Re: Test failures with latest rhdf5
Hi Mike,
thanks a lot for the speedy response!
On Fri, Dec 06, 2019 at 08:06:44AM +0000, Mike Smith wrote:
> Hi Andreas,
> Thanks for the heads up. That's a weird error because really it's just comparing too strings that represent the shape of the datasets, so it's the string creation rather than anything else that's failing.
> This was reported once before (https://support.bioconductor.org/p/101038/ (https://support.bioconductor.org/p/101038/)) but I put it down to using old versions of R/rhdf5 that predated my time as maintainer, and the user never got back to me with more details.
> I presume you have built many previous versions of rhdf5 on your system, and I haven't changed the h5ls() function in years, so it's odd that it's manifesting now.
I need to admit that also the previous version 2.30.0 showed the exact
same issue. However, non of the maintainers team payed sufficient
attention to that issue.
> I'll take a look at the code and see if there's anything wrong in h5ls(), I guess this must be a pretty weird edge case if it doesn't show up anywhere else.
> I'll let you know if I find something.
Thanks a lot again for your quick response. Feel free to ask here if
you need some further information.
Kind regards
Andreas.
> Cheers,
> Mike
>
> On Fri, Dec 6, 2019 at 08:35, Andreas Tille wrote:
> Hi Mike,
>
> I intent to upgrade the Debian package of rhdf5 to version 2.30.1
> but I stumbled about the following issues in the test suite:
>
> library(testthat)
> library(rhdf5)
> .
> test_check("rhdf5")
> ── 1. Failure: h5ls supports native (@test_native.R#21) ───────────────────────
> `object` not equal to "3 x 4".
> 1/1 mismatches
> x[1]: " x 4"
> y[1]: "3 x 4"
>
> ── 2. Failure: h5ls supports native (@test_native.R#23) ───────────────────────
> `object` not equal to "4 x 3".
> 1/1 mismatches
> x[1]: " x 3"
> y[1]: "4 x 3"
>
> ── 3. Failure: h5ls supports native (@test_native.R#27) ───────────────────────
> `object` not equal to "4 x 3".
> 1/1 mismatches
> x[1]: " x 3"
> y[1]: "4 x 3"
>
> ── 4. Failure: h5ls supports native (@test_native.R#29) ───────────────────────
> `object` not equal to "3 x 4".
> 1/1 mismatches
> x[1]: " x 4"
> y[1]: "3 x 4"
>
> ── 5. Failure: h5ls supports native (@test_native.R#38) ───────────────────────
> `object` not equal to "2 x 3 x 4".
> 1/1 mismatches
> x[1]: " x 4"
> y[1]: "2 x 3 x 4"
>
> ── 6. Failure: h5ls supports native (@test_native.R#41) ───────────────────────
> `object` not equal to "4 x 3 x 2".
> 1/1 mismatches
> x[1]: " x 2"
> y[1]: "4 x 3 x 2"
>
> ── 7. Failure: h5ls supports native (@test_native.R#46) ───────────────────────
> `object` not equal to "4 x 3 x 2".
> 1/1 mismatches
> x[1]: " x 2"
> y[1]: "4 x 3 x 2"
>
> ── 8. Failure: h5ls supports native (@test_native.R#49) ───────────────────────
> `object` not equal to "2 x 3 x 4".
> 1/1 mismatches
> x[1]: " x 4"
> y[1]: "2 x 3 x 4"
>
> ══ testthat results ═══════════════════════════════════════════════════════════
> [ OK: 694 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 8 ]
> 1. Failure: h5ls supports native (@test_native.R#21).
> 2. Failure: h5ls supports native (@test_native.R#23).
> 3. Failure: h5ls supports native (@test_native.R#27).
> 4. Failure: h5ls supports native (@test_native.R#29).
> 5. Failure: h5ls supports native (@test_native.R#38).
> 6. Failure: h5ls supports native (@test_native.R#41).
> 7. Failure: h5ls supports native (@test_native.R#46).
> 8. Failure: h5ls supports native (@test_native.R#49).
>
> Error: testthat unit tests failed
> Execution halted
>
> Do you have any idea what might be wrong here?
>
> Kind regards
>
> Andreas.
>
> --
> http://fam-tille.de (http://fam-tille.de)
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