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Can't load BlueprintEncodeData from ExperimentHub
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!
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 I'll bet that you're using some out-of-date packages.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
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
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.