rPackages.hdf5r: fix compile error

[Kupac]

Description of changes

Due to HDFGroup/hdf5#1814
, the package doesn't compile, because it needs h5cc -show and h5cc -showconfig outputs in the config script. Switching back to hdf5_1_10 solved the problem, albeit it's an older version of the hdf5 lib (but seems to work).

Things done

• Built on platform(s)
  • x86_64-linux
  • aarch64-linux
  • x86_64-darwin
  • aarch64-darwin
• Tested, as applicable:
  • NixOS test(s) (look inside nixos/tests)
  • and/or package tests
  • or, for functions and "core" functionality, tests in lib/tests or pkgs/test
  • made sure NixOS tests are linked to the relevant packages
• Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
• Tested basic functionality of all binary files (usually in ./result/bin/)
• 24.05 Release Notes (or backporting 23.05 and 23.11 Release notes)
  • (Package updates) Added a release notes entry if the change is major or breaking
  • (Module updates) Added a release notes entry if the change is significant
  • (Module addition) Added a release notes entry if adding a new NixOS module
• Fits CONTRIBUTING.md.

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[philipp-baumann]

confirm nix-build --pure -A rPackages.rhdf5 compiles successfully on this PR for darwin-aarch64

# ...
/nix/store/k687y4hiraslz65qz8pli1wb5wmcabvn-clang-wrapper-16.0.6/bin/c++ -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/nix/store/1hfs8ylpsyfrrakhyvskr4dgycd0l16c-R-4.3.2/lib/R/lib -L/nix/store/hi4fialjfb9wd2f5al4vpzlyh8dz38fz-libcxx-16.0.6/lib -o rhdf5.so H5.o H5A.o H5D.o H5E.o H5F.o H5G.o H5I.o H5L.o H5O.o H5P.o H5R.o H5S.o H5S_extras.o H5T.o H5T_extras.o H5Z.o H5constants.o HandleList.o HandleListWrap.o bit64conversion.o external_filters.o h5dump.o h5ls.o h5testLock.o h5writeDataFrame.o printdatatype.o utils.o wrap.o -lhdf5 -lhdf5 -L/nix/store/1hfs8ylpsyfrrakhyvskr4dgycd0l16c-R-4.3.2/lib/R/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation
installing to /nix/store/5q2cqvk4ixvpbj9wkni9z1w6l5vk0h9d-r-rhdf5-2.46.1/library/00LOCK-rhdf5/00new/rhdf5/libs
** R
** inst
** byte-compile and prepare package for lazy loading
During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C" 
2: Setting LC_TIME failed, using "C" 
3: Setting LC_MESSAGES failed, using "C" 
4: Setting LC_MONETARY failed, using "C" 
** help
*** installing help indices
*** copying figures
** building package indices
During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C" 
2: Setting LC_TIME failed, using "C" 
3: Setting LC_MESSAGES failed, using "C" 
4: Setting LC_MONETARY failed, using "C" 
** installing vignettes
** testing if installed package can be loaded from temporary location
During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C" 
2: Setting LC_TIME failed, using "C" 
3: Setting LC_MESSAGES failed, using "C" 
4: Setting LC_MONETARY failed, using "C" 
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C" 
2: Setting LC_TIME failed, using "C" 
3: Setting LC_MESSAGES failed, using "C" 
4: Setting LC_MONETARY failed, using "C" 
** testing if installed package keeps a record of temporary installation path
* DONE (rhdf5)
Running phase: fixupPhase
checking for references to /private/tmp/nix-build-r-rhdf5-2.46.1.drv-0/ in /nix/store/5q2cqvk4ixvpbj9wkni9z1w6l5vk0h9d-r-rhdf5-2.46.1...
patching script interpreter paths in /nix/store/5q2cqvk4ixvpbj9wkni9z1w6l5vk0h9d-r-rhdf5-2.46.1
rewriting symlink /nix/store/5q2cqvk4ixvpbj9wkni9z1w6l5vk0h9d-r-rhdf5-2.46.1/nix-support/propagated-user-env-packages to be relative to /nix/store/5q2cqvk4ixvpbj9wkni9z1w6l5vk0h9d-r-rhdf5-2.46.1
/nix/store/5q2cqvk4ixvpbj9wkni9z1w6l5vk0h9d-r-rhdf5-2.46.1

[b-rodrigues]

Built and tested successfully on linux-aarch64 (rpi5):

> hdf5r::h5version()
hdf5r version 1.3.8 with C-library HDF5 Version  1.10.11 
[1] "1.10.11"

[b-rodrigues]

For curiosity's sake, if we wished to be on the latest version, would we need to overlay this definition?

nixpkgs/pkgs/tools/misc/hdf5/1.10.nix

Line 15 in cbc4211

version = "1.10.11";

[Kupac]

For curiosity's sake, if we wished to be on the latest version, would we need to overlay this definition?

For curiosity's sake, I'm overriding the version and src of hdf5_1_10 with those of hdf5. if that works, we'd have the latest version compiled without cmake - best of both worlds. And we wouldn't have to update hash at each version bump ;) Let's see how that works !

[Kupac]

> h5version()
hdf5r version 1.3.8 with C-library HDF5 Version  1.14.3 
[1] "1.14.3"

[Kupac]

I'm gonna push it, and see what @jbedo thinks. I kept it in a separate commit for now, in case we have to roll it back

[b-rodrigues]

Everything seems to be working (tested on linux-aarch64):

> hdf5r::h5version()
hdf5r version 1.3.8 with C-library HDF5 Version  1.14.3 
[1] "1.14.3"

[b-rodrigues]

I think if we keep this, this should likely go all the way down starting at line 944 (where packages with overrides are defined)

[Kupac]

Yes, I'm not sure where it belongs. Just keep in mind that it's not an rPackage itself that's overridden, but one of it's nativeBuildInputs.

[jbedo]

Fixed in #298837 by leveraging Rhdf5lib's library. If we need a newer version we can work on updating Rhdf5lib.