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TODO.md

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Release Checklist

  • [] Add readme for h5 wrapper functions
  • [] Add examples
  • [] Read/Improve Documentation

Release Sunday:

After Release / Marketing:

  • [] Deprecate h5, Release 1.0.0 with deprecation notice in Description and link to hdf5r
  • [] Announce hdf5r at the R-packages mailinglist
  • [] Announce hdf5 at the HDF5 Group (David) and tell them that there's a new package in town ;), maybe inform at HDF5 mailing list.
  • [] Blog at R-Bloggers?
  • [] R-Journal?

Changes from h5 to hdf5r

  • Change subset operator to [[
    • Q: Why [[ instead of [?
    • Q: Implement [ to support multiple arguments?
  • No Support for on-the-fly group creation / Recursive group creation ? e.g. file[["testgroup/testset"]] <- 1:10 without existing testgroup
  • full.names in list.xxx does not return global path name, changed parameters

Missing Features

  • list.attributes (e.g. through H5Aiterate2)
  • Adjust $print() for all HDF5 objects
  • Create dataset without chunking?
    • This should work without setting chunk size: dset1 <- createDataSet(file, "testmat_1", testmat_n, space = dspace)
  • Get Chunk size from dataset
  • Implement follow.link
  • How to set up dataset with specified maximum dimensions, only using set_extent?
  • General: Improve error messages

Issues

  • H5S$new(maxdims = "test") should immediately throw error
  • Check why H5T_STD_I64LE is not mapped to 64bit integer?
  • Check why enum test case ist not working (test-zzz.enum.R)
  • Does array retrieval work?
  • Subsetting allows zero and negative values
  • insert check before expand f <- function() dset2[10:11, 9] <- matrix(rep(0, 2*9), nrow = 2)
  • Reading entire dataset using [] (instead of [,]) for 2-dimensional objects should also work, like in matrix(1:9, nrow = 3)[]
  • Move package startup message to README / doc
  • Check datatype before dataset is extended
  • Fix Issues for HDF5 1.8.12
  • NA handling for strings does not work properly
  • Fix Issues for HDF5 1.8.14
  • Implement test cases DataSet-Select-Elem/DataSet-Select-Hyperslab needs refactoring of H5D$read functions (separate dataspace from read).
    • Should all elements be returned if index is zero for element-wise selection?
    • Subscribt out of bounds not thrown for element-wise selection. Instead, indexing starts at 1.

To be implemented for release:

  • Adjust $print() for all HDF5 objects
    • list.attributes (e.g. through H5Aiterate2)
  • Subsetting allows zero and negative values
  • insert check before expand f <- function() dset2[10:11, 9] <- matrix(rep(0, 2*9), nrow = 2)
  • Move package startup message to README / doc
  • Fix Issues for HDF5 1.8.12
  • Fix Issues for HDF5 1.8.14

Organizational

  • mannau: Set h5 as deprecated, link to hdf5r
  • all: Specify release date (e.g May 1st)
  • mannau: Inform HDF5 Group about new CRAN release (make hdf5r standard HDF5 package)