Re: Test failures with latest rhdf5
Hi Mike,
On Fri, Dec 13, 2019 at 02:43:42PM +0100, Mike Smith wrote:
> Hi Andreas,
>
> I think I've narrowed this down to an unsafe use of sprintf() in that
> function.
>
> There's a modified version of the package at
> https://github.com/grimbough/rhdf5/tree/h5ls_printing
>
> I haven't been able to reproduce the bug on my own system, but if you'd like
> to test that version and report back, that would be great.
>
> I'm not sure what format you need for testing, so if you'd like me to
> provide the source tarball or anything let me know.
The easiest way to verify your changes is a patch against the released
version. I admit I tried a diff between the whole directories but this
is quite large and does not really fit to a simple change in an
sprintf().
So a small diff would be very convenient.
Kind regards and thanks for your support
Andreas.
> On 12/6/19 10:01 AM, Andreas Tille wrote:
> > 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)
>
--
http://fam-tille.de
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