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rPackages.rhdf5: fix installation #43287

Merged
merged 1 commit into from Jul 10, 2018
Merged

rPackages.rhdf5: fix installation #43287

merged 1 commit into from Jul 10, 2018

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iimog
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@iimog iimog commented Jul 10, 2018

Fix #43285

Motivation for this change

Fix installation of rPackages.rhdf5. More precisely rPackages.Rhdf5lib is fixed which is a dependency of rPackages.rhdf5 and many other R packages.

Things done
  • Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS)
  • Built on platform(s)
    • NixOS
    • macOS
    • other Linux distributions
  • Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
  • Tested compilation of all pkgs that depend on this change using nix-shell -p nox --run "nox-review wip"
  • Tested execution of all binary files (usually in ./result/bin/)
  • Determined the impact on package closure size (by running nix path-info -S before and after)
  • Fits CONTRIBUTING.md.

@iimog iimog requested a review from peti as a code owner July 10, 2018 14:42
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peti commented Jul 10, 2018

@GrahamcOfBorg build rPackages.rhdf5

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No attempt on aarch64-linux (full log)

The following builds were skipped because they don't evaluate on aarch64-linux: rPackages.rhdf5

Partial log (click to expand)


a) For `nixos-rebuild` you can set
  { nixpkgs.config.allowUnfree = true; }
in configuration.nix to override this.

b) For `nix-env`, `nix-build`, `nix-shell` or any other Nix command you can add
  { allowUnfree = true; }
to ~/.config/nixpkgs/config.nix.

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Success on x86_64-linux (full log)

Attempted: rPackages.rhdf5

Partial log (click to expand)

** testing if installed package can be loaded
* DONE (rhdf5)
post-installation fixup
shrinking RPATHs of ELF executables and libraries in /nix/store/37q0m8p9p90q9pswv71m5fxc5gq45jk7-r-rhdf5-2.25.4
shrinking /nix/store/37q0m8p9p90q9pswv71m5fxc5gq45jk7-r-rhdf5-2.25.4/library/rhdf5/libs/rhdf5.so
strip is /nix/store/4qvrxzxa535y8304mk195x50b6p9607d-binutils-2.30/bin/strip
patching script interpreter paths in /nix/store/37q0m8p9p90q9pswv71m5fxc5gq45jk7-r-rhdf5-2.25.4
/nix/store/37q0m8p9p90q9pswv71m5fxc5gq45jk7-r-rhdf5-2.25.4/library/rhdf5/downloadHDF5/downloadHDF5.sh: interpreter directive changed from "/bin/bash" to "/nix/store/8zkg9ac4s4alzyf4a8kfrig1j73z66dw-bash-4.4-p23/bin/bash"
checking for references to /build in /nix/store/37q0m8p9p90q9pswv71m5fxc5gq45jk7-r-rhdf5-2.25.4...
/nix/store/37q0m8p9p90q9pswv71m5fxc5gq45jk7-r-rhdf5-2.25.4

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Success on x86_64-darwin (full log)

Attempted: rPackages.rhdf5

Partial log (click to expand)

*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rhdf5)
post-installation fixup
strip is /nix/store/7ddbq63v97nk8gkbf7gcsfmby37h6gbl-cctools-binutils-darwin/bin/strip
patching script interpreter paths in /nix/store/mir34sh2g9z1y1d8z4nmhvjv1yy7ayfl-r-rhdf5-2.25.4
/nix/store/mir34sh2g9z1y1d8z4nmhvjv1yy7ayfl-r-rhdf5-2.25.4/library/rhdf5/downloadHDF5/downloadHDF5.sh: interpreter directive changed from "/bin/bash" to "/nix/store/q2wqq1k20v8kc3vckapqf5nws30brnni-bash-4.4-p23/bin/bash"
/nix/store/mir34sh2g9z1y1d8z4nmhvjv1yy7ayfl-r-rhdf5-2.25.4

@peti peti merged commit ff47879 into NixOS:master Jul 10, 2018
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@peti peti Awaiting requested review from peti

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Error installing rPackages.rhdf5
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@iimog @peti @GrahamcOfBorg