencode_v26")
2022-03-16 13:56:36 downloading and reading the metadata.
2022-03-16 13:56:38 caching file tcga.tcga.UVM.MD.gz.
2022-03-16 13:56:39 caching file tcga.recount_project.UVM.MD.gz.
2022-03-16 13:56:40 caching file tcga.recount_qc.UVM.MD.gz.
2022-03-16 13:56:42 caching file tcga.recount_seq_qc.UVM.MD.gz.
2022-03-16 13:56:44 downloading and reading the feature information.
2022-03-16 13:56:44 caching file human.exon_sums.G026.gtf.gz.
2022-03-16 13:57:06 downloading and reading the counts: 80 samples across 1299686 features.
Error in file(file, "rt") : invalid 'description' argument
In addition: Warning messages:
1: In UseMethod("depth") :
  no applicable method for 'depth' applied to an object of class "NULL"
2: The 'url' <http://duffel.rail.bio/recount3/human/data_sources/tcga/exon_sums/VM/UVM/tcga.exon_sums.UVM.G026.gz> does not exist or is not available. 

should be fixed now, it was a lingering permissions issue that only affected TCGA exon sums