Error when adding column attributes with NAs about loomr HOT 8 OPEN

for(j in 1:ncol([email protected])){
	if(is.factor([email protected][,j]) == T){
	[email protected][,j] = as.character([email protected][,j]) # Force the variable type to be character
	[email protected][,j][is.na([email protected][,j])] <- "N.A"
}
if(is.character([email protected][,j]) == T){
	[email protected][,j][is.na([email protected][,j])] <- "N.A"
 }
}

library(Seurat)

pbmc.data <- Read10X(data.dir = "~/single_cell_projects/resources/seurat_example/filtered_gene_bc_matrices/hg19/")
pbmc <- CreateSeuratObject(counts = pbmc.data, project = "pbmc3k", min.cells = 3, min.features = 200)

cell_names <- colnames(pbmc)

new_char_col <- rep(c("1", NA), length(cell_names)/2)
names(new_char_col) <- cell_names

new_num_col <- rep(c(1, NA), length(cell_names)/2)
names(new_num_col) <- cell_names

pbmc_na_char <- AddMetaData(pbmc, new_char_col, col.name = "test")

pbmc_na_num <- AddMetaData(pbmc, new_num_col, col.name = "test")

pbmc.loom <- as.loom(pbmc, filename = "~/single_cell_projects/resources/seurat_example/pbmc.loom")

pbmc_na_char.loom <- as.loom(pbmc_na_char, filename = "~/single_cell_projects/resources/seurat_example/pbmc_na_char.loom")

pbmc_na_num.loom <- as.loom(pbmc_na_num, filename = "~/single_cell_projects/resources/seurat_example/pbmc_na_num.loom")

> library(Seurat)
> data("pbmc_small")
> lfile <- as.loom(x = pbmc_small, filename = 'pbmc_small.loom')
Transposing input data: loom file will show input columns (cells) as rows and input rows (features) as columns
This is to maintain compatibility with other loom tools
  |======================================================================| 100%
Adding: CellID
Adding: Gene
Adding a layer to norm_data (layer 1 of 1)
  |======================================================================| 100%
Adding: mean
Adding: variance
Adding: variance_expected
Adding: variance_standardized
Adding: Selected
Adding: orig_ident
Adding: nCount_RNA
Adding: nFeature_RNA
Adding: RNA_snn_res_0_8
Adding: letter_idents
Adding: groups
Adding: RNA_snn_res_1
Adding: ClusterID
Adding: ClusterName
Adding scaled data matrix to /layers/scale_data
Adding a layer to scale_data (layer 1 of 1)
  |======================================================================| 100%
Adding dimensional reduction information for pca
Adding cell embedding information for pca
Adding feature loading information for pca
Adding dimensional reduction information for tsne
Adding cell embedding information for tsne
No feature loading information for tsne
Adding graph RNA_snn
> lfile
Class: loom
Filename: /home/paul/Software/loomR/pbmc_small.loom
Access type: H5F_ACC_RDWR
Attributes: version, chunks, LOOM_SPEC_VERSION, assay, last_modified
Listing:
       name    obj_type dataset.dims dataset.type_class
  col_attrs   H5I_GROUP         <NA>               <NA>
 col_graphs   H5I_GROUP         <NA>               <NA>
     layers   H5I_GROUP         <NA>               <NA>
     matrix H5I_DATASET     80 x 230          H5T_FLOAT
  row_attrs   H5I_GROUP         <NA>               <NA>
 row_graphs   H5I_GROUP         <NA>               <NA>
> lfile$mode
[1] "w-"
> newcol <- sample(x = c(1:10, NA), size = ncol(x = pbmc_small), replace = TRUE)
> any(is.na(x = newcol))
[1] TRUE
> lfile$add.col.attribute(attributes = newcol, overwrite = TRUE)
 Show Traceback
 
 Rerun with Debug
 Error in self$add.attribute(attributes = attributes, MARGIN = 2, overwrite = overwrite) : 
  Attributes must be provided as a named list 
> lfile$add.col.attribute(attributes = list('newcol' = newcol), overwrite = TRUE)
Adding: newcol
> any(is.na(x = lfile[['col_attrs/newcol']][]))
[1] TRUE

library(Seurat)
library(loomR)

data("pbmc_small")
lfile <- as.loom(x = pbmc_small, filename = 'pbmc_small.loom', overwrite = TRUE)

x <- list(
  "int" = sample(c(1L, 2L, NA), size = ncol(x = pbmc_small), replace = TRUE),
  "dbl" = sample(c(1.0, 2.0, NA), size = ncol(x = pbmc_small), replace = TRUE),
  "chr" = sample(c("a", "b", NA), size = ncol(x = pbmc_small), replace = TRUE)
)
x$fct <- addNA(factor(x$chr, levels = c("a", "b")))

lfile$add.col.attribute(
  attributes = list(
    # "chr" = x$chr,
    # "fct" = x$fct, 
    "int" = x$int,
    "dbl" = x$dbl
  ),
  overwrite = TRUE
)

R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936  LC_CTYPE=Chinese (Simplified)_China.936   
[3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C                              
[5] LC_TIME=Chinese (Simplified)_China.936    

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

other attached packages:
[1] loomR_0.2.1.9000 hdf5r_1.2.0      R6_2.4.0         Seurat_3.1.0    

loaded via a namespace (and not attached):
 [1] nlme_3.1-141        tsne_0.1-3          bitops_1.0-6        bit64_0.9-7         RcppAnnoy_0.0.12   
 [6] RColorBrewer_1.1-2  httr_1.4.1          sctransform_0.2.0   tools_3.6.1         irlba_2.3.3        
[11] KernSmooth_2.23-15  uwot_0.1.3          lazyeval_0.2.2      colorspace_1.4-1    npsurv_0.4-0       
[16] tidyselect_0.2.5    gridExtra_2.3       bit_1.1-14          compiler_3.6.1      plotly_4.9.0       
[21] caTools_1.17.1.2    scales_1.0.0        lmtest_0.9-37       ggridges_0.5.1      pbapply_1.4-1      
[26] stringr_1.4.0       digest_0.6.20       R.utils_2.9.0       pkgconfig_2.0.2     htmltools_0.3.6    
[31] bibtex_0.4.2        htmlwidgets_1.3     rlang_0.4.0         rstudioapi_0.10     zoo_1.8-6          
[36] jsonlite_1.6        ica_1.0-2           gtools_3.8.1        dplyr_0.8.3         R.oo_1.22.0        
[41] magrittr_1.5        Matrix_1.2-17       Rcpp_1.0.2          munsell_0.5.0       ape_5.3            
[46] reticulate_1.13     R.methodsS3_1.7.1   stringi_1.4.3       gbRd_0.4-11         MASS_7.3-51.4      
[51] gplots_3.0.1.1      Rtsne_0.15          plyr_1.8.4          grid_3.6.1          parallel_3.6.1     
[56] gdata_2.18.0        listenv_0.7.0       ggrepel_0.8.1       crayon_1.3.4        lattice_0.20-38    
[61] cowplot_1.0.0       splines_3.6.1       SDMTools_1.1-221.1  pillar_1.4.2        igraph_1.2.4.1     
[66] future.apply_1.3.0  reshape2_1.4.3      codetools_0.2-16    leiden_0.3.1        glue_1.3.1         
[71] packrat_0.5.0       lsei_1.2-0          metap_1.1           data.table_1.12.2   RcppParallel_4.4.3 
[76] png_0.1-7           Rdpack_0.11-0       gtable_0.3.0        RANN_2.6.1          purrr_0.3.2        
[81] tidyr_0.8.3         future_1.14.0       assertthat_0.2.1    ggplot2_3.2.1       rsvd_1.0.2         
[86] survival_2.44-1.1   viridisLite_0.3.0   tibble_2.1.3        cluster_2.1.0       globals_0.12.4     
[91] fitdistrplus_1.0-14 ROCR_1.0-7