SaveH5Seurat failing on example mouse bone marrow dataset

[GBeattie]

Hey! This issue is linked with the scVelo tutorial which uses seurat-disk.

I used the exact code form the tutorial and came across this error:

> SaveH5Seurat(bm, filename = "mouseBM.h5Seurat")
Creating h5Seurat file for version 3.1.5.9900
Error in attr$write(robj) : HDF5-API Errors:
    error #000: H5A.c in H5Awrite(): line 676: buf parameter can't be NULL
        class: HDF5
        major: Invalid arguments to routine
        minor: Bad value

Thanks in advance for any assistance!

sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
[1] SeuratWrappers_0.3.0  SeuratDisk_0.0.0.9015 Seurat_3.2.3         

loaded via a namespace (and not attached):
  [1] Rtsne_0.15            colorspace_1.4-1      deldir_0.1-29         ellipsis_0.3.1        ggridges_0.5.2       
  [6] rstudioapi_0.11       spatstat.data_1.4-3   leiden_0.3.3          listenv_0.8.0         remotes_2.2.0        
 [11] ggrepel_0.8.2         bit64_4.0.5           RSpectra_0.16-0       fansi_0.4.1           codetools_0.2-16     
 [16] splines_4.0.3         polyclip_1.10-0       jsonlite_1.7.1        ica_1.0-2             cluster_2.1.0        
 [21] png_0.1-7             uwot_0.1.10           shiny_1.5.0           sctransform_0.3.1     BiocManager_1.30.10  
 [26] compiler_4.0.3        httr_1.4.2            assertthat_0.2.1      SeuratObject_4.0.0    Matrix_1.2-18        
 [31] fastmap_1.0.1         lazyeval_0.2.2        cli_2.1.0             later_1.1.0.1         htmltools_0.5.1.1    
 [36] prettyunits_1.1.1     tools_4.0.3           rsvd_1.0.3            igraph_1.2.6          gtable_0.3.0         
 [41] glue_1.4.2            RANN_2.6.1            reshape2_1.4.4        dplyr_1.0.2           rappdirs_0.3.1       
 [46] tinytex_0.26          Rcpp_1.0.6            spatstat_1.64-1       Biobase_2.50.0        scattermore_0.7      
 [51] cellranger_1.1.0      vctrs_0.3.4           nlme_3.1-149          lmtest_0.9-38         xfun_0.18            
 [56] stringr_1.4.0         globals_0.13.1        ps_1.4.0              mime_0.9              miniUI_0.1.1.1       
 [61] lifecycle_0.2.0       irlba_2.3.3           goftest_1.2-2         future_1.19.1         MASS_7.3-53          
 [66] zoo_1.8-8             scales_1.1.1          pcaMethods_1.80.0     promises_1.1.1        spatstat.utils_1.17-0
 [71] parallel_4.0.3        RColorBrewer_1.1-2    reticulate_1.18       pbapply_1.4-3         gridExtra_2.3        
 [76] ggplot2_3.3.2         rpart_4.1-15          stringi_1.5.3         velocyto.R_0.6        BiocGenerics_0.36.0  
 [81] pkgbuild_1.1.0        rlang_0.4.10          pkgconfig_2.0.3       matrixStats_0.57.0    lattice_0.20-41      
 [86] ROCR_1.0-11           purrr_0.3.4           tensor_1.5            patchwork_1.0.1       htmlwidgets_1.5.2    
 [91] cowplot_1.1.0         bit_4.0.4             processx_3.4.4        tidyselect_1.1.0      RcppAnnoy_0.0.18     
 [96] plyr_1.8.6            magrittr_2.0.1        R6_2.5.0              generics_0.1.0        DBI_1.1.0            
[101] pillar_1.4.6          withr_2.3.0           mgcv_1.8-33           fitdistrplus_1.1-1    survival_3.2-7       
[106] abind_1.4-5           tibble_3.0.4          future.apply_1.6.0    crayon_1.3.4          hdf5r_1.3.3          
[111] KernSmooth_2.23-17    plotly_4.9.2.1        grid_4.0.3            readxl_1.3.1          data.table_1.13.2    
[116] callr_3.5.1           digest_0.6.27         xtable_1.8-4          tidyr_1.1.2           httpuv_1.5.4         
[121] munsell_0.5.0         viridisLite_0.3.0    

[webbedfeet]

Same error.

[YitengDang]

I have the same error as well. Any help would be appreciated!

[wang0430]

Same error.