Can't load BlueprintEncodeData from ExperimentHub

[myushen]

Hi,

I get this error while trying to pull data from ExperimentHub by legacy = TRUE.

celldex::BlueprintEncodeData(legacy = TRUE)
snapshotDate(): 2024-04-29
see ?celldex and browseVignettes('celldex') for documentation
loading from cache
Error in DelayedArray:::.get_ans_type(x, must.be.numeric = FALSE) : 
  operation not supported on matrices of type character

The issue did not occur for MonacoImmuneData. Also, I had tried re-download the dataset

fetchReference("blueprint_encode", "2024-02-26", realize.assays = TRUE, overwrite = TRUE)

Thanks for you help!

[LTLA]

I can't reproduce this. I'll bet that you're using some out-of-date packages. For example, I have a different snapshot date when I try the same command:

celldex::BlueprintEncodeData(legacy=TRUE)
##   |======================================================================| 100%
## 
## snapshotDate(): 2024-09-13
## see ?celldex and browseVignettes('celldex') for documentation
## loading from cache
## see ?celldex and browseVignettes('celldex') for documentation
## loading from cache
## class: SummarizedExperiment 
## dim: 19859 259 
## metadata(0):
## assays(1): logcounts
## rownames(19859): TSPAN6 TNMD ... LINC00550 GIMAP1-GIMAP5
## rowData names(0):
## colnames(259): mature.neutrophil
##   CD14.positive..CD16.negative.classical.monocyte ...
##   epithelial.cell.of.umbilical.artery.1
##   dermis.lymphatic.vessel.endothelial.cell.1
## colData names(3): label.main label.fine label.ont

Your snapshot date suggests that you're using the previous BioC version... which should still have worked, but I don't have that installed anymore, so I can't test it easily.

FWIW fetchReference() also works fine for me:

fetchReference("blueprint_encode", "2024-02-26", realize.assays = TRUE, overwrite = TRUE)
## class: SummarizedExperiment 
## dim: 19859 259 
## metadata(0):
## assays(1): logcounts
## rownames(19859): TSPAN6 TNMD ... LINC00550 GIMAP1-GIMAP5
## rowData names(0):
## colnames(259): mature.neutrophil
##   CD14.positive..CD16.negative.classical.monocyte ...
##   epithelial.cell.of.umbilical.artery.1
##   dermis.lymphatic.vessel.endothelial.cell.1
## colData names(3): label.main label.fine label.ont

Session information

R version 4.4.0 Patched (2024-05-20 r86569)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.5 LTS

Matrix products: default
BLAS:   /home/luna/Software/R/R-4-4-branch/lib/libRblas.so 
LAPACK: /home/luna/Software/R/R-4-4-branch/lib/libRlapack.so;  LAPACK version 3.12.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: America/Los_Angeles
tzcode source: system (glibc)

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

other attached packages:
 [1] celldex_1.15.0              SummarizedExperiment_1.35.1
 [3] Biobase_2.65.1              GenomicRanges_1.57.1       
 [5] GenomeInfoDb_1.41.1         IRanges_2.39.2             
 [7] S4Vectors_0.43.2            BiocGenerics_0.51.1        
 [9] MatrixGenerics_1.17.0       matrixStats_1.4.1          

loaded via a namespace (and not attached):
 [1] KEGGREST_1.45.1           httr2_1.0.4              
 [3] rhdf5_2.49.0              lattice_0.22-6           
 [5] rhdf5filters_1.17.0       vctrs_0.6.5              
 [7] tools_4.4.0               generics_0.1.3           
 [9] parallel_4.4.0            curl_5.2.2               
[11] tibble_3.2.1              fansi_1.0.6              
[13] AnnotationDbi_1.67.0      RSQLite_2.3.7            
[15] blob_1.2.4                pkgconfig_2.0.3          
[17] Matrix_1.7-0              dbplyr_2.5.0             
[19] sparseMatrixStats_1.17.2  lifecycle_1.0.4          
[21] GenomeInfoDbData_1.2.12   compiler_4.4.0           
[23] Biostrings_2.73.1         alabaster.se_1.5.3       
[25] gypsum_1.1.6              alabaster.matrix_1.5.8   
[27] yaml_2.3.10               pillar_1.9.0             
[29] crayon_1.5.3              DelayedArray_0.31.11     
[31] cachem_1.1.0              abind_1.4-8              
[33] mime_0.12                 ExperimentHub_2.13.1     
[35] AnnotationHub_3.13.3      tidyselect_1.2.1         
[37] purrr_1.0.2               dplyr_1.1.4              
[39] BiocVersion_3.20.0        fastmap_1.2.0            
[41] grid_4.4.0                cli_3.6.3                
[43] SparseArray_1.5.34        magrittr_2.0.3           
[45] S4Arrays_1.5.7            utf8_1.2.4               
[47] alabaster.base_1.5.7      withr_3.0.1              
[49] DelayedMatrixStats_1.27.3 filelock_1.0.3           
[51] UCSC.utils_1.1.0          rappdirs_0.3.3           
[53] bit64_4.0.5               XVector_0.45.0           
[55] httr_1.4.7                bit_4.0.5                
[57] png_0.1-8                 HDF5Array_1.33.6         
[59] memoise_2.0.1             BiocFileCache_2.13.0     
[61] rlang_1.1.4               Rcpp_1.0.13              
[63] glue_1.7.0                DBI_1.2.3                
[65] BiocManager_1.30.25       alabaster.ranges_1.5.2   
[67] alabaster.schemas_1.5.0   jsonlite_1.8.8           
[69] Rhdf5lib_1.27.0           R6_2.5.1                 
[71] zlibbioc_1.51.1          

[myushen]

I am using the latest celldex Bioc version 1.14.0. Both MonacoImmuneData and BlueprintEncodeData caches the same data version 2024-02-26, however MonacoImmuneData did not produce the same error, which was odd.

This is the issue when I tried to fetchReference the latest data without upgrading the package to the BioC devel version.

fetchReference("blueprint_encode", "2024-09-13")
Error in save_file(bucket_path, destination = out, overwrite = overwrite,  : 
  failed to save 'celldex/blueprint_encode/2024-09-13/..manifest'; HTTP 404 Not Found.
• object not found

sessionInfo()

R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Red Hat Enterprise Linux 9.4 (Plow)

Matrix products: default
BLAS:   /stornext/System/data/software/rhel/9/base/tools/R/4.4.1/lib64/R/lib/libRblas.so 
LAPACK: /stornext/System/data/software/rhel/9/base/tools/R/4.4.1/lib64/R/lib/libRlapack.so;  LAPACK version 3.12.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Australia/Melbourne
tzcode source: system (glibc)

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

other attached packages:
 [1] HPCell_0.3.2                    ensembldb_2.28.0                AnnotationFilter_1.28.0         GenomicFeatures_1.56.0         
 [5] AnnotationDbi_1.66.0            jsonlite_1.8.8                  celldex_1.14.0                  stringr_1.5.1                  
 [9] tidyseurat_0.8.0                SeuratObject_5.0.2              sp_2.1-4                        ggplot2_3.5.1                  
[13] ttservice_0.4.0                 tidyr_1.3.1                     tidySingleCellExperiment_1.15.4 SingleCellExperiment_1.26.0    
[17] SummarizedExperiment_1.34.0     GenomicRanges_1.56.0            GenomeInfoDb_1.40.0             IRanges_2.38.0                 
[21] S4Vectors_0.42.1                MatrixGenerics_1.16.0           matrixStats_1.4.1               crew.cluster_0.3.1             
[25] crew_0.9.2                      tarchetypes_0.9.0               targets_1.7.1                   tibble_3.2.1                   
[29] magrittr_2.0.3                  dplyr_1.1.4                     testthat_3.2.1.1                Biobase_2.64.0                 
[33] BiocGenerics_0.50.0             shinyBS_0.61.1                 

loaded via a namespace (and not attached):
  [1] igraph_2.0.3                      ica_1.0-3                         plotly_4.10.4                    
  [4] SingleR_2.6.0                     scater_1.32.0                     devtools_2.4.5                   
  [7] zlibbioc_1.50.0                   tidyselect_1.2.1                  bit_4.0.5                        
 [10] doParallel_1.0.17                 clue_0.3-65                       lattice_0.22-6                   
 [13] rjson_0.2.23                      urlchecker_1.0.1                  blob_1.2.4                       
 [16] rngtools_1.5.2                    S4Arrays_1.4.0                    parallel_4.4.1                   
 [19] seqLogo_1.70.0                    png_0.1-8                         cli_3.6.3                        
 [22] registry_0.5-1                    ProtGenerics_1.36.0               goftest_1.2-3                    
 [25] gargle_1.5.2                      BiocIO_1.14.0                     bluster_1.14.0                   
 [28] purrr_1.0.2                       BiocNeighbors_1.22.0              ggnetwork_0.5.13                 
 [31] Signac_1.14.0                     uwot_0.2.2                        curl_5.2.2                       
 [34] mime_0.12                         leiden_0.4.3.1                    ComplexHeatmap_2.20.0            
 [37] stringi_1.8.4                     desc_1.4.3                        ids_1.0.1                        
 [40] backports_1.5.0                   XML_3.99-0.16.1                   httpuv_1.6.15                    
 [43] rappdirs_0.3.3                    splines_4.4.1                     CellChat_2.1.2                   
 [46] RcppRoll_0.3.1                    nanonext_1.2.1                    RApiSerialize_0.1.3              
 [49] DT_0.33                           sctransform_0.4.1                 ggbeeswarm_0.7.2                 
 [52] sessioninfo_1.2.2                 HDF5Array_1.32.1                  DBI_1.2.3                        
 [55] jquerylib_0.1.4                   withr_3.0.1                       systemfonts_1.0.6                
 [58] rprojroot_2.0.4                   xgboost_1.7.7.1                   tidySummarizedExperiment_1.14.0  
 [61] lmtest_0.9-40                     brio_1.1.5                        BiocManager_1.30.25              
 [64] rtracklayer_1.64.0                htmlwidgets_1.6.4                 fs_1.6.4                         
 [67] biomaRt_2.60.0                    ggrepel_0.9.6                     statnet.common_4.9.0             
 [70] SparseArray_1.4.3                 cellranger_1.1.0                  annotate_1.82.0                  
 [73] reticulate_1.39.0                 zoo_1.8-12                        JASPAR2020_0.99.10               
 [76] XVector_0.44.0                    knitr_1.46                        network_1.18.2                   
 [79] TFBSTools_1.42.0                  UCSC.utils_1.0.0                  TFMPvalue_0.0.9                  
 [82] secretbase_1.0.2                  foreach_1.5.2                     fansi_1.0.6                      
 [85] patchwork_1.3.0                   caTools_1.18.2                    grid_4.4.1                       
 [88] data.table_1.16.0                 rhdf5_2.48.0                      pwalign_1.0.0                    
 [91] R.oo_1.26.0                       poweRlaw_0.80.0                   RSpectra_0.16-1                  
 [94] irlba_2.3.5.1                     gridGraphics_0.5-1                alabaster.schemas_1.4.0          
 [97] fastDummies_1.7.3                 ellipsis_0.3.2                    base64url_1.4                    
[100] lazyeval_0.2.2                    yaml_2.3.8                        survival_3.7-0                   
[103] scattermore_1.2                   BiocVersion_3.19.1                crayon_1.5.3                     
[106] mirai_1.0.0                       RcppAnnoy_0.0.22                  RColorBrewer_1.1-3               
[109] progressr_0.14.0                  later_1.3.2                       profvis_0.3.8                    
[112] tidybulk_1.17.3                   ggridges_0.5.6                    codetools_0.2-20                 
[115] GlobalOptions_0.1.2               Seurat_5.0.0                      KEGGREST_1.44.0                  
[118] Rtsne_0.17                        shape_1.4.6.1                     limma_3.60.4                     
[121] filelock_1.0.3                    Rsamtools_2.20.0                  pkgconfig_2.0.3                  
[124] xml2_1.3.6                        ggpubr_0.6.0                      GenomicAlignments_1.40.0         
[127] alabaster.base_1.4.2              spatstat.sparse_3.0-3             BSgenome_1.72.0                  
[130] viridisLite_0.4.2                 gridBase_0.4-7                    xtable_1.8-4                     
[133] car_3.1-2                         plyr_1.8.9                        httr_1.4.7                       
[136] tools_4.4.1                       globals_0.16.3                    pkgbuild_1.4.4                   
[139] beeswarm_0.4.0                    broom_1.0.5                       nlme_3.1-166                     
[142] ExperimentHub_2.12.0              dbplyr_2.5.0                      hdf5r_1.3.11                     
[145] shinyjs_2.1.0                     lme4_1.1-35.3                     digest_0.6.37                    
[148] Matrix_1.7-0                      tzdb_0.4.0                        reshape2_1.4.4                   
[151] viridis_0.6.5                     DirichletMultinomial_1.44.0       BiocFileCache_2.12.0             
[154] glue_1.7.0                        cachem_1.0.8                      polyclip_1.10-7                  
[157] generics_0.1.3                    Biostrings_2.72.0                 ggalluvial_0.12.5                
[160] googledrive_2.1.1                 presto_1.0.0                      parallelly_1.38.0                
[163] pkgload_1.4.0                     statmod_1.5.0                     here_1.0.1                       
[166] RcppHNSW_0.6.0                    ScaledMatrix_1.12.0               minqa_1.2.8                      
[169] carData_3.0-5                     pbapply_1.7-2                     httr2_1.0.1                      
[172] vroom_1.6.5                       spam_2.10-0                       dqrng_0.4.1                      
[175] utf8_1.2.4                        scDblFinder_1.18.0                gtools_3.9.5                     
[178] preprocessCore_1.66.0             alabaster.se_1.4.0                ggsignif_0.6.4                   
[181] gridExtra_2.3                     shiny_1.8.1.1                     GenomeInfoDbData_1.2.12          
[184] R.utils_2.12.3                    rhdf5filters_1.16.0               RCurl_1.98-1.14                  
[187] memoise_2.0.1                     scales_1.3.0                      R.methodsS3_1.8.2                
[190] googlesheets4_1.1.1               gypsum_1.0.1                      svglite_2.1.3                    
[193] future_1.33.2                     RANN_2.6.2                        stringfish_0.16.0                
[196] spatstat.data_3.0-4               rstudioapi_0.16.0                 cluster_2.1.6                    
[199] spatstat.utils_3.0-5              hms_1.1.3                         fitdistrplus_1.2-1               
[202] munsell_0.5.1                     cowplot_1.1.3                     colorspace_2.1-1                 
[205] FNN_1.1.4                         rlang_1.1.4                       DelayedMatrixStats_1.26.0        
[208] sparseMatrixStats_1.16.0          dotCall64_1.1-1                   shinydashboard_0.7.2             
[211] circlize_0.4.16                   scuttle_1.14.0                    xfun_0.43                        
[214] alabaster.matrix_1.4.0            coda_0.19-4.1                     sna_2.8                          
[217] CNEr_1.40.0                       remotes_2.5.0                     iterators_1.0.14                 
[220] abind_1.4-8                       EnsDb.Hsapiens.v86_2.99.0         Rhdf5lib_1.26.0                  
[223] readr_2.1.5                       bitops_1.0-8                      ps_1.8.0                         
[226] promises_1.3.0                    RSQLite_2.3.6                     getip_0.1-4                      
[229] DelayedArray_0.30.1               GO.db_3.19.1                      compiler_4.4.1                   
[232] alabaster.ranges_1.4.0            prettyunits_1.2.0                 boot_1.3-30                      
[235] beachmat_2.20.0                   listenv_0.9.1                     BSgenome.Hsapiens.UCSC.hg38_1.4.5
[238] Rcpp_1.0.13                       AnnotationHub_3.12.0              edgeR_4.2.0                      
[241] BiocSingular_1.20.0               tensor_1.5                        usethis_2.2.3                    
[244] progress_1.2.3                    qs_0.26.1                         MASS_7.3-61                      
[247] uuid_1.2-0                        BiocParallel_1.38.0               ggupset_0.4.0                    
[250] spatstat.random_3.2-3             R6_2.5.1                          Azimuth_0.5.0                    
[253] fastmap_1.2.0                     fastmatch_1.1-4                   rstatix_0.7.2                    
[256] vipor_0.4.7                       ROCR_1.0-11                       SeuratDisk_0.0.0.9021            
[259] rsvd_1.0.5                        gtable_0.3.5                      KernSmooth_2.23-24               
[262] miniUI_0.1.1.1                    deldir_2.0-4                      htmltools_0.5.8.1                
[265] RcppParallel_5.1.9                bit64_4.0.5                       spatstat.explore_3.2-7           
[268] lifecycle_1.0.4                   processx_3.8.4                    nloptr_2.1.1                     
[271] callr_3.7.6                       restfulr_0.0.15                   sass_0.4.9                       
[274] vctrs_0.6.5                       spatstat.geom_3.2-9               scran_1.32.0                     
[277] NMF_0.27                          SeuratData_0.2.2.9001             future.apply_1.11.2              
[280] pracma_2.4.4                      bslib_0.7.0                       pillar_1.9.0                     
[283] DropletUtils_1.24.0               metapod_1.12.0                    locfit_1.5-9.10                  
[286] GetoptLong_1.0.5 

[LTLA]

The "date" in fetchReference() is a version number that refers to the upload date for that dataset, not the current date. Valid options for each reference are obtained with:

celldex::surveyReferences()

Both Blueprint and Monaco work fine for me with the correct version:

celldex::fetchReference("blueprint_encode", "2024-02-26")
## class: SummarizedExperiment
## dim: 19859 259
## metadata(0):
## assays(1): logcounts
## rownames(19859): TSPAN6 TNMD ... LINC00550 GIMAP1-GIMAP5
## rowData names(0):
## colnames(259): mature.neutrophil
##   CD14.positive..CD16.negative.classical.monocyte ...
##   epithelial.cell.of.umbilical.artery.1
##   dermis.lymphatic.vessel.endothelial.cell.1
## colData names(3): label.main label.fine label.ont

celldex::fetchReference("monaco_immune", "2024-02-26")
## class: SummarizedExperiment
## dim: 46077 114
## metadata(0):
## assays(1): logcounts
## rownames(46077): A1BG A1BG-AS1 ... ZYX ZZEF1
## rowData names(0):
## colnames(114): DZQV_CD8_naive DZQV_CD8_CM ... G4YW_Neutrophils
##   G4YW_Basophils
## colData names(3): label.main label.fine label.ont

I suggest you try these commands in a fresh R session.