Edited the build.sh and mata.yaml files #52085
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📝 Walkthrough📝 Walkthrough📝 Walkthrough📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces modifications to two files: Possibly related PRs
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
recipes/sfold/build.sh (1)
17-19: Consider adding error handling for the shebang updatesThe shebang updates improve script portability by using
/usr/bin/env perl. However, consider making the script more robust.Here's a suggested improvement:
-sed -i "s:/usr/bin/perl:/usr/bin/env perl:" STarMir/*.pl -sed -i "s:/usr/bin/perl:/usr/bin/env perl:" STarMir/starmiZZer-param/*.pl -sed -i "s:/usr/bin/perl:/usr/bin/env perl:" bin/*.pl +# Update shebang lines in Perl scripts +for dir in "STarMir" "STarMir/starmiZZer-param" "bin"; do + if [ -d "$dir" ]; then + find "$dir" -name "*.pl" -type f -print0 | while IFS= read -r -d '' file; do + if head -n1 "$file" | grep -q "^#!/usr/bin/perl"; then + sed -i "1s:^#!/usr/bin/perl:#!/usr/bin/env perl:" "$file" + fi + done + fi +doneThis version:
- Checks if directories exist before processing
- Only updates files that actually have the old shebang
- Uses find to safely handle filenames with spaces
- Processes files one by one with proper error checking
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📒 Files selected for processing (2)
recipes/sfold/build.sh(1 hunks)recipes/sfold/meta.yaml(2 hunks)
🔇 Additional comments (2)
recipes/sfold/build.sh (1)
16-16: LGTM: Path configuration looks correct
The SFOLDDIR path modification is properly implemented using the conda build system's PREFIX variable.
recipes/sfold/meta.yaml (1)
27-27: Verify the necessity of r-cluster dependency.
The addition of r-cluster as a runtime dependency should be validated against the changes in build.sh and the package's requirements.
#!/bin/bash
# Check build.sh for R cluster usage
echo "Checking build.sh for R cluster usage:"
rg -l "cluster" recipes/sfold/build.sh || echo "No direct references found in build.sh"
# Check if any R scripts in the source use cluster package
echo -e "\nChecking source code for R cluster package usage:"
fd -e R -e r . | xargs rg -l "library.*cluster|require.*cluster" || echo "No R files found using cluster package"
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Resolved conflict in meta.yaml by keeping number: 2 |
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The build.sh file was edited. |
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@BiocondaBot please fetch artifacts |
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