[BUG] Fail to obtain the spe data of DLPFC

[YikaiLou]

hello, thank you for creating such an outstanding work.Recently, I wanted to input the datasets, but it shows an error:
library(spatialLIBD)
library(ExperimentHub)
packageVersion("spatialLIBD")
ehub <- ExperimentHub::ExperimentHub()
spe <- spatialLIBD::fetch_data(type = "spe", eh = ehub)

packageVersion("spatialLIBD")
[1] '1.14.1'
ehub <- ExperimentHub::ExperimentHub()
snapshotDate(): 2023-10-24
spe <- spatialLIBD::fetch_data(type = "spe", eh = ehub)
Error in inherits(ram, "try-error") || length(ram) == 0L || is.na(ram) :
'length = 9' in coercion to 'logical(1)'

Here are the information details:

R version 4.3.3 (2024-02-29 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22000)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8
[2] LC_CTYPE=Chinese (Simplified)_China.utf8
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.utf8

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] ExperimentHub_2.10.0 AnnotationHub_3.10.0
[3] BiocFileCache_2.10.2 dbplyr_2.5.0
[5] spatialLIBD_1.14.1 ggspavis_1.8.1
[7] cowplot_1.1.3 scater_1.30.1
[9] ggplot2_3.5.0 scuttle_1.12.0
[11] data.table_1.15.4 Seurat_5.0.3
[13] SeuratObject_5.0.1 sp_2.1-3
[15] SpatialExperiment_1.12.0 SingleCellExperiment_1.24.0
[17] SummarizedExperiment_1.32.0 Biobase_2.62.0
[19] GenomicRanges_1.54.1 GenomeInfoDb_1.38.8
[21] IRanges_2.36.0 S4Vectors_0.40.2
[23] BiocGenerics_0.48.1 MatrixGenerics_1.14.0
[25] matrixStats_1.2.0 Banksy_0.99.9

loaded via a namespace (and not attached):
[1] spatstat.sparse_3.0-3 bitops_1.0-7
[3] httr_1.4.7 RColorBrewer_1.1-3
[5] doParallel_1.0.17 tools_4.3.3
[7] sctransform_0.4.1 utf8_1.2.4
[9] R6_2.5.1 DT_0.33
[11] lazyeval_0.2.2 uwot_0.1.16
[13] withr_3.0.0 gridExtra_2.3
[15] progressr_0.14.0 cli_3.6.2
[17] spatstat.explore_3.2-7 fastDummies_1.7.3
[19] sass_0.4.9 spatstat.data_3.0-4
[21] ggridges_0.5.6 pbapply_1.7-2
[23] Rsamtools_2.18.0 dbscan_1.1-12
[25] aricode_1.0.3 sessioninfo_1.2.2
[27] parallelly_1.37.1 attempt_0.3.1
[29] maps_3.4.2 limma_3.58.1
[31] RSQLite_2.3.6 BiocIO_1.12.0
[33] generics_0.1.3 ica_1.0-3
[35] spatstat.random_3.2-3 dplyr_1.1.4
[37] Matrix_1.6-5 ggbeeswarm_0.7.2
[39] fansi_1.0.6 abind_1.4-5
[41] lifecycle_1.0.4 yaml_2.3.8
[43] edgeR_4.0.16 SparseArray_1.2.4
[45] Rtsne_0.17 paletteer_1.6.0
[47] grid_4.3.3 blob_1.2.4
[49] promises_1.2.1 crayon_1.5.2
[51] miniUI_0.1.1.1 lattice_0.22-6
[53] beachmat_2.18.1 KEGGREST_1.42.0
[55] magick_2.8.3 pillar_1.9.0
[57] knitr_1.46 rjson_0.2.21
[59] future.apply_1.11.2 codetools_0.2-20
[61] leiden_0.4.3.1 glue_1.7.0
[63] vctrs_0.6.5 png_0.1-8
[65] spam_2.10-0 gtable_0.3.5
[67] rematch2_2.1.2 cachem_1.0.8
[69] xfun_0.43 S4Arrays_1.2.1
[71] mime_0.12 ggside_0.3.1
[73] survival_3.5-8 RcppHungarian_0.3
[75] iterators_1.0.14 fields_15.2
[77] statmod_1.5.0 interactiveDisplayBase_1.40.0
[79] fitdistrplus_1.1-11 ROCR_1.0-11
[81] nlme_3.1-164 bit64_4.0.5
[83] filelock_1.0.3 RcppAnnoy_0.0.22
[85] bslib_0.7.0 irlba_2.3.5.1
[87] vipor_0.4.7 KernSmooth_2.23-22
[89] colorspace_2.1-0 DBI_1.2.2
[91] tidyselect_1.2.1 bit_4.0.5
[93] compiler_4.3.3 curl_5.2.1
[95] BiocNeighbors_1.20.2 DelayedArray_0.28.0
[97] plotly_4.10.4 rtracklayer_1.62.0
[99] scales_1.3.0 lmtest_0.9-40
[101] rappdirs_0.3.3 stringr_1.5.1
[103] digest_0.6.35 goftest_1.2-3
[105] spatstat.utils_3.0-4 benchmarkmeData_1.0.4
[107] XVector_0.42.0 htmltools_0.5.8
[109] pkgconfig_2.0.3 sparseMatrixStats_1.14.0
[111] fastmap_1.1.1 rlang_1.1.3
[113] htmlwidgets_1.6.4 shiny_1.8.1.1
[115] DelayedMatrixStats_1.24.0 jquerylib_0.1.4
[117] zoo_1.8-12 jsonlite_1.8.8
[119] BiocParallel_1.36.0 mclust_6.1
[121] config_0.3.2 BiocSingular_1.18.0
[123] RCurl_1.98-1.14 magrittr_2.0.3
[125] GenomeInfoDbData_1.2.11 dotCall64_1.1-1
[127] patchwork_1.2.0 munsell_0.5.1
[129] Rcpp_1.0.12 viridis_0.6.5
[131] reticulate_1.35.0 leidenAlg_1.1.3
[133] stringi_1.8.3 zlibbioc_1.48.2
[135] MASS_7.3-60.0.1 plyr_1.8.9
[137] parallel_4.3.3 listenv_0.9.1
[139] ggrepel_0.9.5 deldir_2.0-4
[141] Biostrings_2.70.3 sccore_1.0.5
[143] splines_4.3.3 tensor_1.5
[145] locfit_1.5-9.9 igraph_2.0.3
[147] spatstat.geom_3.2-9 RcppHNSW_0.6.0
[149] reshape2_1.4.4 ScaledMatrix_1.10.0
[151] XML_3.99-0.16.1 BiocVersion_3.18.1
[153] golem_0.4.1 BiocManager_1.30.23
[155] foreach_1.5.2 httpuv_1.6.15
[157] RANN_2.6.1 tidyr_1.3.1
[159] purrr_1.0.2 polyclip_1.10-6
[161] future_1.33.2 benchmarkme_1.0.8
[163] scattermore_1.2 rsvd_1.0.5
[165] xtable_1.8-4 restfulr_0.0.15
[167] RSpectra_0.16-1 later_1.3.2
[169] viridisLite_0.4.2 tibble_3.2.1
[171] GenomicAlignments_1.38.2 memoise_2.0.1
[173] beeswarm_0.4.0 AnnotationDbi_1.64.1
[175] cluster_2.1.6 shinyWidgets_0.8.6
[177] globals_0.16.3

[lcolladotor]

Hm.... while trying to reproduce your issue I ran into Bioconductor/BiocFileCache#48 and re-opened that issue with this comment Bioconductor/BiocFileCache#48 (comment).

Try downloading the data manually from

spatialLIBD/R/fetch_data.R

Line 142 in f25860f

"https://www.dropbox.com/s/f4wcvtdq428y73p/Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata?dl=1"

. See #73 (comment) for more details.

[YikaiLou]

ok,I will see the comments, thank you very much!

[YikaiLou]

Hm.... while trying to reproduce your issue I ran into Bioconductor/BiocFileCache#48 and re-opened that issue with this comment Bioconductor/BiocFileCache#48 (comment).

Try downloading the data manually from

spatialLIBD/R/fetch_data.R

Line 142 in f25860f

"https://www.dropbox.com/s/f4wcvtdq428y73p/Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata?dl=1"

. See #73 (comment) for more details.

I have successfully imported the dataset, thank you very much!！

[lcolladotor]

Excellent!

[lcolladotor]

I know realize that this issue is the same one from #89 that is due to a bug in a dependency (csgillespie/benchmarkme#49).