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Interface to the HDF5 Library
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list.groups() does not support H5Link #27

Closed kthr closed 8 years ago

kthr commented 8 years ago

We are using H5link's in our hdf5 file, I realized that they are not supported yet. I changed the code to add the support and also replaced the deprecated H5Giterate by H5Lvisit and H5Literate. There is now less code needed for group traversal. Hope you can and will use it.

Best, Konstantin

add_support_for_h5link.patch.zip

kthr commented 8 years ago

The patch from my previous comment contains an error. The function ExistsGroup always returned true. Here is the patch where this is fixed:

add_support_for_h5link.txt

mannau commented 8 years ago

Hi Konstantin, thanks for your suggestions - I have applied your changes. However, they do not pass all tests:

Running the tests in 'tests/testthat.R' failed. Last 13 lines of output: 9: FUN(X[[i]], ...) 10: list.groups(.Object, x, full.names, recursive) 11: list.groups(.Object, x, full.names, recursive) 12: stop("Specified path does not exist")

testthat results ================================================================ OK: 413 SKIPPED: 0 FAILED: 3

  1. Error: DataSet-list-dataset (@test-DataSet.R#151)
  2. Failure: CommonFG-list-groups (@test-H5Group.R#121)

  3. Error: CommonFG-list-groups (@test-H5Group.R#129)

    Error: testthat unit tests failed Execution halted

(see also travis build log at https://travis-ci.org/mannau/h5/builds/115739922) Unfortunately I have no more time at the moment to look into this, could you please follow the following steps:

  1. fork repo
  2. apply changes
  3. pull request That way it is easier for me to integrate your changes and see if all tests run as expected. I have already created a temporary branch bug-h5link which includes your suggested changes. Looking forward to your pull-request!

best, mario