Error: Other 'type' values are not supported

[JayaniLakshika]

if (!exists("spe")) spe <- fetch_data("spatialDLPFC_Visium")

[boyiguo1]

@JayaniLakshika Thanks for reporting the error. Would you mind providing a minimum replicable example and provide your session information, i.e. sessionInfo()?

I assume that you didn't successfully load the spatialLIBD package. Can you check? Thanks.

[JayaniLakshika]

@boyiguo1 Thanks, Please find the sessionInfo() below.

R version 4.2.3 (2023-03-15) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Ventura 13.0

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib

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

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

other attached packages: [1] spatialLIBD_1.10.1 SpatialExperiment_1.8.1 SingleCellExperiment_1.20.1 [4] SummarizedExperiment_1.28.0 Biobase_2.58.0 GenomicRanges_1.50.2
[7] GenomeInfoDb_1.34.9 IRanges_2.32.0 S4Vectors_0.36.2
[10] BiocGenerics_0.44.0 MatrixGenerics_1.10.0 matrixStats_0.63.0
[13] escheR_0.99.0 ggplot2_3.4.1

loaded via a namespace (and not attached): [1] spam_2.9-1 AnnotationHub_3.6.0 BiocFileCache_2.6.1
[4] lazyeval_0.2.2 BiocParallel_1.32.6 scater_1.26.1
[7] benchmarkme_1.0.8 digest_0.6.31 foreach_1.5.2
[10] htmltools_0.5.5 viridis_0.6.2 magick_2.7.4
[13] fansi_1.0.4 magrittr_2.0.3 memoise_2.0.1
[16] ScaledMatrix_1.6.0 paletteer_1.5.0 config_0.3.1
[19] doParallel_1.0.17 limma_3.54.2 Biostrings_2.66.0
[22] R.utils_2.12.2 colorspace_2.1-0 ggrepel_0.9.3
[25] blob_1.2.4 rappdirs_0.3.3 dplyr_1.1.1
[28] crayon_1.5.2 RCurl_1.98-1.10 jsonlite_1.8.4
[31] iterators_1.0.14 glue_1.6.2 gtable_0.3.3
[34] zlibbioc_1.44.0 XVector_0.38.0 DelayedArray_0.24.0
[37] BiocSingular_1.14.0 DropletUtils_1.18.1 Rhdf5lib_1.20.0
[40] maps_3.4.1 HDF5Array_1.26.0 scales_1.2.1
[43] DBI_1.1.3 edgeR_3.40.2 Rcpp_1.0.10
[46] viridisLite_0.4.1 xtable_1.8-4 dqrng_0.3.0
[49] rsvd_1.0.5 bit_4.0.5 dotCall64_1.0-2
[52] DT_0.27 htmlwidgets_1.6.2 httr_1.4.5
[55] RColorBrewer_1.1-3 ellipsis_0.3.2 pkgconfig_2.0.3
[58] XML_3.99-0.14 R.methodsS3_1.8.2 scuttle_1.8.4
[61] sass_0.4.5 dbplyr_2.3.2 locfit_1.5-9.7
[64] utf8_1.2.3 tidyselect_1.2.0 rlang_1.1.0.9000
[67] later_1.3.0 AnnotationDbi_1.60.2 munsell_0.5.0
[70] BiocVersion_3.16.0 tools_4.2.3 cachem_1.0.7
[73] cli_3.6.1 generics_0.1.3 RSQLite_2.3.0
[76] ExperimentHub_2.6.0 fastmap_1.1.1 yaml_2.3.7
[79] rematch2_2.1.2 bit64_4.0.5 purrr_1.0.1
[82] KEGGREST_1.38.0 sparseMatrixStats_1.10.0 mime_0.12
[85] R.oo_1.25.0 compiler_4.2.3 rstudioapi_0.14
[88] beeswarm_0.4.0 plotly_4.10.1 filelock_1.0.2
[91] curl_5.0.0 png_0.1-8 interactiveDisplayBase_1.36.0 [94] statmod_1.5.0 tibble_3.2.1 bslib_0.4.2
[97] fields_14.1 lattice_0.20-45 Matrix_1.5-3
[100] vctrs_0.6.1 pillar_1.9.0 lifecycle_1.0.3
[103] rhdf5filters_1.10.1 BiocManager_1.30.20 jquerylib_0.1.4
[106] BiocNeighbors_1.16.0 data.table_1.14.8 cowplot_1.1.1
[109] bitops_1.0-7 irlba_2.3.5.1 httpuv_1.6.9
[112] rtracklayer_1.58.0 R6_2.5.1 BiocIO_1.8.0
[115] promises_1.2.0.1 gridExtra_2.3 vipor_0.4.5
[118] sessioninfo_1.2.2 codetools_0.2-19 benchmarkmeData_1.0.4
[121] golem_0.4.0 rhdf5_2.42.0 rjson_0.2.21
[124] shinyWidgets_0.7.6 withr_2.5.0 GenomicAlignments_1.34.1
[127] Rsamtools_2.14.0 GenomeInfoDbData_1.2.9 parallel_4.2.3
[130] grid_4.2.3 beachmat_2.14.0 tidyr_1.3.0
[133] attempt_0.3.1 DelayedMatrixStats_1.20.0 shiny_1.7.4
[136] ggbeeswarm_0.7.1 restfulr_0.0.15

[JayaniLakshika]

@boyiguo1 Thanks..Found it. RCurl had the problem.

[boyiguo1]

Thanks for bringing this to my attention. I will find some other example dataset, such that the replication of the tutorial will be more robust.

[boyiguo1]

Now using STexampleData instead of spatialLIBD to reduce the computational load to replicate the vignettes. See the change via 25446d9.

[boyiguo1]

Meanwhile, since the original error is not a programming problem of the current package. I am closing this issue.