CRAN Package Check Results for Package hdf5r

Last updated on 2020-12-01 00:46:43 CET.

Check Details

Version: 1.3.3
Check: installed package size
Result: NOTE
     installed size is 6.3Mb
     sub-directories of 1Mb or more:
     libs 1.6Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.3.3
Check: examples
Result: ERROR
    Running examples in ‘hdf5r-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: H5A-class
    > ### Title: Class for representing HDF5 attributes
    > ### Aliases: H5A-class H5A
    >
    > ### ** Examples
    >
    > fname <- tempfile(fileext = ".h5")
    > file <- H5File$new(fname, mode = "a")
    > h5attr(file, "attr_numeric") <- rnorm(10)
    > a <- file$attr_open("attr_numeric")
    > a$get_info()
     corder_valid corder cset data_size
    1 0 0 0 80
    > a$attr_name()
    [1] "attr_numeric"
    > a$get_space()
    Class: H5S
    Type: Simple
    Dims: 10
    Maxdims: 10
    > a$get_type()
    Class: H5T_FLOAT
    Datatype: H5T_IEEE_F64LE
    > a$get_storage_size()
    [1] 80
    > a$read()
    Error in H5ToR_Pre(mem_type, nelem) : HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    Calls: <Anonymous> -> H5ToR_Pre
    Execution halted
Flavor: r-patched-solaris-x86

Version: 1.3.3
Check: tests
Result: ERROR
     Running ‘testthat.R’ [39s/44s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(hdf5r)
     >
     > test_check("hdf5r")
     ── ERROR (test-64bit_support.R:43:5): Dataset with more than 2^31 rows ─────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. ├─testthat::expect_equal(...) test-64bit_support.R:43:4
     2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     4. ├─large_ds[(2^32 - 20):(2^32 + 20)]
     5. └─hdf5r:::`[.H5D`(large_ds, (2^32 - 20):(2^32 + 20))
     6. └─x$read(...)
     7. └─self$read_low_level(...)
    
     ── ERROR (test-64bit_support.R:76:5): Datatype conversion with 64bit ───────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. └─hdf5r:::convertRoundTrip(dbl_vec, dtype_uint64, flags = h5const$H5TOR_CONV_NONE) test-64bit_support.R:76:4
     2. └─hdf5r:::H5ToR_Pre(dtype, nelem)
    
     ── ERROR (test-convert.R:33:5): Convert H5T_FLOAT works ────────────────────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. └─hdf5r:::convertRoundTrip(Robj, dtype_double) test-convert.R:33:4
     2. └─hdf5r:::H5ToR_Pre(dtype, nelem)
    
     ── ERROR (test-convert.R:77:5): Convert H5T_INTEGER works ──────────────────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. └─hdf5r:::convertRoundTrip(robj_double, dtype_uint64) test-convert.R:77:4
     2. └─hdf5r:::H5ToR_Pre(dtype, nelem)
    
     ── ERROR (test-convert.R:131:5): Convert H5T_ENUM works ────────────────────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. └─hdf5r:::convertRoundTrip(obj_logical, enum_logical) test-convert.R:131:4
     2. └─hdf5r:::H5ToR_Pre(dtype, nelem)
    
     ── ERROR (test-convert.R:171:5): Convert H5T_STRING works ──────────────────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. └─hdf5r:::convertRoundTrip(string.utf8, dtype_string_unknown) test-convert.R:171:4
     2. └─hdf5r:::H5ToR_Pre(dtype, nelem)
    
     ── ERROR (test-convert.R:222:5): Convert R_Complex works ───────────────────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. └─hdf5r:::convertRoundTrip(r_cmplx, dtype_complex) test-convert.R:222:4
     2. └─hdf5r:::H5ToR_Pre(dtype, nelem)
    
     ── ERROR (test-convert.R:235:5): Convert H5T_COMPOUND works ────────────────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. └─hdf5r:::convertRoundTrip(test_frame, dtype_cpd) test-convert.R:235:4
     2. └─hdf5r:::H5ToR_Pre(dtype, nelem)
    
     ── ERROR (test-convert.R:246:5): Convert H5T_ARRAY works ───────────────────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. └─hdf5r:::convertRoundTrip(test_data, dtype_array, nelem = 20) test-convert.R:246:4
     2. └─hdf5r:::H5ToR_Pre(dtype, nelem)
    
     ── ERROR (test-convert.R:256:5): Convert H5T_VLEN works ────────────────────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. └─hdf5r:::convertRoundTrip(test_data, dtype_vlen) test-convert.R:256:4
     2. └─hdf5r:::H5ToR_Pre(dtype, nelem)
    
     ── ERROR (test-convert.R:379:5): Logical with and without NA ───────────────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. └─hdf5r:::convertRoundTrip(logical_noNA, dtype_logical_noNA) test-convert.R:379:4
     2. └─hdf5r:::H5ToR_Pre(dtype, nelem)
    
     ── ERROR (test-h5a.R:42:5): Basic dataset function ─────────────────────────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. └─hdf5r:::read_write_roundtrip(attr_int64, 1:20) test-h5a.R:42:4
     2. └─h5attr$read() test-h5a.R:22:4
     3. └─hdf5r:::H5ToR_Pre(mem_type, nelem)
    
     ── ERROR (test-h5a.R:151:5): Creating attributes of different types ────────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. └─hdf5r:::read_write_roundtrip(attr_int32, 1:20) test-h5a.R:151:4
     2. └─h5attr$read() test-h5a.R:22:4
     3. └─hdf5r:::H5ToR_Pre(mem_type, nelem)
    
     ── ERROR (test-h5d.R:49:5): Basic dataset function ─────────────────────────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. └─hdf5r:::read_write_roundtrip(ds_int64_chunked, 1:20) test-h5d.R:49:4
     2. └─ds$read() test-h5d.R:24:4
     3. └─self$read_low_level(...)
    
     ── ERROR (test-h5d.R:136:5): Creating datasets of different types ──────────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. └─hdf5r:::read_write_roundtrip(ds_int32, 1:20) test-h5d.R:136:4
     2. └─ds$read() test-h5d.R:24:4
     3. └─self$read_low_level(...)
    
     ── ERROR (test-h5p.R:80:5): H5P_DATASET_CREATE works ───────────────────────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. ├─testthat::expect_equal(h5p_obj$get_fill_value(dtype_int), 1) test-h5p.R:80:4
     2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     4. └─h5p_obj$get_fill_value(dtype_int)
     5. └─hdf5r:::H5ToR_Pre(dtype, 1)
    
     ── FAILURE (test-h5t.R:120:5): native datatypes ────────────────────────────────
     cpd_test_native_c$equal(cpd_native_c) is not TRUE
    
     `actual`: FALSE
     `expected`: TRUE
    
     ── FAILURE (test-h5t.R:121:5): native datatypes ────────────────────────────────
     cpd_test_native_c$describe() not equal to cpd_native_c$describe().
     Component "size": Mean relative difference: 0.1428571
    
     ── Skip (test-h5t.R:147:1): Describe ───────────────────────────────────────────
     Reason: empty test
    
     ── Skip (test-h5t.R:174:1): dtype to text ──────────────────────────────────────
     Reason: empty test
    
     ── ERROR (test-high_level_UI.R:61:5): Names and [[ ─────────────────────────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. ├─testthat::expect_equal(file.h5[["test_dataset2"]]$read(), robj) test-high_level_UI.R:61:4
     2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     4. └─file.h5[["test_dataset2"]]$read()
     5. └─self$read_low_level(...)
    
     ── ERROR (test-high_level_UI.R:269:13): subset_h5.H5D ──────────────────────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. ├─testthat::expect_equal(test[ind1, ind2], robj[ind1, ind2]) test-high_level_UI.R:269:12
     2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     4. ├─test[ind1, ind2]
     5. └─hdf5r:::`[.H5D`(test, ind1, ind2)
     6. └─x$read(...)
     7. └─self$read_low_level(...)
    
     ── ERROR (test-high_level_UI.R:343:5): attributes ──────────────────────────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. └─hdf5r::h5attributes(file.h5) test-high_level_UI.R:343:4
     2. └─attr_obj$read()
     3. └─hdf5r:::H5ToR_Pre(mem_type, nelem)
    
     ── ERROR (test-high_level_UI.R:368:5): Subsetting dimensions, drop and write ───
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. ├─testthat::expect_equal(ex_arr_ds[2, , ], ex_array[2, , ]) test-high_level_UI.R:368:4
     2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     4. ├─ex_arr_ds[2, , ]
     5. └─hdf5r:::`[.H5D`(ex_arr_ds, 2, , )
     6. └─x$read(...)
     7. └─self$read_low_level(...)
    
     ── ERROR (test-reference.R:246:5): Create and dereference references; save in a
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. └─ds_ref_1$dereference(get_value = TRUE) test-reference.R:246:4
     2. └─obj_ds$read_low_level(...)
    
     ── ERROR (test-zzz-Attribute.R:57:3): Attribute-Errors ─────────────────────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. ├─testthat::expect_that(...) test-zzz-Attribute.R:57:2
     2. │ └─testthat:::condition(object)
     3. │ └─testthat::expect_identical(x, expected, expected.label = label)
     4. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     6. └─hdf5r::h5attr(file, "test")
     7. └─attr_obj$read()
     8. └─hdf5r:::H5ToR_Pre(mem_type, nelem)
    
     ── ERROR (test-zzz-Attribute.R:106:5): Attribute-H5Type-File ───────────────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. ├─testthat::expect_that(h5attr(file, aname), is_identical_to(testall[[i]])) test-zzz-Attribute.R:106:4
     2. │ └─testthat:::condition(object)
     3. │ └─testthat::expect_identical(x, expected, expected.label = label)
     4. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     6. └─hdf5r::h5attr(file, aname)
     7. └─attr_obj$read()
     8. └─hdf5r:::H5ToR_Pre(mem_type, nelem)
    
     ── ERROR (test-zzz-Attribute.R:183:3): Attribute-Bug-Scalar-Issue09 ────────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. ├─testthat::expect_that(...) test-zzz-Attribute.R:183:2
     2. │ └─testthat:::condition(object)
     3. │ └─testthat::expect_identical(x, expected, expected.label = label)
     4. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     6. ├─base::substr(h5attr(file[["floats"]], "scalar"), 1, 5)
     7. └─hdf5r::h5attr(file[["floats"]], "scalar")
     8. └─attr_obj$read()
     9. └─hdf5r:::H5ToR_Pre(mem_type, nelem)
    
     ── ERROR (test-zzz-DataSet-IO-NA.R:40:3): DataSet-Vector-NA ────────────────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. └─hdf5r::readDataSet(dset11) test-zzz-DataSet-IO-NA.R:40:2
     2. └─object$read()
     3. └─self$read_low_level(...)
    
     ── ERROR (test-zzz-DataSet-IO.R:36:3): DataSet-Vector ──────────────────────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. └─hdf5r::readDataSet(dset11) test-zzz-DataSet-IO.R:36:2
     2. └─object$read()
     3. └─self$read_low_level(...)
    
     ── ERROR (test-zzz-DataSet-IO.R:105:3): DataSet-Vector-boundaries ──────────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. └─hdf5r::readDataSet(dset1) test-zzz-DataSet-IO.R:105:2
     2. └─object$read()
     3. └─self$read_low_level(...)
    
     ── ERROR (test-zzz-DataSet-IO.R:158:3): datatypes-Matrix ───────────────────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. └─hdf5r::readDataSet(dset11) test-zzz-DataSet-IO.R:158:2
     2. └─object$read()
     3. └─self$read_low_level(...)
    
     ── ERROR (test-zzz-DataSet-IO.R:223:3): datatypes-Array ────────────────────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. └─hdf5r::readDataSet(dset11) test-zzz-DataSet-IO.R:223:2
     2. └─object$read()
     3. └─self$read_low_level(...)
    
     ── ERROR (test-zzz-DataSet-IO.R:271:3): datatypes-Array-BugWithASCII ───────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. ├─testthat::expect_that(file[["test/ascii"]][], is_identical_to(varlength)) test-zzz-DataSet-IO.R:271:2
     2. │ └─testthat:::condition(object)
     3. │ └─testthat::expect_identical(x, expected, expected.label = label)
     4. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     6. ├─file[["test/ascii"]][]
     7. └─hdf5r:::`[.H5D`(file[["test/ascii"]], )
     8. └─x$read(...)
     9. └─self$read_low_level(...)
    
     ── ERROR (test-zzz-DataSet-Select-Subset.R:78:3): DataSet-Select-Subset-vector-r
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. ├─dset1[1:dset1$dims] test-zzz-DataSet-Select-Subset.R:78:2
     2. └─hdf5r:::`[.H5D`(dset1, 1:dset1$dims) test-zzz-DataSet-Select-Subset.R:78:2
     3. └─x$read(...)
     4. └─self$read_low_level(...)
    
     ── ERROR (test-zzz-DataSet-Select-Subset.R:115:7): DataSet-Select-Subset-read-st
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. ├─testthat::expect_that(testvec[1:3], is_identical_to(LETTERS[1:3])) test-zzz-DataSet-Select-Subset.R:115:6
     2. │ └─testthat:::condition(object)
     3. │ └─testthat::expect_identical(x, expected, expected.label = label)
     4. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     6. ├─testvec[1:3]
     7. └─hdf5r:::`[.H5D`(testvec, 1:3)
     8. └─x$read(...)
     9. └─self$read_low_level(...)
    
     ── ERROR (test-zzz-DataSet-Select-Subset.R:149:7): DataSet-Select-Subset-read-st
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. ├─testthat::expect_that(testvec[1:3], is_identical_to(LETTERS[1:3])) test-zzz-DataSet-Select-Subset.R:149:6
     2. │ └─testthat:::condition(object)
     3. │ └─testthat::expect_identical(x, expected, expected.label = label)
     4. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     6. ├─testvec[1:3]
     7. └─hdf5r:::`[.H5D`(testvec, 1:3)
     8. └─x$read(...)
     9. └─self$read_low_level(...)
    
     ── ERROR (test-zzz-DataSet-Select-Subset.R:196:3): DataSet-Select-Subset-vector-
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. ├─dset1[] test-zzz-DataSet-Select-Subset.R:196:2
     2. └─hdf5r:::`[.H5D`(dset1, ) test-zzz-DataSet-Select-Subset.R:196:2
     3. └─x$read(...)
     4. └─self$read_low_level(...)
    
     ── ERROR (test-zzz-DataSet-Select-Subset.R:249:3): DataSet-Select-Subset-matrix-
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. ├─testthat::expect_that(readDataSet(dset1), is_identical_to(testmat_n)) test-zzz-DataSet-Select-Subset.R:249:2
     2. │ └─testthat:::condition(object)
     3. │ └─testthat::expect_identical(x, expected, expected.label = label)
     4. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     6. └─hdf5r::readDataSet(dset1)
     7. └─object$read()
     8. └─self$read_low_level(...)
    
     ── ERROR (test-zzz-DataSet-Select-Subset.R:296:3): DataSet-Select-Subset-matrix-
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. ├─testthat::expect_that(dset2[2, 2], is_identical_to(-2L)) test-zzz-DataSet-Select-Subset.R:296:2
     2. │ └─testthat:::condition(object)
     3. │ └─testthat::expect_identical(x, expected, expected.label = label)
     4. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     6. ├─dset2[2, 2]
     7. └─hdf5r:::`[.H5D`(dset2, 2, 2)
     8. └─x$read(...)
     9. └─self$read_low_level(...)
    
     ── ERROR (test-zzz-DataSet-Select-Subset.R:399:3): DataSet-Select-Subset-array-r
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. ├─testthat::expect_that(readDataSet(dset1), is_identical_to(testmat_n)) test-zzz-DataSet-Select-Subset.R:399:2
     2. │ └─testthat:::condition(object)
     3. │ └─testthat::expect_identical(x, expected, expected.label = label)
     4. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     6. └─hdf5r::readDataSet(dset1)
     7. └─object$read()
     8. └─self$read_low_level(...)
    
     ── ERROR (test-zzz-DataSet-Select-Subset.R:458:3): DataSet-Select-Subset-array-w
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. ├─testthat::expect_that(dset2[2, 2, 2], is_identical_to(-2L)) test-zzz-DataSet-Select-Subset.R:458:2
     2. │ └─testthat:::condition(object)
     3. │ └─testthat::expect_identical(x, expected, expected.label = label)
     4. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     6. ├─dset2[2, 2, 2]
     7. └─hdf5r:::`[.H5D`(dset2, 2, 2, 2)
     8. └─x$read(...)
     9. └─self$read_low_level(...)
    
     ── ERROR (test-zzz-DataSet-extend.R:43:3): DataSet-extend ──────────────────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. ├─testthat::expect_equal(readDataSet(dset2), testmat) test-zzz-DataSet-extend.R:43:2
     2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     4. └─hdf5r::readDataSet(dset2)
     5. └─object$read()
     6. └─self$read_low_level(...)
    
     ── ERROR (test-zzz-DataSet-extend.R:75:3): DataSet-extend-matrix-rbind ─────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. ├─testthat::expect_that(...) test-zzz-DataSet-extend.R:75:2
     2. │ └─testthat:::condition(object)
     3. │ └─testthat::expect_identical(x, expected, expected.label = label)
     4. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     6. └─hdf5r::readDataSet(dset1)
     7. └─object$read()
     8. └─self$read_low_level(...)
    
     ── ERROR (test-zzz-DataSet-extend.R:110:3): DataSet-extend-matrix-cbind ────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. ├─testthat::expect_that(...) test-zzz-DataSet-extend.R:110:2
     2. │ └─testthat:::condition(object)
     3. │ └─testthat::expect_identical(x, expected, expected.label = label)
     4. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     6. └─hdf5r::readDataSet(dset1)
     7. └─object$read()
     8. └─self$read_low_level(...)
    
     ── ERROR (test-zzz-DataSet-extend.R:137:3): DataSet-extend-vector-c ────────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. ├─testthat::expect_that(readDataSet(dset1), is_identical_to(testmat_n_extend)) test-zzz-DataSet-extend.R:137:2
     2. │ └─testthat:::condition(object)
     3. │ └─testthat::expect_identical(x, expected, expected.label = label)
     4. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     6. └─hdf5r::readDataSet(dset1)
     7. └─object$read()
     8. └─self$read_low_level(...)
    
     ── ERROR (test-zzz-DataSet-scalar.R:9:7): datatypes-Array-BugWithScalar ────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. ├─dset[] test-zzz-DataSet-scalar.R:9:6
     2. └─hdf5r:::`[.H5D`(dset, ) test-zzz-DataSet-scalar.R:9:6
     3. └─x$read(...)
     4. └─self$read_low_level(...)
    
     ── ERROR (test-zzz-DataSet.R:182:3): DataSet-list-dataset-link ─────────────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. ├─testthat::expect_that(file[["hardlink/test2"]][], is_identical_to(1:3)) test-zzz-DataSet.R:182:2
     2. │ └─testthat:::condition(object)
     3. │ └─testthat::expect_identical(x, expected, expected.label = label)
     4. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     6. ├─file[["hardlink/test2"]][]
     7. └─hdf5r:::`[.H5D`(file[["hardlink/test2"]], )
     8. └─x$read(...)
     9. └─self$read_low_level(...)
    
     ── ERROR (test-zzz-DataSet.R:203:3): DataSet-Bug-F32-Issue10 ───────────────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. ├─testthat::expect_that(...) test-zzz-DataSet.R:203:2
     2. │ └─testthat:::condition(object)
     3. │ └─testthat::expect_identical(x, expected, expected.label = label)
     4. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     6. ├─file[["floats"]][]
     7. └─hdf5r:::`[.H5D`(file[["floats"]], )
     8. └─x$read(...)
     9. └─self$read_low_level(...)
    
     ── ERROR (test-zzz-H5File-Subset.R:58:3): H5File-Subset-DataSet ────────────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. ├─testthat::expect_that(readDataSet(dset), is_identical_to(1:10)) test-zzz-H5File-Subset.R:58:2
     2. │ └─testthat:::condition(object)
     3. │ └─testthat::expect_identical(x, expected, expected.label = label)
     4. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     6. └─hdf5r::readDataSet(dset)
     7. └─object$read()
     8. └─self$read_low_level(...)
    
     ── Skip (test-zzz-H5File.R:156:1): H5File-flush ────────────────────────────────
     Reason: empty test
    
     ── ERROR (test-zzz-H5Group.R:216:3): CommonFG-unlink ───────────────────────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. ├─testthat::expect_that(file[["testgroup/testset"]][], is_identical_to(5:6)) test-zzz-H5Group.R:216:2
     2. │ └─testthat:::condition(object)
     3. │ └─testthat::expect_identical(x, expected, expected.label = label)
     4. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     6. ├─file[["testgroup/testset"]][]
     7. └─hdf5r:::`[.H5D`(file[["testgroup/testset"]], )
     8. └─x$read(...)
     9. └─self$read_low_level(...)
    
     ── ERROR (test-zzz-io.R:20:2): datatypes-IO ────────────────────────────────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. └─hdf5r::readDataSet(dset) test-zzz-io.R:20:8
     2. └─object$read()
     3. └─self$read_low_level(...)
    
     ── ERROR (test-zzz-vlen.R:69:3): DataSet-VLEN-Vector ───────────────────────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. ├─testthat::expect_that(testlist_n_in[], is_identical_to(testlist_n)) test-zzz-vlen.R:69:2
     2. │ └─testthat:::condition(object)
     3. │ └─testthat::expect_identical(x, expected, expected.label = label)
     4. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     6. ├─testlist_n_in[]
     7. └─hdf5r:::`[.H5D`(testlist_n_in, )
     8. └─x$read(...)
     9. └─self$read_low_level(...)
    
     ── ERROR (test-zzz-vlen.R:117:3): DataSet-VLEN-Vector-Attribute ────────────────
     Error: HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
     Backtrace:
     █
     1. └─hdf5r::h5attr(testgroup, "testlist_n") test-zzz-vlen.R:117:2
     2. └─attr_obj$read()
     3. └─hdf5r:::H5ToR_Pre(mem_type, nelem)
    
     ── Skipped tests ──────────────────────────────────────────────────────────────
     ● empty test (3)
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     ERROR (test-64bit_support.R:43:5): Dataset with more than 2^31 rows
     ERROR (test-64bit_support.R:76:5): Datatype conversion with 64bit
     ERROR (test-convert.R:33:5): Convert H5T_FLOAT works
     ERROR (test-convert.R:77:5): Convert H5T_INTEGER works
     ERROR (test-convert.R:131:5): Convert H5T_ENUM works
     ERROR (test-convert.R:171:5): Convert H5T_STRING works
     ERROR (test-convert.R:222:5): Convert R_Complex works
     ERROR (test-convert.R:235:5): Convert H5T_COMPOUND works
     ERROR (test-convert.R:246:5): Convert H5T_ARRAY works
     ERROR (test-convert.R:256:5): Convert H5T_VLEN works
     ERROR (test-convert.R:379:5): Logical with and without NA
     ERROR (test-h5a.R:42:5): Basic dataset function
     ERROR (test-h5a.R:151:5): Creating attributes of different types
     ERROR (test-h5d.R:49:5): Basic dataset function
     ERROR (test-h5d.R:136:5): Creating datasets of different types
     ERROR (test-h5p.R:80:5): H5P_DATASET_CREATE works
     FAILURE (test-h5t.R:120:5): native datatypes
     FAILURE (test-h5t.R:121:5): native datatypes
     ERROR (test-high_level_UI.R:61:5): Names and [[
     ERROR (test-high_level_UI.R:269:13): subset_h5.H5D
     ERROR (test-high_level_UI.R:343:5): attributes
     ERROR (test-high_level_UI.R:368:5): Subsetting dimensions, drop and write
     ERROR (test-reference.R:246:5): Create and dereference references; save in a dataset
     ERROR (test-zzz-Attribute.R:57:3): Attribute-Errors
     ERROR (test-zzz-Attribute.R:106:5): Attribute-H5Type-File
     ERROR (test-zzz-Attribute.R:183:3): Attribute-Bug-Scalar-Issue09
     ERROR (test-zzz-DataSet-IO-NA.R:40:3): DataSet-Vector-NA
     ERROR (test-zzz-DataSet-IO.R:36:3): DataSet-Vector
     ERROR (test-zzz-DataSet-IO.R:105:3): DataSet-Vector-boundaries
     ERROR (test-zzz-DataSet-IO.R:158:3): datatypes-Matrix
     ERROR (test-zzz-DataSet-IO.R:223:3): datatypes-Array
     ERROR (test-zzz-DataSet-IO.R:271:3): datatypes-Array-BugWithASCII
     ERROR (test-zzz-DataSet-Select-Subset.R:78:3): DataSet-Select-Subset-vector-read
     ERROR (test-zzz-DataSet-Select-Subset.R:115:7): DataSet-Select-Subset-read-string
     ERROR (test-zzz-DataSet-Select-Subset.R:149:7): DataSet-Select-Subset-read-string-fixed
     ERROR (test-zzz-DataSet-Select-Subset.R:196:3): DataSet-Select-Subset-vector-write
     ERROR (test-zzz-DataSet-Select-Subset.R:249:3): DataSet-Select-Subset-matrix-read
     ERROR (test-zzz-DataSet-Select-Subset.R:296:3): DataSet-Select-Subset-matrix-write
     ERROR (test-zzz-DataSet-Select-Subset.R:399:3): DataSet-Select-Subset-array-read
     ERROR (test-zzz-DataSet-Select-Subset.R:458:3): DataSet-Select-Subset-array-write
     ERROR (test-zzz-DataSet-extend.R:43:3): DataSet-extend
     ERROR (test-zzz-DataSet-extend.R:75:3): DataSet-extend-matrix-rbind
     ERROR (test-zzz-DataSet-extend.R:110:3): DataSet-extend-matrix-cbind
     ERROR (test-zzz-DataSet-extend.R:137:3): DataSet-extend-vector-c
     ERROR (test-zzz-DataSet-scalar.R:9:7): datatypes-Array-BugWithScalar
     ERROR (test-zzz-DataSet.R:182:3): DataSet-list-dataset-link
     ERROR (test-zzz-DataSet.R:203:3): DataSet-Bug-F32-Issue10
     ERROR (test-zzz-H5File-Subset.R:58:3): H5File-Subset-DataSet
     ERROR (test-zzz-H5Group.R:216:3): CommonFG-unlink
     ERROR (test-zzz-io.R:20:2): datatypes-IO
     ERROR (test-zzz-vlen.R:69:3): DataSet-VLEN-Vector
     ERROR (test-zzz-vlen.R:117:3): DataSet-VLEN-Vector-Attribute
    
     [ FAIL 52 | WARN 0 | SKIP 3 | PASS 456 ]
     Error: Test failures
     Execution halted
Flavor: r-patched-solaris-x86

Version: 1.3.3
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘hdf5r.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Quitting from lines 159-160 (hdf5r.Rmd)
    Error: processing vignette 'hdf5r.Rmd' failed with diagnostics:
    HDF5-API Errors:
     error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
     class: HDF5
     major: Invalid arguments to routine
     minor: Inappropriate type
    
    --- failed re-building ‘hdf5r.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘hdf5r.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86

Version: 1.3.3
Check: whether package can be installed
Result: ERROR
    Installation failed.
Flavor: r-release-macos-x86_64