On 2020-11-10 08:57:32 +0100, Andreas Tille wrote:
> 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.
Is a fix for that issues in sight? Or should we consider removal of the
r-bioc-rhdf5 and its reverse dependencies to finish the transition once
r-bioc-genomicfiles, r-bioc-degreport, and r-bioc-dexseq have been
uploaded to finish the transition?
Cheers
--
Sebastian Ramacher
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