Treekin

[mwaldl]

Add runtime dependency libgfortran3 to meta,yaml file. This resolves the runtime error "treekin: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory".

Further clean up might be needed, including adding libgfortran as dependency during build.

[coderabbitai]

📝 Walkthrough

📝 Walkthrough

📝 Walkthrough

Walkthrough

The pull request introduces modifications to the meta.yaml file for the treekin package. The primary change is the update of the build number from 4 to 5. Additionally, a new section called run_exports has been added under the build section, which includes a reference to a subpackage myrecipe with a maximum pinning constraint. A new runtime requirement specifying libgfortran with a version constraint of =3 has also been included under the run section. Furthermore, the indentation for the run section has been corrected to align with YAML formatting standards. No other alterations to the logic, error handling, or control flow have been made in this update.

Possibly related PRs

• 2024.4 #50977: This PR updates the meta.yaml file and emphasizes the importance of specifying run_exports, which is directly related to the changes made in the main PR regarding the introduction of a run_exports section.

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[martin-g]

@bgruening @aliciaaevans This PR fails with:

13:51:51 �[36mBIOCONDA DEBUG�[0m Found: LintMessage(recipe=Recipe "treekin", check=<class 'bioconda_utils.lint.check_build_help.should_use_compilers'>, severity=<Severity.ERROR: 30>, title='The recipe requires a compiler directly', body="\nSince version 3, `conda-build` uses a special syntax to require\ncompilers for a given language matching the architecture for which\na package is being build. Please use:\n\n    requirements:\n       build:\n         - {{ compiler('language') }}\n\nWhere language is one of `c`, `cxx`, `fortran`, `go` or\n`cgo`. You can specify multiple compilers if needed.\n\nThere is no need to add `libgfortran`, `libgcc`, or\n`toolchain` to the dependencies as this will be handled by\nconda-build itself.", start_line=33, end_line=34, fname='recipes/treekin/meta.yaml', canfix=False)�[0m

but the recipe properly uses - {{ compiler("cxx") }} and - {{ compiler("fortran") }}.

In addition the linting error probably should mention rust too.

[mwaldl]

@martin-g @bgruening @aliciaaevans Does the linter fail because libgfortran is defined as a runtime dependency?
The build dependency is properly defined as - {{ compiler("fortran") }}, however it appears to also be required at runtime. Any suggestions on how to resolve this?

[martin-g]

@mwaldl According to https://github.com/bioconda/bioconda-utils/blob/5910a1009b8b783eb4a3e1a9b15ab71b9794899a/bioconda_utils/lint/check_build_help.py#L13-L47 it is not allowed to use libgfortran as a dependency.
Let's try with - compiler("fortran") as a run dependency!

[martin-g]

Now it fails with

09:30:20 BIOCONDA DEBUG Found: LintMessage(recipe=Recipe "treekin", check=<class 'bioconda_utils.lint.check_build_help.compilers_must_be_in_build'>, severity=<Severity.ERROR: 30>, title='The recipe requests a compiler in a section other than build', body="\nPlease move the `{{ compiler('language') }}` line into the\n`requirements: build:` section.", start_line=33, end_line=34, fname='recipes/treekin/meta.yaml', canfix=False)