Debian Patches

Status for r-bioc-rhdf5/2.48.0+dfsg-3

Patch Description Author Forwarded Bugs Origin Last update
hack_to_use_H5private.h.patch r-bioc-rhdf5 is using H5private.h While this is totally broken to use this private header file
it is provided here as a copy of the source code of
libhdf5-dev 1.10.4+repack-10
which is provided as a code copy
Andreas Tille <tille@debian.org> no 2019-04-25
use_debian_packaged_libhdf5.patch Use Debian packaged libhdf5 Andreas Tille <tille@debian.org> no 2019-04-25
fix-hdf5deref.patch Default H5Rdereference to H5Rdereference2 if it has been defined Nilesh Patra <nilesh@debian.org> no 2022-05-14
skip_failing_tests.patch Skip three tests due to
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_external_filters.R:74:5'): BLOSC filter works when reading ───
H5Dget_storage_size(did) is not strictly less than 4 * 2000. Difference: 0
── Error ('test_h5read.R:357:5'): Failing to read BLOSC ────────────────────────
Not all required filters available.
Missing filters: blosc

1. ├─testthat::expect_silent(h5read(blosc_file, "dset")) at test_h5read.R:357:4
2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
3. │ ├─testthat (local) .capture(...)
4. │ │ ├─withr::with_output_sink(...)
5. │ │ │ └─base::force(code)
6. │ │ ├─base::withCallingHandlers(...)
7. │ │ └─base::withVisible(code)
8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
9. └─rhdf5::h5read(blosc_file, "dset")
10. └─rhdf5:::h5readDataset(...)
11. └─base::tryCatch(...)
12. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. └─value[[3L]](cond)
── Error ('test_h5read.R:357:5'): Failing to read BLOSC ────────────────────────

1. ├─testthat::expect_silent(h5read(blosc_file, "dset")) at test_h5read.R:357:4
2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
3. │ ├─testthat (local) .capture(...)
4. │ │ ├─withr::with_output_sink(...)
5. │ │ │ └─base::force(code)
6. │ │ ├─base::withCallingHandlers(...)
7. │ │ └─base::withVisible(code)
8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
9. └─rhdf5::h5read(blosc_file, "dset")
10. └─rhdf5::H5Dclose(h5dataset)
11. └─rhdf5:::h5checktype(h5dataset, "dataset")

[ FAIL 3 | WARN 0 | SKIP 2 | PASS 1058 ]
Andreas Tille <tille@debian.org> no 2023-07-22

All known versions for source package 'r-bioc-rhdf5'

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