Update zol to 1.5.0 #51673
Update zol to 1.5.0 #51673
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📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces an update to the The Possibly related PRs
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/zol/meta.yaml (1)
Line range hint
13-14: Consider pinning critical dependenciesThe package has extensive bioinformatics dependencies. While the current configuration is functional, consider:
- Pinning version ranges for critical dependencies to ensure reproducibility
- Adding upper bounds for dependencies known to have breaking changes
For example:
run: - diamond >=2.1.7,<3.0 - pyhmmer <2.0 - pandas >=2.0,<3.0Also applies to: 19-54
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
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📒 Files selected for processing (1)
- recipes/zol/meta.yaml (1 hunks)
🔇 Additional comments (2)
recipes/zol/meta.yaml (2)
2-2: LGTM: Version update is consistentThe version bump to 1.5.0 matches the PR objectives and follows semantic versioning.
9-10: Verify release availability and checksumLet's verify that the GitHub release exists and the checksum matches the source tarball.
| cp zol/njTree.R ${PREFIX}/bin/ | ||
| cp zol/phyloHeatmap.R ${PREFIX}/bin/ | ||
| cp zol/salt_gc_vs_ribo_aai.R ${PREFIX}/bin/ | ||
| export LDFLAGS= |
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Avoid clearing LDFLAGS in conda build scripts.
Setting LDFLAGS to empty could override important system-specific linker flags that conda-build provides. This might cause linking issues on some platforms.
Either remove this line or preserve existing flags:
-export LDFLAGS=
+export LDFLAGS="${LDFLAGS} -Wl,-headerpad_max_install_names"📝 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.
| export LDFLAGS= | |
| export LDFLAGS="${LDFLAGS} -Wl,-headerpad_max_install_names" |
| ${CXX} -std=c++11 -Wl,-headerpad_max_install_names -o ${PREFIX}/bin/runRBH src/zol/orthologs/runRBH.cpp | ||
| ${CXX} -std=c++11 -Wl,-headerpad_max_install_names -o ${PREFIX}/bin/splitDiamondResults src/zol/orthologs/splitDiamondResults.cpp | ||
| ${CXX} -std=c++11 -Wl,-headerpad_max_install_names -o ${PREFIX}/bin/splitDiamondResultsForFai src/zol/splitDiamondResultsForFai.cpp |
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💡 Codebase verification
Platform-specific linker flags should be handled by conda-forge's compiler configuration
From the meta.yaml, we can see that the package properly uses conda-forge's C++ compiler configuration ({{ compiler('cxx') }}). This means we don't need to manually handle platform-specific flags as conda-forge's compiler infrastructure will handle this automatically.
The source files referenced in build.sh don't exist in the expected locations, suggesting they might be part of the downloaded source archive. Since we can't verify the C++11 requirements in the source code, we should rely on conda-forge's default compiler settings.
- Remove the macOS-specific
-Wl,-headerpad_max_install_namesflag and let conda-forge handle platform-specific linking - Keep using C++11 as we can't verify if newer features are used in the source code
- Simplify the build script to use conda-forge's compiler configuration
-${CXX} -std=c++11 -Wl,-headerpad_max_install_names -o ${PREFIX}/bin/runRBH src/zol/orthologs/runRBH.cpp
-${CXX} -std=c++11 -Wl,-headerpad_max_install_names -o ${PREFIX}/bin/splitDiamondResults src/zol/orthologs/splitDiamondResults.cpp
-${CXX} -std=c++11 -Wl,-headerpad_max_install_names -o ${PREFIX}/bin/splitDiamondResultsForFai src/zol/splitDiamondResultsForFai.cpp
+${CXX} -std=c++11 -o ${PREFIX}/bin/runRBH src/zol/orthologs/runRBH.cpp
+${CXX} -std=c++11 -o ${PREFIX}/bin/splitDiamondResults src/zol/orthologs/splitDiamondResults.cpp
+${CXX} -std=c++11 -o ${PREFIX}/bin/splitDiamondResultsForFai src/zol/splitDiamondResultsForFai.cpp🔗 Analysis chain
Consider cross-platform compatibility for linker flags.
The -Wl,-headerpad_max_install_names flag is specific to macOS and may cause issues on other platforms. Additionally, the hardcoded C++11 standard might be outdated for newer compilers.
Let's verify the compiler requirements in the package metadata:
Consider these improvements:
- Make the linker flags conditional based on the platform
- Use the conda-forge compiler standards
- Consider upgrading to a newer C++ standard
Here's a suggested implementation:
-${CXX} -std=c++11 -Wl,-headerpad_max_install_names -o ${PREFIX}/bin/runRBH src/zol/orthologs/runRBH.cpp
-${CXX} -std=c++11 -Wl,-headerpad_max_install_names -o ${PREFIX}/bin/splitDiamondResults src/zol/orthologs/splitDiamondResults.cpp
-${CXX} -std=c++11 -Wl,-headerpad_max_install_names -o ${PREFIX}/bin/splitDiamondResultsForFai src/zol/splitDiamondResultsForFai.cpp
+# Set platform-specific flags
+LINKER_FLAGS=""
+if [[ "$OSTYPE" == "darwin"* ]]; then
+ LINKER_FLAGS="-Wl,-headerpad_max_install_names"
+fi
+
+# Compile C++ programs
+for prog in runRBH splitDiamondResults splitDiamondResultsForFai; do
+ ${CXX} -std=c++14 ${LINKER_FLAGS} \
+ -o ${PREFIX}/bin/${prog} \
+ src/zol/orthologs/${prog}.cpp
+done🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if there are any compiler requirements specified
rg "compiler:" recipes/zol/meta.yaml
Length of output: 36
Script:
#!/bin/bash
# Let's check the entire meta.yaml file to understand build requirements
cat recipes/zol/meta.yaml
# Also check if there are any other build scripts that might set compiler flags
fd "build.*" recipes/zol/
# Let's also check for any C++ source files to understand minimum required features
fd ".+\.cpp$" -x head -n 20 {}
Length of output: 1558
Script:
#!/bin/bash
# Let's check the actual C++ source files content to understand C++11 requirements
rg -l "std::" src/zol/orthologs/runRBH.cpp src/zol/orthologs/splitDiamondResults.cpp src/zol/splitDiamondResultsForFai.cpp || true
# Let's also check if these files exist at the specified paths
fd -t f "runRBH.cpp|splitDiamondResults.cpp|splitDiamondResultsForFai.cpp"
# Check if there are any platform-specific build configurations
rg "OSTYPE|darwin|linux" recipes/zol/
Length of output: 475
Update
zol: 1.4.12 → 1.5.0recipes/zol(click to view/edit other files)@Kalan-LabThis pull request was automatically generated (see docs).