[R-pkg-team] Bug#1104158: r-cran-testthat breaks r-cran-hdf5r autopkgtest
Paul Gevers
elbrus at debian.org
Sat Apr 26 10:28:08 BST 2025
Source: r-cran-testthat, r-cran-hdf5r
Control: found -1 r-cran-testthat/3.2.3-1
Control: found -1 r-cran-hdf5r/1.3.12+dfsg-1
Severity: serious
Tags: sid trixie
User: debian-ci at lists.debian.org
Usertags: breaks needs-update
Dear maintainer(s),
With a recent upload of r-cran-testthat the autopkgtest of r-cran-hdf5r
fails in testing when that autopkgtest is run with the binary packages
of r-cran-testthat from unstable. It passes when run with only packages
from testing. In tabular form:
pass fail
r-cran-testthat from testing 3.2.3-1
r-cran-hdf5r from testing 1.3.12+dfsg-1
all others from testing from testing
I copied some of the output at the bottom of this report.
Currently this regression is blocking the migration of r-cran-testthat
to testing [1]. Due to the nature of this issue, I filed this bug report
against both packages. Can you please investigate the situation and
reassign the bug to the right package?
More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation
Paul
[1] https://qa.debian.org/excuses.php?package=r-cran-testthat
https://ci.debian.net/data/autopkgtest/testing/armel/r/r-cran-hdf5r/60239896/log.gz
59s dpkg-architecture: warning: cannot determine CC system type,
falling back to default (native compilation)
59s BEGIN TEST testthat.R
59s 59s R version 4.4.3 (2025-02-28) -- "Trophy Case"
59s Copyright (C) 2025 The R Foundation for Statistical Computing
59s Platform: arm-unknown-linux-gnueabi (32-bit)
59s 59s R is free software and comes with ABSOLUTELY NO WARRANTY.
59s You are welcome to redistribute it under certain conditions.
59s Type 'license()' or 'licence()' for distribution details.
59s 59s R is a collaborative project with many contributors.
59s Type 'contributors()' for more information and
59s 'citation()' on how to cite R or R packages in publications.
59s 59s Type 'demo()' for some demos, 'help()' for on-line help, or
59s 'help.start()' for an HTML browser interface to help.
59s Type 'q()' to quit R.
59s 59s > library(testthat)
59s > library(hdf5r)
60s > 60s > test_check("hdf5r")
73s [ FAIL 49 | WARN 0 | SKIP 3 | PASS 449 ]
73s 73s ══ Skipped tests (3)
═══════════════════════════════════════════════════════════
73s • empty test (3): 'test-h5t.R:147:1', 'test-h5t.R:174:1',
73s 'test-zzz-H5File.R:156:1'
73s 74s ══ Failed tests
════════════════════════════════════════════════════════════════
75s ── Error ('test-64bit_support.R:43:5'): Dataset with more than
2^31 rows ───────
75s Error in `self$read_low_level(file_space = self_space_id,
mem_space = mem_space_id, 75s dataset_xfer_pl = dataset_xfer_pl,
set_dim = TRUE, dim_to_set = dim_to_set, 75s drop = drop)`:
HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. ├─testthat::expect_equal(...) at test-64bit_support.R:43:5
75s 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
75s 3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
75s 4. ├─large_ds[(2^32 - 20):(2^32 + 20)]
75s 5. └─hdf5r:::`[.H5D`(large_ds, (2^32 - 20):(2^32 + 20))
75s 6. └─x$read(...)
75s 7. └─self$read_low_level(...)
75s ── Error ('test-convert.R:33:5'): Convert H5T_FLOAT works
──────────────────────
75s Error in `H5ToR_Pre(dtype, nelem)`: HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. └─hdf5r:::convertRoundTrip(Robj, dtype_double) at
test-convert.R:33:5
75s 2. └─hdf5r:::H5ToR_Pre(dtype, nelem)
75s ── Error ('test-convert.R:77:5'): Convert H5T_INTEGER works
────────────────────
75s Error in `H5ToR_Pre(dtype, nelem)`: HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. └─hdf5r:::convertRoundTrip(robj_double, dtype_uint64) at
test-convert.R:77:5
75s 2. └─hdf5r:::H5ToR_Pre(dtype, nelem)
75s ── Error ('test-convert.R:118:5'): Convert H5T_STRING works
────────────────────
75s Error in `H5ToR_Pre(dtype, nelem)`: HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. └─hdf5r:::convertRoundTrip(string.utf8, dtype_string_unknown)
at test-convert.R:118:5
75s 2. └─hdf5r:::H5ToR_Pre(dtype, nelem)
75s ── Error ('test-convert.R:169:5'): Convert R_Complex works
─────────────────────
75s Error in `H5ToR_Pre(dtype, nelem)`: HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. └─hdf5r:::convertRoundTrip(r_cmplx, dtype_complex) at
test-convert.R:169:5
75s 2. └─hdf5r:::H5ToR_Pre(dtype, nelem)
75s ── Error ('test-convert.R:183:5'): Convert H5T_COMPOUND works
──────────────────
75s Error in `H5ToR_Pre(dtype, nelem)`: HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. └─hdf5r:::convertRoundTrip(test_frame, dtype_cpd) at
test-convert.R:183:5
75s 2. └─hdf5r:::H5ToR_Pre(dtype, nelem)
75s ── Error ('test-convert.R:194:5'): Convert H5T_ARRAY works
─────────────────────
75s Error in `H5ToR_Pre(dtype, nelem)`: HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. └─hdf5r:::convertRoundTrip(test_data, dtype_array, nelem = 20)
at test-convert.R:194:5
75s 2. └─hdf5r:::H5ToR_Pre(dtype, nelem)
75s ── Error ('test-convert.R:204:5'): Convert H5T_VLEN works
──────────────────────
75s Error in `H5ToR_Pre(dtype, nelem)`: HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. └─hdf5r:::convertRoundTrip(test_data, dtype_vlen) at
test-convert.R:204:5
75s 2. └─hdf5r:::H5ToR_Pre(dtype, nelem)
75s ── Error ('test-convert.R:327:5'): Logical with and without NA
─────────────────
75s Error in `H5ToR_Pre(dtype, nelem)`: HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. └─hdf5r:::convertRoundTrip(logical_noNA, dtype_logical_noNA)
at test-convert.R:327:5
75s 2. └─hdf5r:::H5ToR_Pre(dtype, nelem)
75s ── Error ('test-h5a.R:42:5'): Basic dataset function
───────────────────────────
75s Error in `H5ToR_Pre(mem_type, nelem)`: HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. └─hdf5r (local) read_write_roundtrip(attr_int64, 1:20) at
test-h5a.R:42:5
75s 2. └─h5attr$read() at test-h5a.R:22:5
75s 3. └─hdf5r:::H5ToR_Pre(mem_type, nelem)
75s ── Error ('test-h5a.R:151:5'): Creating attributes of different
types ──────────
75s Error in `H5ToR_Pre(mem_type, nelem)`: HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. └─hdf5r (local) read_write_roundtrip(attr_int32, 1:20) at
test-h5a.R:151:5
75s 2. └─h5attr$read() at test-h5a.R:22:5
75s 3. └─hdf5r:::H5ToR_Pre(mem_type, nelem)
75s ── Error ('test-h5a.R:226:5'): Creating attributes of different
types of length 0 ──
75s Error in `H5ToR_Pre(mem_type, nelem)`: HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. └─hdf5r (local) read_write_roundtrip(attr_int32, integer(0))
at test-h5a.R:226:5
75s 2. └─h5attr$read() at test-h5a.R:22:5
75s 3. └─hdf5r:::H5ToR_Pre(mem_type, nelem)
75s ── Error ('test-h5d.R:49:5'): Basic dataset function
───────────────────────────
75s Error in `self$read_low_level(file_space = self_space_id,
mem_space = mem_space_id, 75s dataset_xfer_pl = dataset_xfer_pl,
set_dim = TRUE, dim_to_set = dim_to_set, 75s drop = drop)`:
HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. └─hdf5r (local) read_write_roundtrip(ds_int64_chunked, 1:20)
at test-h5d.R:49:5
75s 2. └─ds$read() at test-h5d.R:24:5
75s 3. └─self$read_low_level(...)
75s ── Error ('test-h5d.R:136:5'): Creating datasets of different
types ────────────
75s Error in `self$read_low_level(file_space = self_space_id,
mem_space = mem_space_id, 75s dataset_xfer_pl = dataset_xfer_pl,
set_dim = TRUE, dim_to_set = dim_to_set, 75s drop = drop)`:
HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. └─hdf5r (local) read_write_roundtrip(ds_int32, 1:20) at
test-h5d.R:136:5
75s 2. └─ds$read() at test-h5d.R:24:5
75s 3. └─self$read_low_level(...)
75s ── Error ('test-h5p.R:80:5'): H5P_DATASET_CREATE works
─────────────────────────
75s Error in `H5ToR_Pre(dtype, 1)`: HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. ├─testthat::expect_equal(h5p_obj$get_fill_value(dtype_int), 1)
at test-h5p.R:80:5
75s 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
75s 3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
75s 4. └─h5p_obj$get_fill_value(dtype_int)
75s 5. └─hdf5r:::H5ToR_Pre(dtype, 1)
75s ── Error ('test-high_level_UI.R:61:5'): Names and [[
───────────────────────────
75s Error in `self$read_low_level(file_space = self_space_id,
mem_space = mem_space_id, 75s dataset_xfer_pl = dataset_xfer_pl,
set_dim = TRUE, dim_to_set = dim_to_set, 75s drop = drop)`:
HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. ├─testthat::expect_equal(file.h5[["test_dataset2"]]$read(),
robj) at test-high_level_UI.R:61:5
75s 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
75s 3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
75s 4. └─file.h5[["test_dataset2"]]$read()
75s 5. └─self$read_low_level(...)
75s ── Error ('test-high_level_UI.R:269:13'): subset_h5.H5D
────────────────────────
75s Error in `self$read_low_level(file_space = self_space_id,
mem_space = mem_space_id, 75s dataset_xfer_pl = dataset_xfer_pl,
set_dim = TRUE, dim_to_set = dim_to_set, 75s drop = drop)`:
HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. ├─testthat::expect_equal(test[ind1, ind2], robj[ind1, ind2])
at test-high_level_UI.R:269:13
75s 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
75s 3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
75s 4. ├─test[ind1, ind2]
75s 5. └─hdf5r:::`[.H5D`(test, ind1, ind2)
75s 6. └─x$read(...)
75s 7. └─self$read_low_level(...)
75s ── Error ('test-high_level_UI.R:343:5'): attributes
────────────────────────────
75s Error in `H5ToR_Pre(mem_type, nelem)`: HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. └─hdf5r::h5attributes(file.h5) at test-high_level_UI.R:343:5
75s 2. └─attr_obj$read()
75s 3. └─hdf5r:::H5ToR_Pre(mem_type, nelem)
75s ── Error ('test-high_level_UI.R:368:5'): Subsetting dimensions,
drop and write ──
75s Error in `self$read_low_level(file_space = self_space_id,
mem_space = mem_space_id, 75s dataset_xfer_pl = dataset_xfer_pl,
set_dim = TRUE, dim_to_set = dim_to_set, 75s drop = drop)`:
HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. ├─testthat::expect_equal(ex_arr_ds[2, , ], ex_array[2, , ]) at
test-high_level_UI.R:368:5
75s 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
75s 3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
75s 4. ├─ex_arr_ds[2, , ]
75s 5. └─hdf5r:::`[.H5D`(ex_arr_ds, 2, , )
75s 6. └─x$read(...)
75s 7. └─self$read_low_level(...)
75s ── Error ('test-reference.R:246:5'): Create and dereference
references; save in a dataset ──
75s Error in `obj_ds$read_low_level(file_space = obj_space, mem_type =
obj_ds_dtype, 75s set_dim = TRUE, dim_to_set = dim_to_set)`:
HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. └─ds_ref_1$dereference(get_value = TRUE) at test-reference.R:246:5
75s 2. └─obj_ds$read_low_level(...)
75s ── Error ('test-zzz-Attribute.R:57:3'): Attribute-Errors
───────────────────────
75s Error in `H5ToR_Pre(mem_type, nelem)`: HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. ├─testthat::expect_that(...) at test-zzz-Attribute.R:57:3
75s 2. │ └─testthat (local) condition(object)
75s 3. │ └─testthat::expect_identical(x, expected, expected.label =
label)
75s 4. │ └─testthat::quasi_label(enquo(object), label, arg =
"object")
75s 5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
75s 6. └─hdf5r::h5attr(file, "test")
75s 7. └─attr_obj$read()
75s 8. └─hdf5r:::H5ToR_Pre(mem_type, nelem)
75s ── Error ('test-zzz-Attribute.R:106:5'): Attribute-H5Type-File
─────────────────
75s Error in `H5ToR_Pre(mem_type, nelem)`: HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. ├─testthat::expect_that(h5attr(file, aname),
is_identical_to(testall[[i]])) at test-zzz-Attribute.R:106:5
75s 2. │ └─testthat (local) condition(object)
75s 3. │ └─testthat::expect_identical(x, expected, expected.label =
label)
75s 4. │ └─testthat::quasi_label(enquo(object), label, arg =
"object")
75s 5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
75s 6. └─hdf5r::h5attr(file, aname)
75s 7. └─attr_obj$read()
75s 8. └─hdf5r:::H5ToR_Pre(mem_type, nelem)
75s ── Error ('test-zzz-Attribute.R:183:3'):
Attribute-Bug-Scalar-Issue09 ──────────
75s Error in `H5ToR_Pre(mem_type, nelem)`: HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. ├─testthat::expect_that(...) at test-zzz-Attribute.R:183:3
75s 2. │ └─testthat (local) condition(object)
75s 3. │ └─testthat::expect_identical(x, expected, expected.label =
label)
75s 4. │ └─testthat::quasi_label(enquo(object), label, arg =
"object")
75s 5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
75s 6. ├─base::substr(h5attr(file[["floats"]], "scalar"), 1, 5)
75s 7. └─hdf5r::h5attr(file[["floats"]], "scalar")
75s 8. └─attr_obj$read()
75s 9. └─hdf5r:::H5ToR_Pre(mem_type, nelem)
75s ── Error ('test-zzz-DataSet-extend.R:43:3'): DataSet-extend
────────────────────
75s Error in `self$read_low_level(file_space = self_space_id,
mem_space = mem_space_id, 75s dataset_xfer_pl = dataset_xfer_pl,
set_dim = TRUE, dim_to_set = dim_to_set, 75s drop = drop)`:
HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. ├─testthat::expect_equal(readDataSet(dset2), testmat) at
test-zzz-DataSet-extend.R:43:3
75s 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
75s 3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
75s 4. └─hdf5r::readDataSet(dset2)
75s 5. └─object$read()
75s 6. └─self$read_low_level(...)
75s ── Error ('test-zzz-DataSet-extend.R:75:3'):
DataSet-extend-matrix-rbind ───────
75s Error in `self$read_low_level(file_space = self_space_id,
mem_space = mem_space_id, 75s dataset_xfer_pl = dataset_xfer_pl,
set_dim = TRUE, dim_to_set = dim_to_set, 75s drop = drop)`:
HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. ├─testthat::expect_that(...) at test-zzz-DataSet-extend.R:75:3
75s 2. │ └─testthat (local) condition(object)
75s 3. │ └─testthat::expect_identical(x, expected, expected.label =
label)
75s 4. │ └─testthat::quasi_label(enquo(object), label, arg =
"object")
75s 5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
75s 6. └─hdf5r::readDataSet(dset1)
75s 7. └─object$read()
75s 8. └─self$read_low_level(...)
75s ── Error ('test-zzz-DataSet-extend.R:110:3'):
DataSet-extend-matrix-cbind ──────
75s Error in `self$read_low_level(file_space = self_space_id,
mem_space = mem_space_id, 75s dataset_xfer_pl = dataset_xfer_pl,
set_dim = TRUE, dim_to_set = dim_to_set, 75s drop = drop)`:
HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. ├─testthat::expect_that(...) at test-zzz-DataSet-extend.R:110:3
75s 2. │ └─testthat (local) condition(object)
75s 3. │ └─testthat::expect_identical(x, expected, expected.label =
label)
75s 4. │ └─testthat::quasi_label(enquo(object), label, arg =
"object")
75s 5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
75s 6. └─hdf5r::readDataSet(dset1)
75s 7. └─object$read()
75s 8. └─self$read_low_level(...)
75s ── Error ('test-zzz-DataSet-extend.R:137:3'):
DataSet-extend-vector-c ──────────
75s Error in `self$read_low_level(file_space = self_space_id,
mem_space = mem_space_id, 75s dataset_xfer_pl = dataset_xfer_pl,
set_dim = TRUE, dim_to_set = dim_to_set, 75s drop = drop)`:
HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. ├─testthat::expect_that(readDataSet(dset1),
is_identical_to(testmat_n_extend)) at test-zzz-DataSet-extend.R:137:3
75s 2. │ └─testthat (local) condition(object)
75s 3. │ └─testthat::expect_identical(x, expected, expected.label =
label)
75s 4. │ └─testthat::quasi_label(enquo(object), label, arg =
"object")
75s 5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
75s 6. └─hdf5r::readDataSet(dset1)
75s 7. └─object$read()
75s 8. └─self$read_low_level(...)
75s ── Error ('test-zzz-DataSet-IO-NA.R:40:3'): DataSet-Vector-NA
──────────────────
75s Error in `self$read_low_level(file_space = self_space_id,
mem_space = mem_space_id, 75s dataset_xfer_pl = dataset_xfer_pl,
set_dim = TRUE, dim_to_set = dim_to_set, 75s drop = drop)`:
HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. └─hdf5r::readDataSet(dset11) at test-zzz-DataSet-IO-NA.R:40:3
75s 2. └─object$read()
75s 3. └─self$read_low_level(...)
75s ── Error ('test-zzz-DataSet-IO.R:36:3'): DataSet-Vector
────────────────────────
75s Error in `self$read_low_level(file_space = self_space_id,
mem_space = mem_space_id, 75s dataset_xfer_pl = dataset_xfer_pl,
set_dim = TRUE, dim_to_set = dim_to_set, 75s drop = drop)`:
HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. └─hdf5r::readDataSet(dset11) at test-zzz-DataSet-IO.R:36:3
75s 2. └─object$read()
75s 3. └─self$read_low_level(...)
75s ── Error ('test-zzz-DataSet-IO.R:105:3'):
DataSet-Vector-boundaries ────────────
75s Error in `self$read_low_level(file_space = self_space_id,
mem_space = mem_space_id, 75s dataset_xfer_pl = dataset_xfer_pl,
set_dim = TRUE, dim_to_set = dim_to_set, 75s drop = drop)`:
HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. └─hdf5r::readDataSet(dset1) at test-zzz-DataSet-IO.R:105:3
75s 2. └─object$read()
75s 3. └─self$read_low_level(...)
75s ── Error ('test-zzz-DataSet-IO.R:158:3'): datatypes-Matrix
─────────────────────
75s Error in `self$read_low_level(file_space = self_space_id,
mem_space = mem_space_id, 75s dataset_xfer_pl = dataset_xfer_pl,
set_dim = TRUE, dim_to_set = dim_to_set, 75s drop = drop)`:
HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. └─hdf5r::readDataSet(dset11) at test-zzz-DataSet-IO.R:158:3
75s 2. └─object$read()
75s 3. └─self$read_low_level(...)
75s ── Error ('test-zzz-DataSet-IO.R:223:3'): datatypes-Array
──────────────────────
75s Error in `self$read_low_level(file_space = self_space_id,
mem_space = mem_space_id, 75s dataset_xfer_pl = dataset_xfer_pl,
set_dim = TRUE, dim_to_set = dim_to_set, 75s drop = drop)`:
HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. └─hdf5r::readDataSet(dset11) at test-zzz-DataSet-IO.R:223:3
75s 2. └─object$read()
75s 3. └─self$read_low_level(...)
75s ── Error ('test-zzz-DataSet-IO.R:271:3'):
datatypes-Array-BugWithASCII ─────────
75s Error in `self$read_low_level(file_space = self_space_id,
mem_space = mem_space_id, 75s dataset_xfer_pl = dataset_xfer_pl,
set_dim = TRUE, dim_to_set = dim_to_set, 75s drop = drop)`:
HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. ├─testthat::expect_that(file[["test/ascii"]][],
is_identical_to(varlength)) at test-zzz-DataSet-IO.R:271:3
75s 2. │ └─testthat (local) condition(object)
75s 3. │ └─testthat::expect_identical(x, expected, expected.label =
label)
75s 4. │ └─testthat::quasi_label(enquo(object), label, arg =
"object")
75s 5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
75s 6. ├─file[["test/ascii"]][]
75s 7. └─hdf5r:::`[.H5D`(file[["test/ascii"]], )
75s 8. └─x$read(...)
75s 9. └─self$read_low_level(...)
75s ── Error ('test-zzz-DataSet-scalar.R:9:7'):
datatypes-Array-BugWithScalar ──────
75s Error in `self$read_low_level(file_space = self_space_id,
mem_space = self_space_id, 75s dataset_xfer_pl = dataset_xfer_pl)`:
HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. ├─dset[] at test-zzz-DataSet-scalar.R:9:7
75s 2. └─hdf5r:::`[.H5D`(dset, ) at test-zzz-DataSet-scalar.R:9:7
75s 3. └─x$read(...)
75s 4. └─self$read_low_level(...)
75s ── Error ('test-zzz-DataSet-Select-Subset.R:78:3'):
DataSet-Select-Subset-vector-read ──
75s Error in `self$read_low_level(file_space = self_space_id,
mem_space = mem_space_id, 75s dataset_xfer_pl = dataset_xfer_pl,
set_dim = TRUE, dim_to_set = dim_to_set, 75s drop = drop)`:
HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. ├─dset1[1:dset1$dims] at test-zzz-DataSet-Select-Subset.R:78:3
75s 2. └─hdf5r:::`[.H5D`(dset1, 1:dset1$dims) at
test-zzz-DataSet-Select-Subset.R:78:3
75s 3. └─x$read(...)
75s 4. └─self$read_low_level(...)
75s ── Error ('test-zzz-DataSet-Select-Subset.R:115:7'):
DataSet-Select-Subset-read-string ──
75s Error in `self$read_low_level(file_space = self_space_id,
mem_space = mem_space_id, 75s dataset_xfer_pl = dataset_xfer_pl,
set_dim = TRUE, dim_to_set = dim_to_set, 75s drop = drop)`:
HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. ├─testthat::expect_that(testvec[1:3],
is_identical_to(LETTERS[1:3])) at test-zzz-DataSet-Select-Subset.R:115:7
75s 2. │ └─testthat (local) condition(object)
75s 3. │ └─testthat::expect_identical(x, expected, expected.label =
label)
75s 4. │ └─testthat::quasi_label(enquo(object), label, arg =
"object")
75s 5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
75s 6. ├─testvec[1:3]
75s 7. └─hdf5r:::`[.H5D`(testvec, 1:3)
75s 8. └─x$read(...)
75s 9. └─self$read_low_level(...)
75s ── Error ('test-zzz-DataSet-Select-Subset.R:149:7'):
DataSet-Select-Subset-read-string-fixed ──
75s Error in `self$read_low_level(file_space = self_space_id,
mem_space = mem_space_id, 75s dataset_xfer_pl = dataset_xfer_pl,
set_dim = TRUE, dim_to_set = dim_to_set, 75s drop = drop)`:
HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. ├─testthat::expect_that(testvec[1:3],
is_identical_to(LETTERS[1:3])) at test-zzz-DataSet-Select-Subset.R:149:7
75s 2. │ └─testthat (local) condition(object)
75s 3. │ └─testthat::expect_identical(x, expected, expected.label =
label)
75s 4. │ └─testthat::quasi_label(enquo(object), label, arg =
"object")
75s 5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
75s 6. ├─testvec[1:3]
75s 7. └─hdf5r:::`[.H5D`(testvec, 1:3)
75s 8. └─x$read(...)
75s 9. └─self$read_low_level(...)
75s ── Error ('test-zzz-DataSet-Select-Subset.R:196:3'):
DataSet-Select-Subset-vector-write ──
75s Error in `self$read_low_level(file_space = self_space_id,
mem_space = mem_space_id, 75s dataset_xfer_pl = dataset_xfer_pl,
set_dim = TRUE, dim_to_set = dim_to_set, 75s drop = drop)`:
HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. ├─dset1[] at test-zzz-DataSet-Select-Subset.R:196:3
75s 2. └─hdf5r:::`[.H5D`(dset1, ) at
test-zzz-DataSet-Select-Subset.R:196:3
75s 3. └─x$read(...)
75s 4. └─self$read_low_level(...)
75s ── Error ('test-zzz-DataSet-Select-Subset.R:249:3'):
DataSet-Select-Subset-matrix-read ──
75s Error in `self$read_low_level(file_space = self_space_id,
mem_space = mem_space_id, 75s dataset_xfer_pl = dataset_xfer_pl,
set_dim = TRUE, dim_to_set = dim_to_set, 75s drop = drop)`:
HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. ├─testthat::expect_that(readDataSet(dset1),
is_identical_to(testmat_n)) at test-zzz-DataSet-Select-Subset.R:249:3
75s 2. │ └─testthat (local) condition(object)
75s 3. │ └─testthat::expect_identical(x, expected, expected.label =
label)
75s 4. │ └─testthat::quasi_label(enquo(object), label, arg =
"object")
75s 5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
75s 6. └─hdf5r::readDataSet(dset1)
75s 7. └─object$read()
75s 8. └─self$read_low_level(...)
75s ── Error ('test-zzz-DataSet-Select-Subset.R:296:3'):
DataSet-Select-Subset-matrix-write ──
75s Error in `self$read_low_level(file_space = self_space_id,
mem_space = mem_space_id, 75s dataset_xfer_pl = dataset_xfer_pl,
set_dim = TRUE, dim_to_set = dim_to_set, 75s drop = drop)`:
HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. ├─testthat::expect_that(dset2[2, 2], is_identical_to(-2L)) at
test-zzz-DataSet-Select-Subset.R:296:3
75s 2. │ └─testthat (local) condition(object)
75s 3. │ └─testthat::expect_identical(x, expected, expected.label =
label)
75s 4. │ └─testthat::quasi_label(enquo(object), label, arg =
"object")
75s 5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
75s 6. ├─dset2[2, 2]
75s 7. └─hdf5r:::`[.H5D`(dset2, 2, 2)
75s 8. └─x$read(...)
75s 9. └─self$read_low_level(...)
75s ── Error ('test-zzz-DataSet-Select-Subset.R:399:3'):
DataSet-Select-Subset-array-read ──
75s Error in `self$read_low_level(file_space = self_space_id,
mem_space = mem_space_id, 75s dataset_xfer_pl = dataset_xfer_pl,
set_dim = TRUE, dim_to_set = dim_to_set, 75s drop = drop)`:
HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. ├─testthat::expect_that(readDataSet(dset1),
is_identical_to(testmat_n)) at test-zzz-DataSet-Select-Subset.R:399:3
75s 2. │ └─testthat (local) condition(object)
75s 3. │ └─testthat::expect_identical(x, expected, expected.label =
label)
75s 4. │ └─testthat::quasi_label(enquo(object), label, arg =
"object")
75s 5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
75s 6. └─hdf5r::readDataSet(dset1)
75s 7. └─object$read()
75s 8. └─self$read_low_level(...)
75s ── Error ('test-zzz-DataSet-Select-Subset.R:458:3'):
DataSet-Select-Subset-array-write ──
75s Error in `self$read_low_level(file_space = self_space_id,
mem_space = mem_space_id, 75s dataset_xfer_pl = dataset_xfer_pl,
set_dim = TRUE, dim_to_set = dim_to_set, 75s drop = drop)`:
HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. ├─testthat::expect_that(dset2[2, 2, 2], is_identical_to(-2L))
at test-zzz-DataSet-Select-Subset.R:458:3
75s 2. │ └─testthat (local) condition(object)
75s 3. │ └─testthat::expect_identical(x, expected, expected.label =
label)
75s 4. │ └─testthat::quasi_label(enquo(object), label, arg =
"object")
75s 5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
75s 6. ├─dset2[2, 2, 2]
75s 7. └─hdf5r:::`[.H5D`(dset2, 2, 2, 2)
75s 8. └─x$read(...)
75s 9. └─self$read_low_level(...)
75s ── Error ('test-zzz-DataSet.R:182:3'): DataSet-list-dataset-link
───────────────
75s Error in `self$read_low_level(file_space = self_space_id,
mem_space = mem_space_id, 75s dataset_xfer_pl = dataset_xfer_pl,
set_dim = TRUE, dim_to_set = dim_to_set, 75s drop = drop)`:
HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. ├─testthat::expect_that(file[["hardlink/test2"]][],
is_identical_to(1:3)) at test-zzz-DataSet.R:182:3
75s 2. │ └─testthat (local) condition(object)
75s 3. │ └─testthat::expect_identical(x, expected, expected.label =
label)
75s 4. │ └─testthat::quasi_label(enquo(object), label, arg =
"object")
75s 5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
75s 6. ├─file[["hardlink/test2"]][]
75s 7. └─hdf5r:::`[.H5D`(file[["hardlink/test2"]], )
75s 8. └─x$read(...)
75s 9. └─self$read_low_level(...)
75s ── Error ('test-zzz-DataSet.R:203:3'): DataSet-Bug-F32-Issue10
─────────────────
75s Error in `self$read_low_level(file_space = self_space_id,
mem_space = mem_space_id, 75s dataset_xfer_pl = dataset_xfer_pl,
set_dim = TRUE, dim_to_set = dim_to_set, 75s drop = drop)`:
HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. ├─testthat::expect_that(...) at test-zzz-DataSet.R:203:3
75s 2. │ └─testthat (local) condition(object)
75s 3. │ └─testthat::expect_identical(x, expected, expected.label =
label)
75s 4. │ └─testthat::quasi_label(enquo(object), label, arg =
"object")
75s 5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
75s 6. ├─file[["floats"]][]
75s 7. └─hdf5r:::`[.H5D`(file[["floats"]], )
75s 8. └─x$read(...)
75s 9. └─self$read_low_level(...)
75s ── Error ('test-zzz-H5File-Subset.R:58:3'): H5File-Subset-DataSet
──────────────
75s Error in `self$read_low_level(file_space = self_space_id,
mem_space = mem_space_id, 75s dataset_xfer_pl = dataset_xfer_pl,
set_dim = TRUE, dim_to_set = dim_to_set, 75s drop = drop)`:
HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. ├─testthat::expect_that(readDataSet(dset),
is_identical_to(1:10)) at test-zzz-H5File-Subset.R:58:3
75s 2. │ └─testthat (local) condition(object)
75s 3. │ └─testthat::expect_identical(x, expected, expected.label =
label)
75s 4. │ └─testthat::quasi_label(enquo(object), label, arg =
"object")
75s 5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
75s 6. └─hdf5r::readDataSet(dset)
75s 7. └─object$read()
75s 8. └─self$read_low_level(...)
75s ── Error ('test-zzz-H5Group.R:216:3'): CommonFG-unlink
─────────────────────────
75s Error in `self$read_low_level(file_space = self_space_id,
mem_space = mem_space_id, 75s dataset_xfer_pl = dataset_xfer_pl,
set_dim = TRUE, dim_to_set = dim_to_set, 75s drop = drop)`:
HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. ├─testthat::expect_that(file[["testgroup/testset"]][],
is_identical_to(5:6)) at test-zzz-H5Group.R:216:3
75s 2. │ └─testthat (local) condition(object)
75s 3. │ └─testthat::expect_identical(x, expected, expected.label =
label)
75s 4. │ └─testthat::quasi_label(enquo(object), label, arg =
"object")
75s 5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
75s 6. ├─file[["testgroup/testset"]][]
75s 7. └─hdf5r:::`[.H5D`(file[["testgroup/testset"]], )
75s 8. └─x$read(...)
75s 9. └─self$read_low_level(...)
75s ── Error ('test-zzz-io.R:20:2'): datatypes-IO
──────────────────────────────────
75s Error in `self$read_low_level(file_space = self_space_id,
mem_space = mem_space_id, 75s dataset_xfer_pl = dataset_xfer_pl,
set_dim = TRUE, dim_to_set = dim_to_set, 75s drop = drop)`:
HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. └─hdf5r::readDataSet(dset) at test-zzz-io.R:20:9
75s 2. └─object$read()
75s 3. └─self$read_low_level(...)
75s ── Error ('test-zzz-vlen.R:69:3'): DataSet-VLEN-Vector
─────────────────────────
75s Error in `self$read_low_level(file_space = self_space_id,
mem_space = mem_space_id, 75s dataset_xfer_pl = dataset_xfer_pl,
set_dim = TRUE, dim_to_set = dim_to_set, 75s drop = drop)`:
HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. ├─testthat::expect_that(testlist_n_in[],
is_identical_to(testlist_n)) at test-zzz-vlen.R:69:3
75s 2. │ └─testthat (local) condition(object)
75s 3. │ └─testthat::expect_identical(x, expected, expected.label =
label)
75s 4. │ └─testthat::quasi_label(enquo(object), label, arg =
"object")
75s 5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
75s 6. ├─testlist_n_in[]
75s 7. └─hdf5r:::`[.H5D`(testlist_n_in, )
75s 8. └─x$read(...)
75s 9. └─self$read_low_level(...)
75s ── Error ('test-zzz-vlen.R:117:3'): DataSet-VLEN-Vector-Attribute
──────────────
75s Error in `H5ToR_Pre(mem_type, nelem)`: HDF5-API Errors:
75s error #000: ../../../src/H5T.c in H5Tget_class(): line 2221:
not a datatype
75s class: HDF5
75s major: Invalid arguments to routine
75s minor: Inappropriate type
75s 75s Backtrace:
75s ▆
75s 1. └─hdf5r::h5attr(testgroup, "testlist_n") at test-zzz-vlen.R:117:3
75s 2. └─attr_obj$read()
75s 3. └─hdf5r:::H5ToR_Pre(mem_type, nelem)
75s 75s [ FAIL 49 | WARN 0 | SKIP 3 | PASS 449 ]
75s Error: Test failures
75s Execution halted
75s autopkgtest [12:08:36]: test run-unit-test
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