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LieberInstitute / spatialLIBD

Code for the spatialLIBD R/Bioconductor package and shiny app
http://LieberInstitute.github.io/spatialLIBD/
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[BUG] fetch_data fails #85

Closed stemangiola closed 2 months ago

stemangiola commented 2 months ago

Please ask questions about how to use spatialLIBD on the Bioconductor Support Site using the appropriate tag(s) including the one for this package.

Note. Update the issue title to concisely describe the bug.

Describe the bug

Hello Team. fetch_data(type = "spe") fails (Thanks for the support)

Provide a minimally reproducible example (reprex)

snapshotDate(): 2024-04-29
adding rname 'https://www.dropbox.com/s/f4wcvtdq428y73p/Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata?dl=1'
  |========================================================================================================================================| 100%
  |========================================================================================================================================| 100%

Error in BiocFileCache::bfcrpath(bfc, url) : 
  not all 'rnames' found or unique.
In addition: Warning message:
In value[[3L]](cond) : 
trying to add rname 'https://www.dropbox.com/s/f4wcvtdq428y73p/Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata?dl=1' produced error:
  HTTP/2 stream 1 was not closed cleanly: PROTOCOL_ERROR (err 1)
> sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: x86_64-apple-darwin20
Running under: macOS Sonoma 14.6.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/Helsinki
tzcode source: internal

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

other attached packages:
 [1] spatialLIBD_1.17.8          SpatialExperiment_1.14.0    SingleCellExperiment_1.26.0 SummarizedExperiment_1.34.0 Biobase_2.64.0             
 [6] GenomicRanges_1.56.1        GenomeInfoDb_1.40.1         IRanges_2.38.1              S4Vectors_0.42.1            BiocGenerics_0.50.0        
[11] MatrixGenerics_1.16.0       matrixStats_1.4.1           here_1.0.1                 

loaded via a namespace (and not attached):
  [1] later_1.3.2               BiocIO_1.14.0             bitops_1.0-8              filelock_1.0.3            fields_16.2              
  [6] R.oo_1.26.0               tibble_3.2.1              XML_3.99-0.17             lifecycle_1.0.4           edgeR_4.2.1              
 [11] doParallel_1.0.17         rprojroot_2.0.4           lattice_0.22-6            magrittr_2.0.3            limma_3.60.4             
 [16] plotly_4.10.4             sass_0.4.9                jquerylib_0.1.4           yaml_2.3.10               httpuv_1.6.15            
 [21] spam_2.10-0               sessioninfo_1.2.2         cowplot_1.1.3             DBI_1.2.3                 RColorBrewer_1.1-3       
 [26] golem_0.5.1               maps_3.4.2                abind_1.4-8               zlibbioc_1.50.0           R.utils_2.12.3           
 [31] purrr_1.0.2               RCurl_1.98-1.16           rappdirs_0.3.3            GenomeInfoDbData_1.2.12   ggrepel_0.9.6            
 [36] irlba_2.3.5.1             dqrng_0.4.1               DelayedMatrixStats_1.26.0 codetools_0.2-20          DropletUtils_1.24.0      
 [41] DelayedArray_0.30.1       DT_0.33                   scuttle_1.14.0            tidyselect_1.2.1          UCSC.utils_1.0.0         
 [46] ScaledMatrix_1.12.0       viridis_0.6.5             shinyWidgets_0.8.6        BiocFileCache_2.12.0      GenomicAlignments_1.40.0 
 [51] jsonlite_1.8.8            BiocNeighbors_1.22.0      scater_1.32.1             iterators_1.0.14          foreach_1.5.2            
 [56] tools_4.4.1               Rcpp_1.0.13               glue_1.7.0                gridExtra_2.3             SparseArray_1.4.8        
 [61] xfun_0.47                 dplyr_1.1.4               HDF5Array_1.32.1          withr_3.0.1               BiocManager_1.30.25      
 [66] fastmap_1.2.0             rhdf5filters_1.16.0       fansi_1.0.6               digest_0.6.37             rsvd_1.0.5               
 [71] R6_2.5.1                  mime_0.12                 colorspace_2.1-1          RSQLite_2.3.7             R.methodsS3_1.8.2        
 [76] config_0.3.2              utf8_1.2.4                tidyr_1.3.1               generics_0.1.3            data.table_1.16.0        
 [81] rtracklayer_1.65.0        httr_1.4.7                htmlwidgets_1.6.4         S4Arrays_1.4.1            pkgconfig_2.0.3          
 [86] gtable_0.3.5              blob_1.2.4                XVector_0.44.0            htmltools_0.5.8.1         dotCall64_1.1-1          
 [91] scales_1.3.0              png_0.1-8                 attempt_0.3.1             knitr_1.48                rstudioapi_0.16.0        
 [96] rjson_0.2.22              curl_5.2.2                rhdf5_2.48.0              cachem_1.1.0              stringr_1.5.1            
[101] BiocVersion_3.19.1        parallel_4.4.1            vipor_0.4.7               AnnotationDbi_1.66.0      restfulr_0.0.15          
[106] pillar_1.9.0              grid_4.4.1                vctrs_0.6.5               promises_1.3.0            BiocSingular_1.20.0      
[111] dbplyr_2.5.0              beachmat_2.20.0           xtable_1.8-4              beeswarm_0.4.0            paletteer_1.6.0          
[116] magick_2.8.4              cli_3.6.3                 locfit_1.5-9.10           compiler_4.4.1            Rsamtools_2.20.0         
[121] rlang_1.1.4               crayon_1.5.3              rematch2_2.1.2            ggbeeswarm_0.7.2          stringi_1.8.4            
[126] viridisLite_0.4.2         BiocParallel_1.38.0       munsell_0.5.1             Biostrings_2.72.1         lazyeval_0.2.2           
[131] Matrix_1.7-0              ExperimentHub_2.12.0      benchmarkme_1.0.8         sparseMatrixStats_1.16.0  bit64_4.0.5              
[136] Rhdf5lib_1.26.0           ggplot2_3.5.1             KEGGREST_1.44.1           statmod_1.5.0             shiny_1.9.1              
[141] AnnotationHub_3.12.0      memoise_2.0.1             bslib_0.8.0               benchmarkmeData_1.0.4     bit_4.0.5
lcolladotor commented 2 months ago

Hi @stemangiola,

Check https://github.com/LieberInstitute/spatialLIBD/issues/84#issuecomment-2319113667 and run curl::curl_version(). I suspect that you have the same issue about your system curl version.

best, Leo

stemangiola commented 2 months ago

Thanks Leo, apologies for not checking, I'm in a rush for a workshop :) 🙏