Problem with processed counts GCBC

[massonix]

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]

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