Re: Help needed for r-bioc-rhdf5 in BioConductor transition

[Nilesh Patra <nilesh@tchncs.de>]

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Hi Andreas,

> Hi,
> when trying to build r-bioc-rhdf5 in Git I get
> ...
> installing to /build/r-bioc-rhdf5-2.36.0+dfsg/debian/r-bioc-rhdf5/usr/lib/R/site-library/00LOCK-r-bioc-rhdf5-2.36.0+dfsg/00new/rhdf5/libs
> ** R
> [...]
> unable to load shared object '/build/r-bioc-rhdf5-2.36.0+dfsg/debian/r-bioc-rhdf5/usr/lib/R/site-library/00LOCK-r-bioc-rhdf5-2.36.0+dfsg/00new/rhdf5/libs/rhdf5.so':
>  /build/r-bioc-rhdf5-2.36.0+dfsg/debian/r-bioc-rhdf5/usr/lib/R/site-library/00LOCK-r-bioc-rhdf5-2.36.0+dfsg/00new/rhdf5/libs/rhdf5.so: undefined symbol: H5Scombine_select

I think I _probably_ did find out the problem(I'm not 100% sure). The problem likely is that this function has been introduced in 1.10.7 release of hdf5 (which vendors lib
and the one we have in archive is 1.10.6 (older than what we need)
This answer is also hidden in the news file of this very source package here[1]
And the release notes of 1.10.7 of hdf5 also say the same[2] about adding more hyperslab functions.

So maybe we new update of hdf5 in the acrhive to 1.10.7 to proceed with rhdf5 update for bioconductor.
Or, is there some interim version between 1.34.0->1.36.0 that might build with current state?

[1]: https://salsa.debian.org/r-pkg-team/r-bioc-rhdf5/-/blob/master/inst/NEWS.Rd#L8-9
[2]: https://www.hdfgroup.org/2020/09/release-of-hdf5-1-10-7-newsletter-175/

Nilesh