Add rdeval

[richard-burhans]

Add rdeval from The Vertebrate Genome Lab.

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Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes.
This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe.
If not already present in the meta.yaml, make sure to specify run_exports (see here for the rationale and comprehensive explanation).
Add a run_exports section like this:

build:
  run_exports:
    - ...

with ... being one of:

Case	run_exports statement
semantic versioning	{{ pin_subpackage("myrecipe", max_pin="x") }}
semantic versioning (0.x.x)	{{ pin_subpackage("myrecipe", max_pin="x.x") }}
known breakage in minor versions	{{ pin_subpackage("myrecipe", max_pin="x.x") }} (in such a case, please add a note that shortly mentions your evidence for that)
known breakage in patch versions	{{ pin_subpackage("myrecipe", max_pin="x.x.x") }} (in such a case, please add a note that shortly mentions your evidence for that)
calendar versioning	{{ pin_subpackage("myrecipe", max_pin=None) }}

while replacing "myrecipe" with either name if a name|lower variable is defined in your recipe or with the lowercase name of the package in quotes.

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[coderabbitai]

Actionable comments posted: 1

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between e3a192a and 6ab51c5.

📒 Files selected for processing (3)

• recipes/rdeval/Makefile.patch (1 hunks)
• recipes/rdeval/gfalibs-Makefile.patch (1 hunks)
• recipes/rdeval/meta.yaml (1 hunks)

🚧 Files skipped from review as they are similar to previous changes (1)

• recipes/rdeval/meta.yaml

🔇 Additional comments (6)

recipes/rdeval/Makefile.patch (2)

7-12: LGTM! Improved LDFLAGS handling

The conditional assignment of LDFLAGS is a good improvement as it:

1. Preserves any existing LDFLAGS from the build environment
2. Ensures -pthread is always included
3. Follows Conda best practices for respecting build environment variables

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1-25: Consider ABI compatibility requirements

Since this is a Bioconda recipe and the changes affect compilation flags, please ensure that:

1. The package's meta.yaml includes appropriate run_exports to handle ABI compatibility
2. The version constraints in run_exports account for potential ABI breaks from these build changes

✅ Verification successful

ABI compatibility is properly handled

The package already has appropriate run_exports configuration with max_pin="x.x", which correctly handles ABI compatibility for the build flag changes. The pinning ensures that users get compatible versions when the package is updated.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Check if meta.yaml has run_exports section
rg -A 5 "run_exports:" recipes/rdeval/meta.yaml || echo "No run_exports found"

Length of output: 168

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Script:

#!/bin/bash
# Check the package version and build number
rg "version:|build:" recipes/rdeval/meta.yaml

# Check if there are any shared libraries being built
fd -e so -e dylib -e dll . recipes/rdeval || echo "No shared libraries found"

# Check if the package links against core C++ libraries
rg "stdlib|stdcxx|c\+\+|libstdc\+\+" recipes/rdeval/meta.yaml

Length of output: 197

---

Script:

#!/bin/bash
# Check the actual build output targets in the Makefile
rg "^all:|\.o:|\.a:|\.so:" recipes/rdeval/Makefile.patch

# Check if there are any install targets that might reveal the built artifacts
rg "^install:" recipes/rdeval/Makefile.patch

# Look for the package version in the recipe
cat recipes/rdeval/meta.yaml

Length of output: 1118

recipes/rdeval/gfalibs-Makefile.patch (4)

4-5: LGTM: Improved compiler variable assignment

The change from = to ?= for CXX assignment is a good practice, allowing the compiler to be overridden from the environment while maintaining a default value. This is particularly useful for cross-compilation and platform-specific builds.

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18-18: LGTM: Improved build rules

The changes improve the build rules by:

1. Removing unnecessary empty command after the 'all' target
2. Correctly using CPPFLAGS for the compilation stage instead of LDFLAGS

This better reflects the proper usage of compiler flags during the build process.

Also applies to: 21-22

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1-25: Verify Bioconda build system compatibility

Please ensure these Makefile changes align with Bioconda's build requirements and don't impact downstream packages.

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13-13: Verify linking requirements

While removing the empty LDFLAGS is reasonable, please verify that no linking flags are needed for this library, especially considering potential dependencies declared in the recipe's meta.yaml.

[richard-burhans]

@BiocondaBot please add label

[richard-burhans]

@BiocondaBot please add label