Re: Help needed for r-bioc-rhdf5 in BioConductor transition
Hi,
[libhdf5 maintainer in CC]
On Mon, Sep 06, 2021 at 06:33:34PM +0530, Nilesh Patra wrote:
> ------------------------------------------------------------------------
>
> 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.
This sounds pretty convincing.
> 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?
I do not think that we have this option. So I wonder if we can upgrade
libhdf5 pretty soon. May be it makes sense we file some "new upstream
version available" bug agains src:hdf5 and make this bug blocking the
BioConductor transition.
Gilles, do you see any chance to bump the minor version of hdf5 which
should be hopefully easier than just upgrade to the latest upstream
(1.12.0). This would help us a lot.
Kind regards
Andreas.
> [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
>
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