grimbough / rhdf5

Package providing an interface between HDF5 and R

Home Page:http://bioconductor.org/packages/rhdf5

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support for variable length data type

fyangwang opened this issue · comments

Hi, I'm getting a dtype not supported message when reading a file with variable length string type. Values replaced by NA's. Is this something planned to implement in the future? Thanks you!

> df <- h5read(file_path,"/cn")
Warning message:
In H5Dread(h5dataset = h5dataset, h5spaceFile = h5spaceFile, h5spaceMem = h5spaceMem,  :
  h5read for type 'VLEN' not yet implemented. Values replaced by NA's.
> sessionInfo()
R version 4.2.3 (2023-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               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    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] rhdf5_2.42.1

loaded via a namespace (and not attached):
[1] BiocManager_1.30.20 compiler_4.2.3      tools_4.2.3         rhdf5filters_1.10.1 Rhdf5lib_1.20.0  ```