SingleR-inc / celldex

Collection of cell type reference datasets.
https://bioconductor.org/packages/devel/data/experiment/html/celldex.html
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Can't load DICE #12

Closed f6v closed 2 years ago

f6v commented 2 years ago

I'm trying to use the DICE reference, however, there's an error when I'm trying to load it:

celldex::DatabaseImmuneCellExpressionData()
snapshotDate(): 2021-05-18
see ?celldex and browseVignettes('celldex') for documentation
loading from cache
Error: failed to load resource
  name: EH3488
  title: DICE RNA-seq logcounts
  reason: error reading from connection
Session info ```R R version 4.1.1 (2021-08-10) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 11.6 Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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] parallel stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] SingleR_1.6.1 celldex_1.2.0 pheatmap_1.0.12 ggpubr_0.4.0 [5] rstatix_0.7.0 scales_1.1.1 slingshot_2.1.1 TrajectoryUtils_1.0.0 [9] princurve_2.1.6 schex_1.6.3 shiny_1.7.1 SingleCellExperiment_1.14.1 [13] SummarizedExperiment_1.22.0 Biobase_2.52.0 GenomicRanges_1.44.0 GenomeInfoDb_1.28.4 [17] IRanges_2.26.0 S4Vectors_0.30.2 BiocGenerics_0.38.0 MatrixGenerics_1.4.3 [21] matrixStats_0.61.0 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7 [25] purrr_0.3.4 readr_2.0.2 tidyr_1.1.4 tibble_3.1.5 [29] ggplot2_3.3.5 tidyverse_1.3.1 SeuratObject_4.0.2 Seurat_4.0.5 loaded via a namespace (and not attached): [1] utf8_1.2.2 reticulate_1.22 tidyselect_1.1.1 [4] RSQLite_2.2.8 AnnotationDbi_1.54.1 htmlwidgets_1.5.4 [7] BiocParallel_1.26.2 grid_4.1.1 Rtsne_0.15 [10] ScaledMatrix_1.0.0 munsell_0.5.0 codetools_0.2-18 [13] ica_1.0-2 future_1.22.1 miniUI_0.1.1.1 [16] withr_2.4.2 colorspace_2.0-2 filelock_1.0.2 [19] knitr_1.36 rstudioapi_0.13 ROCR_1.0-11 [22] ggsignif_0.6.3 tensor_1.5 listenv_0.8.0 [25] GenomeInfoDbData_1.2.6 polyclip_1.10-0 farver_2.1.0 [28] bit64_4.0.5 parallelly_1.28.1 vctrs_0.3.8 [31] generics_0.1.0 xfun_0.27 BiocFileCache_2.0.0 [34] R6_2.5.1 rsvd_1.0.5 concaveman_1.1.0 [37] bitops_1.0-7 spatstat.utils_2.2-0 cachem_1.0.6 [40] DelayedArray_0.18.0 assertthat_0.2.1 promises_1.2.0.1 [43] gtable_0.3.0 beachmat_2.8.1 globals_0.14.0 [46] goftest_1.2-3 rlang_0.4.12 splines_4.1.1 [49] lazyeval_0.2.2 hexbin_1.28.2 spatstat.geom_2.3-0 [52] broom_0.7.9 BiocManager_1.30.16 yaml_2.2.1 [55] reshape2_1.4.4 abind_1.4-5 modelr_0.1.8 [58] backports_1.2.1 httpuv_1.6.3 tools_4.1.1 [61] ellipsis_0.3.2 spatstat.core_2.3-0 RColorBrewer_1.1-2 [64] ggridges_0.5.3 Rcpp_1.0.7 plyr_1.8.6 [67] sparseMatrixStats_1.4.2 zlibbioc_1.38.0 RCurl_1.98-1.5 [70] rpart_4.1-15 deldir_1.0-5 pbapply_1.5-0 [73] cowplot_1.1.1 zoo_1.8-9 haven_2.4.3 [76] ggrepel_0.9.1 cluster_2.1.2 fs_1.5.0 [79] magrittr_2.0.1 data.table_1.14.2 scattermore_0.7 [82] openxlsx_4.2.4 lmtest_0.9-38 reprex_2.0.1 [85] RANN_2.6.1 fitdistrplus_1.1-6 hms_1.1.1 [88] patchwork_1.1.1 mime_0.12 evaluate_0.14 [91] xtable_1.8-4 rio_0.5.27 readxl_1.3.1 [94] gridExtra_2.3 compiler_4.1.1 KernSmooth_2.23-20 [97] crayon_1.4.1 htmltools_0.5.2 entropy_1.3.1 [100] mgcv_1.8-38 later_1.3.0 tzdb_0.1.2 [103] lubridate_1.8.0 DBI_1.1.1 tweenr_1.0.2 [106] ExperimentHub_2.0.0 dbplyr_2.1.1 MASS_7.3-54 [109] rappdirs_0.3.3 car_3.0-11 Matrix_1.3-4 [112] cli_3.0.1 igraph_1.2.7 pkgconfig_2.0.3 [115] foreign_0.8-81 plotly_4.10.0 spatstat.sparse_2.0-0 [118] xml2_1.3.2 XVector_0.32.0 rvest_1.0.2 [121] digest_0.6.28 sctransform_0.3.2 RcppAnnoy_0.0.19 [124] spatstat.data_2.1-0 Biostrings_2.60.2 rmarkdown_2.11 [127] cellranger_1.1.0 leiden_0.3.9 uwot_0.1.10 [130] DelayedMatrixStats_1.14.3 curl_4.3.2 lifecycle_1.0.1 [133] nlme_3.1-153 jsonlite_1.7.2 BiocNeighbors_1.10.0 [136] carData_3.0-4 viridisLite_0.4.0 fansi_0.5.0 [139] pillar_1.6.4 lattice_0.20-45 KEGGREST_1.32.0 [142] fastmap_1.1.0 httr_1.4.2 survival_3.2-13 [145] interactiveDisplayBase_1.30.0 glue_1.4.2 zip_2.2.0 [148] png_0.1-7 BiocVersion_3.13.1 bit_4.0.4 [151] ggforce_0.3.3 stringi_1.7.5 blob_1.2.2 [154] BiocSingular_1.8.1 AnnotationHub_3.0.2 memoise_2.0.0 [157] irlba_2.3.3 future.apply_1.8.1 ```

Would appreciate any suggestions!

LTLA commented 2 years ago

I have no idea. Maybe your cached copy of the file was corrupted; try re-downloading it with:

library(ExperimentHub)
ExperimentHub()[["EH3488", force=TRUE]]