Re: Test failures with latest rhdf5

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/) 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'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.

Cheers,

Mike

On Fri, Dec 6, 2019 at 08:35, Andreas Tille <andreas@an3as.eu> 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.

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