tomyputw
commented
4 months ago DICE <- celldex::DatabaseImmuneCellExpressionData() Error in method(object) : object 'validate_dim_slot' not found rlang::last_trace() Error: Can't show last error because no error was recorded yet sessionInfo() R version 4.3.0 (2023-04-21 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 17763)
Matrix products: default
locale: [1] LC_COLLATE=Chinese (Simplified)_China.936 LC_CTYPE=Chinese (Simplified)_China.936 LC_MONETARY=Chinese (Simplified)_China.936 [4] LC_NUMERIC=C LC_TIME=Chinese (Simplified)_China.936
time zone: Asia/Shanghai tzcode source: internal
attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base
other attached packages: [1] DelayedArray_0.30.1 SparseArray_1.2.4 S4Arrays_1.4.1 abind_1.4-5 IRanges_2.38.0 S4Vectors_0.42.0 MatrixGenerics_1.16.0 [8] matrixStats_1.2.0 BiocGenerics_0.48.1 Matrix_1.6-5
loaded via a namespace (and not attached):
[1] RcppAnnoy_0.0.22 splines_4.3.0 later_1.3.2 bitops_1.0-7 filelock_1.0.3
[6] tibble_3.2.1 polyclip_1.10-6 fastDummies_1.7.3 httr2_1.0.0 lifecycle_1.0.4
[11] globals_0.16.3 lattice_0.22-6 MASS_7.3-60.0.1 alabaster.base_1.4.1 magrittr_2.0.3
[16] plotly_4.10.4 yaml_2.3.8 httpuv_1.6.14 Seurat_5.0.3 sctransform_0.4.1
[21] spam_2.10-0 sp_2.1-3 spatstat.sparse_3.0-3 reticulate_1.35.0 cowplot_1.1.3
[26] pbapply_1.7-2 DBI_1.2.2 RColorBrewer_1.1-3 zlibbioc_1.40.0 Rtsne_0.17
[31] GenomicRanges_1.54.1 purrr_1.0.2 RCurl_1.98-1.14 rappdirs_0.3.3 GenomeInfoDbData_1.2.7
[36] ggrepel_0.9.5 irlba_2.3.5.1 listenv_0.9.1 spatstat.utils_3.0-4 goftest_1.2-3
[41] RSpectra_0.16-1 spatstat.random_3.2-3 fitdistrplus_1.1-11 parallelly_1.37.1 DelayedMatrixStats_1.24.0
[46] leiden_0.4.3.1 codetools_0.2-19 tidyselect_1.2.1 BiocFileCache_2.10.1 spatstat.explore_3.2-7
[51] jsonlite_1.8.8 ellipsis_0.3.2 progressr_0.14.0 ggridges_0.5.6 survival_3.5-8
[56] tools_4.3.0 ica_1.0-3 Rcpp_1.0.12 glue_1.7.0 gridExtra_2.3
[61] GenomeInfoDb_1.38.8 HDF5Array_1.22.1 gypsum_1.0.1 dplyr_1.1.4 withr_3.0.0
[66] BiocManager_1.30.23 fastmap_1.1.1 rhdf5filters_1.16.0 fansi_1.0.6 digest_0.6.35
[71] R6_2.5.1 mime_0.12 colorspace_2.1-0 scattermore_1.2 tensor_1.5
[76] spatstat.data_3.0-4 RSQLite_2.3.5 celldex_1.14.0 utf8_1.2.4 tidyr_1.3.1
[81] generics_0.1.3 data.table_1.15.2 httr_1.4.7 htmlwidgets_1.6.4 uwot_0.1.16
[86] pkgconfig_2.0.3 gtable_0.3.5 blob_1.2.4 lmtest_0.9-40 XVector_0.34.0
[91] htmltools_0.5.8 dotCall64_1.1-1 alabaster.matrix_1.4.0 SeuratObject_5.0.1 scales_1.3.0
[96] Biobase_2.62.0 png_0.1-8 rstudioapi_0.16.0 reshape2_1.4.4 nlme_3.1-164
[101] curl_5.2.1 cachem_1.0.8 zoo_1.8-12 rhdf5_2.48.0 stringr_1.5.1
[106] BiocVersion_3.18.1 KernSmooth_2.23-22 parallel_4.3.0 miniUI_0.1.1.1 AnnotationDbi_1.64.1
[111] pillar_1.9.0 grid_4.3.0 alabaster.schemas_1.4.0 vctrs_0.6.5 RANN_2.6.1
[116] promises_1.2.1 dbplyr_2.5.0 xtable_1.8-4 cluster_2.1.6 cli_3.6.2
[121] compiler_4.3.0 rlang_1.1.3 crayon_1.5.2 future.apply_1.11.1 plyr_1.8.9
[126] stringi_1.8.3 alabaster.se_1.4.1 viridisLite_0.4.2 deldir_2.0-4 munsell_0.5.1
[131] Biostrings_2.70.3 lazyeval_0.2.2 spatstat.geom_3.2-9 ExperimentHub_2.10.0 RcppHNSW_0.6.0
[136] patchwork_1.2.0 sparseMatrixStats_1.16.0 bit64_4.0.5 future_1.33.1 ggplot2_3.5.0
[141] Rhdf5lib_1.16.0 KEGGREST_1.34.0 shiny_1.8.0 alabaster.ranges_1.4.1 SummarizedExperiment_1.24.0
[146] interactiveDisplayBase_1.32.0 AnnotationHub_3.10.0 ROCR_1.0-11 igraph_2.0.3 memoise_2.0.1
[151] bit_4.0.5
DICE <- celldex::DatabaseImmuneCellExpressionData() Error in method(object) : object 'validate_dim_slot' not found traceback() 21: method(object) 20: validityMethod(object) 19: isTRUE(x) 18: anyStrings(validityMethod(object)) 17: validObject(.Object) 16: initialize(value, ...) 15: initialize(value, ...) 14: new(...) 13: new2("HDF5ArraySeed", filepath = filepath, name = name, as_sparse = as.sparse, type = type, dim = dim, chunkdim = chunkdim, first_val = first_val) 12: HDF5ArraySeed(filepath, name, as.sparse = as.sparse, type = type) 11: HDF5Array(filepath = fpath, name = "dense_array/data") 10: meth(path, metadata = metadata, ...) 9: readObject(path, metadata = metadata, celldex.realize.assays = celldex.realize.assays, ...) 8: FUN(...) 7: altReadObject(file.path(path, "assays", y - 1L), ...) 6: meth(path, metadata = metadata, ...) 5: readObject(path, metadata = metadata, celldex.realize.assays = celldex.realize.assays, ...) 4: FUN(...) 3: altReadObject(obj_path, celldex.realize.assays = realize.assays, ...) 2: fetchReference("dice", "2024-02-26", realize.assays = TRUE) 1: celldex::DatabaseImmuneCellExpressionData()
I check the code and comfirm that validate_dim_slot is not a function of celldex. Actually I should not ask here but I try a lot and could not solve it.
I use MatrixGenerics 1.16 celldex 1.14 S4Arrays 1.4.1 S4Vectors 0.42.0