Update smudgeplot to 0.4.0 #51904
Update smudgeplot to 0.4.0 #51904
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
recipes/smudgeplot/build.sh (1)
5-5: Add error handling for make command.While the make command is well-structured with proper parallelization and prefix setting, it should include error handling to ensure build failures are caught.
-make -s INSTALL_PREFIX="${PREFIX}" -j"${CPU_COUNT}" +set -e +make -s INSTALL_PREFIX="${PREFIX}" -j"${CPU_COUNT}" || exit 1
| install -C exec/hetmers $PREFIX/bin | ||
| install -C exec/smudgeplot_plot.R $PREFIX/bin | ||
| install -C exec/centrality_plot.R $PREFIX/bin |
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💡 Codebase verification
Files referenced in install commands do not exist
The files hetmers, smudgeplot_plot.R, and centrality_plot.R that are being installed in the build.sh script do not exist in the repository. The installation commands will fail as the source files are missing from the expected exec/ directory.
install -C exec/hetmers $PREFIX/binwill failinstall -C exec/smudgeplot_plot.R $PREFIX/binwill failinstall -C exec/centrality_plot.R $PREFIX/binwill fail
🔗 Analysis chain
Verify executable permissions for new files.
The new executables hetmers and centrality_plot.R have been added. Please ensure they have the correct executable permissions set.
Let me verify if these files exist in a different location since the exec directory wasn't found.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check if the new executables have proper permissions in the source directory
# Test: Check executable permissions
echo "Checking executable permissions:"
ls -l exec/hetmers exec/centrality_plot.R
# Test: Verify if files exist and are executable
for file in "hetmers" "centrality_plot.R"; do
if [[ -x "exec/$file" ]]; then
echo "$file is executable"
else
echo "WARNING: $file is not executable"
fi
done
Length of output: 572
Script:
#!/bin/bash
# Search for the files in the repository
echo "Searching for files:"
fd "hetmers|centrality_plot.R|smudgeplot_plot.R" --type f
# If found, check their permissions
find . -type f -name "hetmers" -o -name "centrality_plot.R" -o -name "smudgeplot_plot.R" -exec ls -l {} \;
Length of output: 216
Update
smudgeplot: 0.3.0 → 0.4.0recipes/smudgeplot(click to view/edit other files)@KamilSJaronThis pull request was automatically generated (see docs).