[BUG] fetch data spe failed

[hym97]

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

I tried to download the data using fetch_data() function, but it failed.

Provide a minimally reproducible example

spe <- fetch_data(type = "spe")

Error message 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)

Expected behavior

Download the data successfully.

R Session Information

Please report the output of either sessionInfo() or

```R options(width = 120) R version 4.4.1 (2024-06-14) Platform: aarch64-apple-darwin20 Running under: macOS Sonoma 14.6.1 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/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: America/Los_Angeles tzcode source: internal attached base packages: [1] stats4 stats graphics grDevices utils datasets methods [8] base other attached packages: [1] spatialLIBD_1.16.2 SpatialExperiment_1.14.0 [3] SingleCellExperiment_1.26.0 SummarizedExperiment_1.34.0 [5] Biobase_2.64.0 GenomicRanges_1.56.1 [7] GenomeInfoDb_1.40.1 IRanges_2.38.1 [9] S4Vectors_0.42.1 BiocGenerics_0.50.0 [11] MatrixGenerics_1.16.0 matrixStats_1.3.0 loaded via a namespace (and not attached): [1] RColorBrewer_1.1-3 rstudioapi_0.16.0 [3] jsonlite_1.8.8 magrittr_2.0.3 [5] ggbeeswarm_0.7.2 magick_2.8.4 [7] BiocIO_1.14.0 fields_16.2 [9] zlibbioc_1.50.0 vctrs_0.6.5 [11] memoise_2.0.1 config_0.3.2 [13] Rsamtools_2.20.0 DelayedMatrixStats_1.26.0 [15] paletteer_1.6.0 RCurl_1.98-1.16 [17] benchmarkme_1.0.8 htmltools_0.5.8.1 [19] S4Arrays_1.4.1 AnnotationHub_3.12.0 [21] curl_5.2.2 BiocNeighbors_1.22.0 [23] SparseArray_1.4.8 sass_0.4.9 [25] bslib_0.8.0 htmlwidgets_1.6.4 [27] plotly_4.10.4 cachem_1.1.0 [29] GenomicAlignments_1.40.0 mime_0.12 [31] lifecycle_1.0.4 iterators_1.0.14 [33] pkgconfig_2.0.3 rsvd_1.0.5 [35] Matrix_1.7-0 R6_2.5.1 [37] fastmap_1.2.0 GenomeInfoDbData_1.2.12 [39] shiny_1.9.1 digest_0.6.37 [41] colorspace_2.1-1 rematch2_2.1.2 [43] AnnotationDbi_1.66.0 scater_1.32.1 [45] irlba_2.3.5.1 ExperimentHub_2.12.0 [47] RSQLite_2.3.7 beachmat_2.20.0 [49] filelock_1.0.3 fansi_1.0.6 [51] httr_1.4.7 abind_1.4-5 [53] compiler_4.4.1 withr_3.0.1 [55] bit64_4.0.5 doParallel_1.0.17 [57] attempt_0.3.1 BiocParallel_1.38.0 [59] viridis_0.6.5 DBI_1.2.3 [61] maps_3.4.2 sessioninfo_1.2.2 [63] rappdirs_0.3.3 DelayedArray_0.30.1 [65] rjson_0.2.22 tools_4.4.1 [67] vipor_0.4.7 beeswarm_0.4.0 [69] httpuv_1.6.15 glue_1.7.0 [71] restfulr_0.0.15 promises_1.3.0 [73] grid_4.4.1 generics_0.1.3 [75] gtable_0.3.5 tidyr_1.3.1 [77] data.table_1.16.0 ScaledMatrix_1.12.0 [79] BiocSingular_1.20.0 utf8_1.2.4 [81] XVector_0.44.0 stringr_1.5.1 [83] ggrepel_0.9.5 BiocVersion_3.19.1 [85] foreach_1.5.2 pillar_1.9.0 [87] spam_2.10-0 limma_3.60.4 [89] later_1.3.2 benchmarkmeData_1.0.4 [91] dplyr_1.1.4 BiocFileCache_2.12.0 [93] lattice_0.22-6 rtracklayer_1.64.0 [95] bit_4.0.5 tidyselect_1.2.1 [97] locfit_1.5-9.10 Biostrings_2.72.1 [99] scuttle_1.14.0 gridExtra_2.3 [101] edgeR_4.2.1 statmod_1.5.0 [103] DT_0.33 stringi_1.8.4 [105] UCSC.utils_1.0.0 lazyeval_0.2.2 [107] yaml_2.3.10 shinyWidgets_0.8.6 [109] codetools_0.2-20 tibble_3.2.1 [111] BiocManager_1.30.25 cli_3.6.3 [113] xtable_1.8-4 jquerylib_0.1.4 [115] munsell_0.5.1 golem_0.5.1 [117] Rcpp_1.0.13 dbplyr_2.5.0 [119] png_0.1-8 XML_3.99-0.17 [121] parallel_4.4.1 ggplot2_3.5.1 [123] blob_1.2.4 dotCall64_1.1-1 [125] sparseMatrixStats_1.16.0 bitops_1.0-8 [127] viridisLite_0.4.2 scales_1.3.0 [129] purrr_1.0.2 crayon_1.5.3 [131] rlang_1.1.4 cowplot_1.1.3 [133] KEGGREST_1.44.1 ```

Indicate whether BiocManager::valid() returns TRUE.

• [x] BiocManager::valid() is TRUE

Note. To avoid potential issues with version mixing and reproducibility, do not install packages from GitHub.

Is the package installed via bioconda?

No, I am using

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("spatialLIBD")

[hym97]

I was able to resolve the issue by manually downloading the data, but I wanted to bring this behavior to your attention.

[lcolladotor]

Hi,

What's the output of curl::curl_version()? I'm guessing that your curl::curl_version()$version will be 8.6.0. If so, the root issue is https://github.com/curl/curl/issues/13725 which has been fixed in curl (system, not R package) version 8.8.0. As a macOS user, you can install version 8.8.0 using homebrew https://formulae.brew.sh/formula/curl.

You will need to compile your R package curl following https://github.com/jeroen/curl?tab=readme-ov-file#macos-using-curl-from-homebrew. Note that the path to pkgconfig is different for Apple Silicon macs. Aka, pay attention to where homebrew installs pkgconfig when you run brew install curl pkg-config.

Best, Leo

[hym97]

I changed the curl to 8.9.1 and it worked. Thank you for your quick response!

Best, Yimeng

[lcolladotor]

Excellent :)