Error in saveHDF5SummarizedExperiment

[fernandafranca]

Hello, I am encoutering an error when trying to use saveHDF5SummarizedExperiment.

> saveHDF5SummarizedExperiment (se, dir = "GSE205037/files") -> h5se
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'type': attempt to set an attribute on NULL
In addition: Warning message:
Layer ‘NA’ is empty 

I haven't found anyone reporting this error for this function so I'm pretty lost as to what I might me doing wrong. Thoughts?

> sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.3.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

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

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] HDF5Array_1.30.0            rhdf5_2.46.1                DelayedArray_0.28.0         SparseArray_1.2.3          
 [5] S4Arrays_1.2.0              abind_1.4-5                 Matrix_1.6-5                SeuratDisk_0.0.0.9021      
 [9] scran_1.30.2                scuttle_1.12.0              SingleCellExperiment_1.24.0 SummarizedExperiment_1.32.0
[13] Biobase_2.62.0              GenomicRanges_1.54.1        GenomeInfoDb_1.38.5         IRanges_2.36.0             
[17] S4Vectors_0.40.2            BiocGenerics_0.48.1         MatrixGenerics_1.14.0       matrixStats_1.2.0          
[21] Seurat_5.0.1                SeuratObject_5.0.1          sp_2.1-3                    lubridate_1.9.3            
[25] forcats_1.0.0               stringr_1.5.1               dplyr_1.1.4                 purrr_1.0.2                
[29] readr_2.1.5                 tidyr_1.3.1                 tibble_3.2.1                ggplot2_3.4.4              
[33] tidyverse_2.0.0            

loaded via a namespace (and not attached):
  [1] RcppAnnoy_0.0.22          splines_4.3.2             later_1.3.2               bitops_1.0-7             
  [5] polyclip_1.10-6           fastDummies_1.7.3         lifecycle_1.0.4           edgeR_4.0.14             
  [9] hdf5r_1.3.9               globals_0.16.2            lattice_0.22-5            MASS_7.3-60.0.1          
 [13] magrittr_2.0.3            limma_3.58.1              plotly_4.10.4             metapod_1.10.1           
 [17] httpuv_1.6.14             sctransform_0.4.1         spam_2.10-0               spatstat.sparse_3.0-3    
 [21] reticulate_1.35.0         cowplot_1.1.3             pbapply_1.7-2             RColorBrewer_1.1-3       
 [25] pkgload_1.3.4             zlibbioc_1.48.0           Rtsne_0.17                RCurl_1.98-1.14          
 [29] GenomeInfoDbData_1.2.11   ggrepel_0.9.5             irlba_2.3.5.1             listenv_0.9.1            
 [33] spatstat.utils_3.0-4      goftest_1.2-3             RSpectra_0.16-1           dqrng_0.3.2              
 [37] spatstat.random_3.2-2     fitdistrplus_1.1-11       parallelly_1.36.0         DelayedMatrixStats_1.24.0
 [41] leiden_0.4.3.1            codetools_0.2-19          tidyselect_1.2.0          farver_2.1.1             
 [45] ScaledMatrix_1.10.0       viridis_0.6.5             spatstat.explore_3.2-6    jsonlite_1.8.8           
 [49] BiocNeighbors_1.20.2      ellipsis_0.3.2            progressr_0.14.0          ggridges_0.5.6           
 [53] survival_3.5-7            scater_1.30.1             tools_4.3.2               ica_1.0-3                
 [57] Rcpp_1.0.12               glue_1.7.0                gridExtra_2.3             withr_3.0.0              
 [61] BiocManager_1.30.22       fastmap_1.1.1             rhdf5filters_1.14.1       bluster_1.12.0           
 [65] fansi_1.0.6               digest_0.6.34             rsvd_1.0.5                timechange_0.3.0         
 [69] R6_2.5.1                  mime_0.12                 colorspace_2.1-0          scattermore_1.2          
 [73] tensor_1.5                spatstat.data_3.0-4       utf8_1.2.4                generics_0.1.3           
 [77] data.table_1.15.0         httr_1.4.7                htmlwidgets_1.6.4         uwot_0.1.16              
 [81] pkgconfig_2.0.3           gtable_0.3.4              lmtest_0.9-40             XVector_0.42.0           
 [85] htmltools_0.5.7           dotCall64_1.1-1           scales_1.3.0              png_0.1-8                
 [89] rstudioapi_0.15.0         tzdb_0.4.0                reshape2_1.4.4            nlme_3.1-164             
 [93] zoo_1.8-12                KernSmooth_2.23-22        parallel_4.3.2            miniUI_0.1.1.1           
 [97] vipor_0.4.7               pillar_1.9.0              grid_4.3.2                vctrs_0.6.5              
[101] RANN_2.6.1                promises_1.2.1            BiocSingular_1.18.0       beachmat_2.18.0          
[105] xtable_1.8-4              cluster_2.1.6             beeswarm_0.4.0            locfit_1.5-9.8           
[109] cli_3.6.2                 compiler_4.3.2            rlang_1.1.3               crayon_1.5.2             
[113] future.apply_1.11.1       labeling_0.4.3            plyr_1.8.9                ggbeeswarm_0.7.2         
[117] stringi_1.8.3             viridisLite_0.4.2         deldir_2.0-2              BiocParallel_1.36.0      
[121] munsell_0.5.0             lazyeval_0.2.2            spatstat.geom_3.2-8       RcppHNSW_0.6.0           
[125] hms_1.1.3                 patchwork_1.2.0           bit64_4.0.5               sparseMatrixStats_1.14.0 
[129] future_1.33.1             Rhdf5lib_1.24.1           statmod_1.5.0             shiny_1.8.0              
[133] ROCR_1.0-11               igraph_2.0.1.1            bit_4.0.5   

[hpages]

We don't have access to se so we can't reproduce the error. Please provide an MRE (Minimal Reproducible Example) , that is, code that we can run that reproduces the error. Thanks!

[LiNk-NY]

@fernandafranca Any updates on this?