Add libgff recipe #51706
Add libgff recipe #51706
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📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces two significant changes related to the Second, a new configuration file called Possibly related PRs
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Actionable comments posted: 3
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (2)
- recipes/libgff/build.sh (1 hunks)
- recipes/libgff/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/libgff/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (2)
recipes/libgff/build.sh (2)
5-9: LGTM: Proper OS-specific CMake configurationThe Darwin-specific CMake configuration is correct and follows best practices by disabling framework and bundle finding, which can cause issues on macOS builds.
1-16: Consider adding build artifact verificationAfter the build completes, it would be beneficial to verify that essential build artifacts are present.
#!/bin/bash # Check if the recipe includes test commands in meta.yaml echo "Checking for test commands in meta.yaml..." rg "test:" -A 5 recipes/libgff/meta.yaml # Verify if libgff.a is listed in the test commands echo "Checking if libgff.a is being tested..." rg "libgff\.a" recipes/libgff/meta.yaml
| -DCMAKE_CXX_FLAGS="${CXXFLAGS}" \ | ||
| "${CONFIG_ARGS}" | ||
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| cmake --build build --target install -j "${CPU_COUNT}" -v |
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Add error checking for build step
The build command should include error checking to ensure the build process completes successfully.
-cmake --build build --target install -j "${CPU_COUNT}" -v
+if ! cmake --build build --target install -j "${CPU_COUNT}" -v; then
+ echo "Build failed"
+ exit 1
+fi📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| cmake --build build --target install -j "${CPU_COUNT}" -v | |
| if ! cmake --build build --target install -j "${CPU_COUNT}" -v; then | |
| echo "Build failed" | |
| exit 1 | |
| fi |
| cmake -S . -B build -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ | ||
| -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER="${CXX}" \ | ||
| -DCMAKE_CXX_FLAGS="${CXXFLAGS}" \ | ||
| "${CONFIG_ARGS}" |
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🛠️ Refactor suggestion
Consider adding additional CMake configuration options
While the basic CMake configuration is correct, consider adding these improvements for better build control:
- Enable position-independent code (-DCMAKE_POSITION_INDEPENDENT_CODE=ON)
- Set RPATH handling (-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE)
cmake -S . -B build -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
-DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER="${CXX}" \
-DCMAKE_CXX_FLAGS="${CXXFLAGS}" \
+ -DCMAKE_POSITION_INDEPENDENT_CODE=ON \
+ -DCMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE \
"${CONFIG_ARGS}"📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| cmake -S . -B build -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ | |
| -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER="${CXX}" \ | |
| -DCMAKE_CXX_FLAGS="${CXXFLAGS}" \ | |
| "${CONFIG_ARGS}" | |
| cmake -S . -B build -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ | |
| -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER="${CXX}" \ | |
| -DCMAKE_CXX_FLAGS="${CXXFLAGS}" \ | |
| -DCMAKE_POSITION_INDEPENDENT_CODE=ON \ | |
| -DCMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE \ | |
| "${CONFIG_ARGS}" |
| #!/bin/bash | ||
|
|
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| export M4="${BUILD_PREFIX}/bin/m4" |
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💡 Codebase verification
M4 dependency missing from build requirements
The build script uses M4 macro processor (${BUILD_PREFIX}/bin/m4) but it's not listed as a build requirement in meta.yaml. This needs to be added to prevent potential build failures.
- Add
m4to thebuild:section inrecipes/libgff/meta.yaml:
requirements:
build:
- make
- cmake
- {{ compiler('cxx') }}
- m4 # Required for build process🔗 Analysis chain
Verify M4 macro processor availability
The script assumes M4 is available in BUILD_PREFIX, but we should verify its presence to prevent build failures.
Let me gather more information about the build requirements to verify if m4 is properly listed as a dependency.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if m4 is listed as a build requirement in meta.yaml
rg -l "m4" recipes/libgff/meta.yaml
# Verify the path exists in typical Bioconda builds
if [ ! -f "${BUILD_PREFIX}/bin/m4" ]; then
echo "Warning: M4 path not found at expected location"
fi
Length of output: 406
Script:
#!/bin/bash
# Check build requirements in meta.yaml
echo "Checking build requirements..."
rg "requirements:" -A 10 recipes/libgff/meta.yaml
# Also check if m4 is mentioned anywhere else in meta.yaml
echo -e "\nChecking for m4 mentions..."
rg "m4" recipes/libgff/meta.yaml
Length of output: 345
Describe your pull request here
Please read the guidelines for Bioconda recipes before opening a pull request (PR).
General instructions
@BiocondaBot please add labelcommand.@bioconda/corein a comment.Instructions for avoiding API, ABI, and CLI breakage issues
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If not already present in the meta.yaml, make sure to specify
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run_exportssection like this:with
...being one of:{{ pin_subpackage("myrecipe", max_pin="x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin="x.x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin=None) }}while replacing
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