Update ucsc-twobittofa to 472 #51654
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📝 WalkthroughWalkthroughThe pull request introduces several modifications across multiple files related to the Possibly related PRs
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (2)
recipes/ucsc-twobittofa/build.sh (1)
20-21: LGTM: Proper executable handling.The change to set permissions before moving the binary is correct. The chmod 755 ensures proper executable permissions (rwxr-xr-x).
Consider adding error checking for the binary operations:
-chmod 0755 bin/twoBitToFa -mv bin/twoBitToFa "${PREFIX}/bin" +if [ -f bin/twoBitToFa ]; then + chmod 0755 bin/twoBitToFa + mv bin/twoBitToFa "${PREFIX}/bin" +else + echo "Error: twoBitToFa binary not found" + exit 1 +firecipes/ucsc-twobittofa/include.macos.patch (1)
1-27: Consider generalizing the include path modificationsWhile this patch is named
include.macos.patch, the modifications to include paths are generally beneficial for all platforms. Consider:
- Making these changes part of the main build system rather than a macOS-specific patch
- Using a more generic patch name if these changes are indeed needed for all platforms
📜 Review details
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📒 Files selected for processing (4)
- recipes/ucsc-twobittofa/build.sh (1 hunks)
- recipes/ucsc-twobittofa/htmshell.patch (0 hunks)
- recipes/ucsc-twobittofa/include.macos.patch (1 hunks)
- recipes/ucsc-twobittofa/meta.yaml (3 hunks)
💤 Files with no reviewable changes (1)
- recipes/ucsc-twobittofa/htmshell.patch
🔇 Additional comments (9)
recipes/ucsc-twobittofa/build.sh (1)
12-12: LGTM: Optimization flag addition matches CFLAGS.The addition of
-O3optimization flag to CXXFLAGS is consistent with the existing CFLAGS configuration, which should improve runtime performance.Let's verify the optimization flags are consistently applied:
✅ Verification successful
Let me gather more information to verify the optimization flags across both CFLAGS and CXXFLAGS:
Optimization flags are consistently applied in both CFLAGS and CXXFLAGS
The verification confirms that
-O3optimization level is consistently set for both C and C++ compilation flags, with CXXFLAGS appropriately including the additional include path requirement. This is the correct configuration for optimal performance.🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Check if optimization flags are consistently used across make commands rg "CXXFLAGS.*-O[0-3]" recipes/ucsc-twobittofa/Length of output: 147
Script:
#!/bin/bash # Check both CFLAGS and CXXFLAGS settings in the build script rg "^export C(XX)?FLAGS.*=.*" recipes/ucsc-twobittofa/Length of output: 228
recipes/ucsc-twobittofa/include.macos.patch (3)
7-8: LGTM: Standard conda build configuration updateThe addition of
${PREFIX}/includetoHG_INCis the correct approach for conda packages, ensuring that headers from the conda environment are properly located during build.
15-16: LGTM: Consistent include path configurationThe modification to
KENT_INCmaintains consistency with the global build configuration, properly integrating with the conda build environment.
23-24: Verify Python 3 compatibility of the scriptThe shebang change from
python2.7topythonsuggests this script will now run with any Python version. This could lead to compatibility issues if the script contains Python 2-specific code.recipes/ucsc-twobittofa/meta.yaml (5)
31-31: LGTM! Appropriate addition of clangdev for macOS builds.The addition of clangdev as a host requirement for macOS is correct and follows Bioconda's best practices for C/C++ packages.
Line range hint
19-21: Verify run_exports pinning strategy.The
run_exportssection usesmax_pin=None, which means no automatic version constraints will be added to downstream dependencies. Given that this is a binary package, consider if version pinning would be beneficial to prevent potential ABI incompatibilities.#!/bin/bash # Description: Check if other UCSC tools use version pinning rg -l "run_exports" recipes/ucsc-**/meta.yaml
45-45: Verify the versioned documentation URL.The changes to the documentation URLs are good improvements:
- Removed trailing slash from home URL
- Added proper punctuation to summary
- Using versioned documentation path
#!/bin/bash # Description: Verify if the versioned README exists # Test the documentation URL curl -s -I "https://github.com/ucscGenomeBrowser/kent/blob/master/v472_base/README" | head -n 1Also applies to: 47-47, 49-49
14-15: Verify the existence of both patch files.✅ Verification successful
Both patch files exist and are properly configured
The verification confirms that both patch files are present in the recipe directory:
include.patch(1241 bytes) for Linux systemsinclude.macos.patch(1223 bytes) for macOS systems🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check if both patch files exist in the recipe directory fd "include.*\.patch$" recipes/ucsc-twobittofa/Length of output: 18690
Script:
#!/bin/bash # Let's check if the patch files exist in the recipe directory ls -la recipes/ucsc-twobittofa/include*.patchLength of output: 270
3-4: Verify the SHA256 checksum for version 472.
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