Unable to reproduce the example Convert AnnData to Seurat

[lldelisle]

Hello, I tried to reproduce the example you provided in: https://mojaveazure.github.io/seurat-disk/articles/convert-anndata.html#converting-from-anndata-to-seurat-via-h5seurat

> library(SeuratDisk)
> url <- "https://seurat.nygenome.org/pbmc3k_final.h5ad"
> curl::curl_download(url, basename(url))
> Convert("pbmc3k_final.h5ad", dest = "h5seurat", overwrite = TRUE)
Warning: Unknown file type: h5ad
Warning: 'assay' not set, setting to 'RNA'
Creating h5Seurat file for version 3.1.5.9900
Adding X as scale.data
Adding raw/X as data
Adding raw/X as counts
Adding meta.features from raw/var
Adding dispersions from scaled feature-level metadata
Adding dispersions_norm from scaled feature-level metadata
Merging gene_ids from scaled feature-level metadata
Adding highly_variable from scaled feature-level metadata
Adding means from scaled feature-level metadata
Merging n_cells from scaled feature-level metadata
Error in dfile$obj_copy_from(src_loc = source, src_name = "obs", dst_name = "meta.data") : 
  HDF5-API Errors:
    error #000: H5Ocopy.c in H5Ocopy(): line 251: unable to copy object
        class: HDF5
        major: Object header
        minor: Unable to copy object

    error #001: H5VLcallback.c in H5VL_object_copy(): line 5530: object copy failed
        class: HDF5
        major: Virtual Object Layer
        minor: Unable to copy object

    error #002: H5VLcallback.c in H5VL__object_copy(): line 5491: object copy failed
        class: HDF5
        major: Virtual Object Layer
        minor: Unable to copy object

    error #003: H5VLnative_object.c in H5VL__native_object_copy(): line 126: unable to copy object
        class: HDF5
        major: Symbol table
        minor: Unable to copy object

    error #004: H5Ocopy.c in H5O_copy(): line 313: unable to copy object
        class: HDF5
        major: Object header
        minor: Unable to copy object

    error #005: H5Ocopy.c in H5O__copy_obj(): line 1217: unable to copy object
        class: HDF5
        major
Error in private$closeFun(id) : HDF5-API Errors:
    error #000: H5F.c in H5Fclose(): line 886: decrementing file ID failed
        class: HDF5
        major: Object atom
        minor: Unable to close file

    error #001: H5I.c in H5I_dec_app_ref(): line 1422: can't decrement ID ref count
        class: HDF5
        major: Object atom
        minor: Unable to decrement reference count

    error #002: H5F.c in H5F__close_cb(): line 243: unable to close file
        class: HDF5
        major: File accessibility
        minor: Unable to close file

    error #003: H5VLcallback.c in H5VL_file_close(): line 3977: file close failed
        class: HDF5
        major: Virtual Object Layer
        minor: Unable to close file

    error #004: H5VLcallback.c in H5VL__file_close(): line 3945: file close failed
        class: HDF5
        major: Virtual Object Layer
        minor: Unable to close file

    error #005: H5VLnative_file.c in H5VL__native_file_close(): line 884: can't close file
        class: HDF5
     
> sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Arch Linux

Matrix products: default
BLAS:   /usr/lib/libblas.so.3.9.1
LAPACK: /usr/lib/liblapack.so.3.9.1

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       

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

other attached packages:
[1] SeuratDisk_0.0.0.9019

loaded via a namespace (and not attached):
  [1] nlme_3.1-152         matrixStats_0.58.0   bit64_4.0.5         
  [4] RcppAnnoy_0.0.18     RColorBrewer_1.1-2   httr_1.4.2          
  [7] sctransform_0.3.2    tools_4.0.5          R6_2.5.0            
 [10] irlba_2.3.3          rpart_4.1-15         KernSmooth_2.23-18  
 [13] uwot_0.1.10          mgcv_1.8-34          DBI_1.1.1           
 [16] lazyeval_0.2.2       colorspace_2.0-0     withr_2.4.1         
 [19] tidyselect_1.1.0     gridExtra_2.3        curl_4.3            
 [22] bit_4.0.4            compiler_4.0.5       cli_2.3.0           
 [25] hdf5r_1.3.3          plotly_4.9.3         Seurat_4.0.0        
 [28] scales_1.1.1         lmtest_0.9-38        spatstat.data_2.1-0 
 [31] ggridges_0.5.3       pbapply_1.4-3        spatstat_1.64-1     
 [34] goftest_1.2-2        stringr_1.4.0        digest_0.6.27       
 [37] spatstat.utils_2.1-0 pkgconfig_2.0.3      htmltools_0.5.1.1   
 [40] parallelly_1.23.0    fastmap_1.1.0        htmlwidgets_1.5.3   
 [43] rlang_0.4.10         shiny_1.6.0          generics_0.1.0      
 [46] zoo_1.8-8            jsonlite_1.7.2       ica_1.0-2           
 [49] dplyr_1.0.4          magrittr_2.0.1       patchwork_1.1.1     
 [52] Matrix_1.3-2         Rcpp_1.0.6           munsell_0.5.0       
 [55] abind_1.4-5          reticulate_1.18      lifecycle_1.0.0     
 [58] stringi_1.5.3        MASS_7.3-53.1        Rtsne_0.15          
 [61] plyr_1.8.6           grid_4.0.5           parallel_4.0.5      
 [64] listenv_0.8.0        promises_1.2.0.1     ggrepel_0.9.1       
 [67] crayon_1.4.1         miniUI_0.1.1.1       deldir_0.2-10       
 [70] lattice_0.20-41      cowplot_1.1.1        splines_4.0.5       
 [73] tensor_1.5           pillar_1.4.7         igraph_1.2.6        
 [76] future.apply_1.7.0   reshape2_1.4.4       codetools_0.2-18    
 [79] leiden_0.3.7         glue_1.4.2           SeuratObject_4.0.0  
 [82] data.table_1.13.6    vctrs_0.3.6          png_0.1-7           
 [85] httpuv_1.5.5         gtable_0.3.0         RANN_2.6.1          
 [88] purrr_0.3.4          polyclip_1.10-0      tidyr_1.1.2         
 [91] scattermore_0.7      future_1.21.0        assertthat_0.2.1    
 [94] ggplot2_3.3.3        mime_0.10            xtable_1.8-4        
 [97] later_1.1.0.1        survival_3.2-10      viridisLite_0.3.0   
[100] tibble_3.0.6         cluster_2.1.1        globals_0.14.0      
[103] fitdistrplus_1.1-3   ellipsis_0.3.1       ROCR_1.0-11         

[alevax]

Hi, I get the very same error.