Can't load DICE
f6v opened this issue · comments
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 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!
I have no idea. Maybe your cached copy of the file was corrupted; try re-downloading it with:
library(ExperimentHub)
ExperimentHub()[["EH3488", force=TRUE]]