On Tue, Nov 03, 2020 at 12:06:11PM +0100, Andreas Tille wrote:
> there is a new dependency r-bioc-rhdf5filters[1] which needed some work
> to exclude code copies of Debian packaged libs. The current packaging
> is *not* *finished* since the actual libraries are not properly linked.
> There are also some failures in autopkgtest.
I think my suspicion that r-bioc-rhdf5filters is not correct is proven
by the fact that r-bioc-rhdf5 is stumbling in its test upon missing
bzip2 and blosc - which is exactly what is introduced in
r-bioc-rhdf5filters:
> library(testthat)
> library(rhdf5)
>
> test_check("rhdf5")
── 1. Failure: BZIP2 filter works when reading (@test_external_filters.R#49) ──
H5Dget_storage_size(did) is not strictly less than 4 * 2000. Difference: 0
── 2. Failure: BLOSC filter works when reading (@test_external_filters.R#57) ──
H5Dget_storage_size(did) is not strictly less than 4 * 2000. Difference: 0
── 3. Error: Failing to read BLOSC (@test_h5read.R#342) ───────────────────────
Unable to read dataset.
Not all required filters available.
Missing filters: blosc
Backtrace:
1. testthat::expect_silent(h5read(blosc_file, "dset"))
9. rhdf5::h5read(blosc_file, "dset")
10. rhdf5:::h5readDataset(...)
11. base::tryCatch(...)
12. base:::tryCatchList(expr, classes, parentenv, handlers)
13. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. value[[3L]](cond)
── 4. Error: Failing to read BLOSC (@test_h5read.R#342) ───────────────────────
Error in h5checktype(). H5Identifier not valid.
Backtrace:
1. testthat::expect_silent(h5read(blosc_file, "dset"))
9. rhdf5::h5read(blosc_file, "dset")
10. rhdf5::H5Dclose(h5dataset)
11. rhdf5:::h5checktype(h5dataset, "dataset")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 776 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 4 ]
1. Failure: BZIP2 filter works when reading (@test_external_filters.R#49)
2. Failure: BLOSC filter works when reading (@test_external_filters.R#57)
3. Error: Failing to read BLOSC (@test_h5read.R#342)
4. Error: Failing to read BLOSC (@test_h5read.R#342)
Error: testthat unit tests failed
Execution halted
I think we should clarify this before uploading r-bioc-rhdf5 with a
broken test which will prevent the migration.
Any help would be welcome
Andreas.
--
http://fam-tille.de
