Rebuild MaSuRCA recipe #51662
Rebuild MaSuRCA recipe #51662
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📝 WalkthroughWalkthroughThis pull request introduces several changes across three main files related to the Masurca software installation and build process. In the Possibly related PRs
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/masurca/0001-install.sh.patch (1)
13-14: Consider simplifying the cp command flagsThe change from
cp -atocp -arfadds redundant flags, as-aalready implies recursive copying (-r). Additionally, the force flag (-f) might mask potential issues during installation.Consider keeping just
cp -aunless there's a specific reason for the force flag:-(cd Flye && make && cp -a ../Flye $DEST); +(cd Flye && make && cp -a ../Flye $DEST);
📜 Review details
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Review profile: CHILL
📒 Files selected for processing (3)
- recipes/masurca/0001-install.sh.patch (1 hunks)
- recipes/masurca/build.sh (1 hunks)
- recipes/masurca/meta.yaml (2 hunks)
🧰 Additional context used
🪛 Shellcheck
recipes/masurca/build.sh
[warning] 4-4: BOOST_ROOT appears unused. Verify use (or export if used externally).
(SC2034)
🔇 Additional comments (8)
recipes/masurca/build.sh (3)
5-5: LGTM! Environment variables are properly configured.The changes improve the build configuration by:
- Using consistent quoting for all path variables
- Correctly appending to
LDFLAGSinstead of overwriting- Setting appropriate paths relative to
${PREFIX}Also applies to: 8-11
7-7: 🛠️ Refactor suggestionConsider the implications of aggressive optimization.
The change from
-O2to-O3enables more aggressive optimization. While this might improve performance, it can potentially:
- Increase build time
- Cause larger binary size
- Lead to unexpected behavior in some cases
The
-I${PREFIX}/includeinCXXFLAGSis redundant sinceCPATHis already set.#!/bin/bash # Check if other bioconda recipes use -O3 echo "Checking optimization levels in other bioconda recipes..." rg -l "export CXXFLAGS.*-O3" recipes/Consider these changes:
-export PERL_EXT_LDFLAGS="-shared -O3 -fstack-protector" +export PERL_EXT_LDFLAGS="-shared -O2 -fstack-protector" -export CFLAGS="${CFLAGS} -O3 -std=gnu90 ${LDFLAGS}" +export CFLAGS="${CFLAGS} -O2 -std=gnu90 ${LDFLAGS}" -export CXXFLAGS="${CXXFLAGS} -O3 -std=c++14 -I${PREFIX}/include ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -O2 -std=c++14 ${LDFLAGS}"Also applies to: 12-13
4-4: Verify BOOST_ROOT usage in the build process.The
BOOST_ROOTvariable is set but appears to be unused. Let's verify if this is required by the MaSuRCA build system.🧰 Tools
🪛 Shellcheck
[warning] 4-4: BOOST_ROOT appears unused. Verify use (or export if used externally).
(SC2034)
recipes/masurca/0001-install.sh.patch (1)
9-10: LGTM: Good addition ofautoreconfThe addition of
autoreconf -ifis a good practice when rebuilding packages, as it ensures the build system is properly regenerated with current autotools versions.recipes/masurca/meta.yaml (4)
25-28: LGTM: Build dependencies align with autotools usageThe addition of autotools-related build dependencies (automake, autoconf, libtool, pkg-config) is appropriate given the use of
autoreconfin the installation process.
47-52: LGTM: Improved metadata documentationThe changes enhance the recipe metadata by:
- Using consistent quoting for URLs
- Adding development and documentation URLs
- Specifying a more precise license family (GPL3)
15-15: Consider impact of looser version pinningThe change from
max_pin='x.x'tomax_pin='x'makes the version constraint less strict. This means downstream packages will accept any minor version updates, which could potentially lead to compatibility issues if there are breaking changes in minor releases.Also applies to: 18-18
11-12: Verify patch file existence and contentsThe addition of the patch file aligns with the new build dependencies. However, let's verify its presence in the repository.
✅ Verification successful
Let me generate additional shell scripts to verify the patch file existence and its contents.
Patch file exists and is properly formatted
The patch file exists and contains valid modifications to the installation script:
- Adds
autoreconf -ifstep for proper autotools configuration- Changes
cp -atocp -arffor more reliable file copyingThe patch file is present and properly formatted, addressing the concern in the review comment.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Check if the patch file exists and show its contents if [ -f recipes/masurca/0001-install.sh.patch ]; then echo "Patch file exists. Contents:" cat recipes/masurca/0001-install.sh.patch else echo "ERROR: Patch file not found!" fiLength of output: 322020
Script:
#!/bin/bash # Check if the patch file exists and show its contents ls -l recipes/masurca/0001-install.sh.patch cat recipes/masurca/0001-install.sh.patchLength of output: 924
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