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Update bioconductor-rhdf5lib: include libcurl dep and revert to default configure script #43930

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dlaehnemann
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From a discussion on bioconductor-rhdf5 in its original respository, I take it that including libcurl as a definite dependency over here will solve the underlying problem. This problem is documented in that issue and basically consists of inconsistent usage of openssl, where in the past the bioconda recipes dependent on rhdf5lib seem to have picked up the build system's libcurl and openssl1.1, which is now incompatible with newer host operating system openssl3 version.

As a bonus, I'll revert to using the default configure script. The patches previously in this recipe were for proper handling of ZLIB dependencies, but this seems to have been fixed in the original configure script since. And by reverting to the default, we ensure that we also pick up all the other improvements that have happened there.

And I'll include the pin_subpackage syntax, according to what I wrote here.


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@dlaehnemann dlaehnemann merged commit ba682a7 into master Oct 27, 2023
5 checks passed
@dlaehnemann dlaehnemann deleted the bioconductor-rhdf5lib-include-libcurl-dep-and-cleanup-configure branch October 27, 2023 12:58
johanneskoester pushed a commit that referenced this pull request Oct 30, 2023
… downstream in bioconductor-rhdf5lib, include pin_subpackage syntax (#43900)

* fix: [bioconductor-rhdf5] explicitly include libcurl dependency

I think that this will fix an issue with `libcrypto.so` not being found that I reported over at `rhdf5`:
grimbough/rhdf5#131

* bump version number

* Update bioconductor-rhdf5: include `run_exports` with `pin_subpackage`

* introduce full_name variable to include `bioconductor-` prefix

* remove libcurl again, as this is handled downstream in bioconductor-rhd5flib

This is the PR that handles this:
#43930

And here's the discussion that pinpoints where the libcurl dependency belongs:
grimbough/rhdf5#131 (comment)

* clean up full_name usage

* include comment about pinning not necessarily being decided, yet

* move the build section to the start of requirements

* fix typo
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