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massonix / HCATonsilData

Provide programmatic access to the tonsil cell atlas datasets
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Problem with processed counts GCBC #3

Open massonix opened 2 years ago

massonix commented 2 years ago

Installing GCBC with processedCounts =TRUE gives the following error:

gcbc <- HCATonsilData(assayType = "RNA", cellType = "GCBC", processedCounts = TRUE)
snapshotDate(): 2022-04-26
see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation
loading from cache
see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation
loading from cache
see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation
loading from cache
see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation
loading from cache
see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation
loading from cache
see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation
loading from cache
see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation
loading from cache
Error in H5Fopen(filepath, flags = "H5F_ACC_RDONLY") : 
  HDF5. File accessibility. Unable to open file.

Which doesn't happen with processedCounts = FALSE. Need to look in depth for future versions

federicomarini commented 2 years ago

FWIW, this works "perfectly fine" on my machine. Which, in turn, makes the whole thing a little more puzzling...

Code and session info ``` > gcbc <- HCATonsilData::HCATonsilData(assayType = "RNA", cellType = "GCBC", processedCounts = TRUE) |=====================================================================================| 100% snapshotDate(): 2022-04-26 see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation downloading 1 resources retrieving 1 resource |=====================================================================================| 100% loading from cache see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation downloading 1 resources retrieving 1 resource |=====================================================================================| 100% loading from cache see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation downloading 1 resources retrieving 1 resource |=====================================================================================| 100% loading from cache see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation downloading 1 resources retrieving 1 resource |=====================================================================================| 100% loading from cache see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation downloading 1 resources retrieving 1 resource |=====================================================================================| 100% loading from cache see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation downloading 1 resources retrieving 1 resource |=====================================================================================| 100% loading from cache see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation downloading 1 resources retrieving 1 resource |=====================================================================================| 100% loading from cache > gcbc class: SingleCellExperiment dim: 37378 72174 metadata(0): assays(2): counts logcounts rownames(37378): AL627309.1 AL627309.3 ... AC136616.1 AC023491.2 rowData names(3): gene_name highly_variable gene_id colnames(72174): bw94nf57_vm85woki_AAACCCAAGAGGCCAT-1 bw94nf57_vm85woki_AAACCCAAGATTGCGG-1 ... bs2e7lr7_mdfwypvz_TTTGACCGTACCCACC-1 bs2e7lr7_mdfwypvz_TTTGTCTAGCAAGGAC-1 colData names(30): barcode donor_id ... UMAP_1_20220215 UMAP_2_20220215 reducedDimNames(3): PCA UMAP HARMONY mainExpName: NULL altExpNames(0): > sessionInfo() R version 4.2.0 (2022-04-22) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Monterey 12.3.1 Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.2/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] stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] shinydashboard_0.7.2 shinyAce_0.4.2 dplyr_1.0.9 [4] rhdf5_2.40.0 HCATonsilData_0.0.0.9000 scran_1.24.0 [7] scater_1.24.0 ggplot2_3.3.6 scuttle_1.6.2 [10] scRNAseq_2.10.0 SingleCellExperiment_1.18.0 SummarizedExperiment_1.26.1 [13] Biobase_2.56.0 GenomicRanges_1.48.0 GenomeInfoDb_1.32.2 [16] IRanges_2.30.0 S4Vectors_0.34.0 BiocGenerics_0.42.0 [19] MatrixGenerics_1.8.0 matrixStats_0.62.0 shiny_1.7.1 loaded via a namespace (and not attached): [1] utf8_1.2.2 ggstance_0.3.5 tidyselect_1.1.2 [4] RSQLite_2.2.14 AnnotationDbi_1.58.0 htmlwidgets_1.5.4 [7] grid_4.2.0 BiocParallel_1.30.2 munsell_0.5.0 [10] ScaledMatrix_1.4.0 statmod_1.4.36 DT_0.23 [13] withr_2.5.0 colorspace_2.0-3 filelock_1.0.2 [16] knitr_1.39 rstudioapi_0.13 labeling_0.4.2 [19] GenomeInfoDbData_1.2.8 polyclip_1.10-0 bit64_4.0.5 [22] farver_2.1.0 vctrs_0.4.1 generics_0.1.2 [25] xfun_0.31 geepack_1.3.3 BiocFileCache_2.4.0 [28] R6_2.5.1 ggbeeswarm_0.6.0 rsvd_1.0.5 [31] locfit_1.5-9.5 AnnotationFilter_1.20.0 bitops_1.0-7 [34] rhdf5filters_1.8.0 cachem_1.0.6 DelayedArray_0.22.0 [37] assertthat_0.2.1 promises_1.2.0.1 BiocIO_1.6.0 [40] scales_1.2.0 beeswarm_0.4.0 gtable_0.3.0 [43] beachmat_2.12.0 ensembldb_2.20.1 rlang_1.0.2 [46] rtracklayer_1.56.0 lazyeval_0.2.2 mosaicCore_0.9.0 [49] broom_0.8.0 BiocManager_1.30.18 yaml_2.3.5 [52] GenomicFeatures_1.48.1 crosstalk_1.2.0 backports_1.4.1 [55] httpuv_1.6.5 rsconnect_0.8.25 tools_4.2.0 [58] ellipsis_0.3.2 jquerylib_0.1.4 geeM_0.10.1 [61] ggformula_0.10.1 ggridges_0.5.3 Rcpp_1.0.8.3 [64] plyr_1.8.7 sparseMatrixStats_1.8.0 progress_1.2.2 [67] zlibbioc_1.42.0 purrr_0.3.4 RCurl_1.98-1.6 [70] prettyunits_1.1.1 viridis_0.6.2 cowplot_1.1.1 [73] fontawesome_0.2.2 haven_2.5.0 ggrepel_0.9.1 [76] cluster_2.1.3 magrittr_2.0.3 ProtGenerics_1.28.0 [79] hms_1.1.1 mime_0.12 evaluate_0.15 [82] xtable_1.8-4 XML_3.99-0.9 gridExtra_2.3 [85] compiler_4.2.0 biomaRt_2.52.0 tibble_3.1.7 [88] crayon_1.5.1 htmltools_0.5.2 later_1.3.0 [91] tidyr_1.2.0 DBI_1.1.2 tweenr_1.0.2 [94] ExperimentHub_2.4.0 dbplyr_2.1.1 MASS_7.3-57 [97] rappdirs_0.3.3 Matrix_1.4-1 cli_3.3.0 [100] parallel_4.2.0 metapod_1.4.0 igraph_1.3.1 [103] forcats_0.5.1 pkgconfig_2.0.3 GenomicAlignments_1.32.0 [106] xml2_1.3.3 vipor_0.4.5 bslib_0.3.1 [109] dqrng_0.3.0 labelle_0.0.0.9000 XVector_0.36.0 [112] stringr_1.4.0 digest_0.6.29 Biostrings_2.64.0 [115] rmarkdown_2.14 edgeR_3.38.1 DelayedMatrixStats_1.18.0 [118] MESS_0.5.7 restfulr_0.0.13 curl_4.3.2 [121] Rsamtools_2.12.0 rjson_0.2.21 lifecycle_1.0.1 [124] jsonlite_1.8.0 Rhdf5lib_1.18.2 BiocNeighbors_1.14.0 [127] viridisLite_0.4.0 limma_3.52.1 fansi_1.0.3 [130] labelled_2.9.1 pillar_1.7.0 lattice_0.20-45 [133] KEGGREST_1.36.0 fastmap_1.1.0 httr_1.4.3 [136] interactiveDisplayBase_1.34.0 glue_1.6.2 png_0.1-7 [139] bluster_1.6.0 BiocVersion_3.15.2 bit_4.0.4 [142] ggforce_0.3.3 stringi_1.7.6 sass_0.4.1 [145] HDF5Array_1.24.0 blob_1.2.3 BiocSingular_1.12.0 [148] AnnotationHub_3.4.0 memoise_2.0.1 irlba_2.3.5 ```