Rebuild breseq #51221
Rebuild breseq #51221
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (3)
recipes/breseq/build.sh (2)
5-7: Good environment setup, but consider modifying LDFLAGSThe environment variable setup looks good and uses $PREFIX correctly. However, there's a potential issue with LDFLAGS.
Consider modifying the LDFLAGS line to avoid potential duplication:
-export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export LDFLAGS="-L${PREFIX}/lib ${LDFLAGS}"This ensures that the new path is prepended rather than appended, which can help avoid potential conflicts or duplications.
9-13: Good configure setup, but consider removing explicit optimization flagThe configure and build setup looks good overall. Running
autoreconfbefore./configureis a good practice.Consider removing the
-O3flag from CXXFLAGS:- CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" \ + CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include" \Conda-build often sets its own optimization flags, and explicitly setting
-O3might override those. Letting conda-build handle optimization can lead to more consistent builds across different packages.recipes/breseq/meta.yaml (1)
46-50: LGTM: Addition of identifiers enhances package metadata.The new identifiers field improves the discoverability and cross-referencing of the package. This is a valuable addition to the metadata.
Consider adding a brief comment explaining the significance of these identifiers, especially the distinction between the different biotools entries (breseq, breseq_bam2aln, breseq_bam2cov). This would help users understand the various components or versions referenced by these identifiers.
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📒 Files selected for processing (2)
- recipes/breseq/build.sh (1 hunks)
- recipes/breseq/meta.yaml (2 hunks)
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🔇 Additional comments (7)
recipes/breseq/build.sh (3)
1-4: LGTM: Good script setupThe script starts with the correct shebang and uses
set -euxfor strict error handling and debugging, which are good practices for build scripts.
14-14: LGTM: Efficient build processThe make commands are well-structured. Using
"${CPU_COUNT}"for parallel building is good for efficiency, and the subsequentmake installis appropriate for installing the built package.
1-14: Overall, the build script looks good with minor suggestions for improvementThe script follows good practices for a conda build script, including proper environment setup, use of autoreconf, and efficient make commands. The suggested improvements (modifying LDFLAGS and removing the explicit -O3 flag) are minor and aimed at ensuring better consistency and avoiding potential issues in the conda build environment.
recipes/breseq/meta.yaml (4)
12-12: LGTM: Build number increment is appropriate.The build number has been correctly incremented from 1 to 2. This is the proper approach when making changes to a package without altering its version number.
37-38: LGTM: Summary reformatting improves readability.The summary has been reformatted as a multi-line string, which improves readability in the YAML file. The content remains unchanged, which is appropriate.
40-40: LGTM: Addition of dev_url is beneficial.The new dev_url field, pointing to the GitHub repository, has been added. This is a positive change as it provides users with a direct link to the development repository, following best practices for package metadata.
Line range hint
16-26: Verify removal of C compiler and zlib dependencies.The C compiler requirement and zlib run dependency have been removed. Please confirm that:
- The package no longer requires C compilation.
- zlib is not needed at runtime.
These changes could potentially affect the package's functionality or dependencies.
To verify these changes, please run the following script:
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@BiocondaBot please fetch artifacts |
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Package(s) built are ready for inspection:
Docker image(s) built:
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@jeffreybarrick mind testing the |
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Both of these |
Describe your pull request here
Fixes #51177
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