Update table2asn to 1.28.1179 #51951
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📝 WalkthroughWalkthroughThe pull request includes updates to two main files: In Possibly related PRs
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (2)
recipes/table2asn/build.sh (1)
6-7: LGTM! Consider standardizing indentation.The changes to use double brackets and force copy are good improvements. However, consider using spaces instead of tabs for indentation to follow common shell scripting conventions.
- cp -f mac.table2asn ${PREFIX}/bin/table2asn + cp -f mac.table2asn ${PREFIX}/bin/table2asnrecipes/table2asn/meta.yaml (1)
Line range hint
39-41: Consider updating skip-lints documentation.The skip-lints section indicates this package shouldn't be noarch. It would be helpful to add a comment explaining why these lints are skipped (e.g., because of platform-specific binaries).
extra: skip-lints: - - should_be_noarch_generic - - should_not_be_noarch_source + - should_be_noarch_generic # Package contains platform-specific binaries + - should_not_be_noarch_source # Package contains platform-specific binaries🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
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📒 Files selected for processing (2)
recipes/table2asn/build.sh(2 hunks)recipes/table2asn/meta.yaml(1 hunks)
🔇 Additional comments (6)
recipes/table2asn/build.sh (2)
Line range hint 18-24: LGTM! The RPATH modifications look correct.
The change to double brackets is a good improvement. The RPATH modifications are properly handled for both Darwin and non-Darwin systems, ensuring the correct linking of the bzip2 library.
9-9: 🛠️ Refactor suggestion
Verify single file matching for wildcard pattern.
While adding the -f flag is good, using the wildcard pattern *.table2asn could be problematic if multiple matching files exist. This could lead to unpredictable behavior in which file gets copied.
Consider being more specific with the file name or add a check to ensure only one file matches:
- cp -f *.table2asn ${PREFIX}/bin/table2asn
+ # Ensure only one file matches
+ table2asn_files=( *.table2asn )
+ if [ ${#table2asn_files[@]} -ne 1 ]; then
+ echo "Error: Expected exactly one table2asn file, found ${#table2asn_files[@]}"
+ exit 1
+ fi
+ cp -f "${table2asn_files[0]}" "${PREFIX}/bin/table2asn"recipes/table2asn/meta.yaml (4)
Line range hint 17-19: LGTM: Appropriate dependency pinning strategy.
The run_exports section correctly pins the package with max_pin="x", which is appropriate for this type of tool where minor version updates shouldn't break compatibility.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
Line range hint 21-24: Verify if runtime dependencies need updates.
The host requirements remain unchanged. Given this is a version update, please verify if any of the dependencies (libidn11, zlib, bzip2) require version updates.
#!/bin/bash
# Description: Check for any dependency changes in the new version's documentation
curl -sL "https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/2024-10-23/by_program/table2asn/DOCUMENTATION/table2asn_readme.txt" | grep -i "requirement\|depend\|version"🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
2-3: Verify the package version and checksum.
The version has been updated to 1.28.1179. Let's verify the Linux checksum against the source.
#!/bin/bash
# Description: Verify the Linux package checksum
# Download the file and compute its checksum
curl -sL "https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/2024-10-23/by_program/table2asn/linux64.table2asn.gz" | sha256sum11-12: Verify the macOS source configuration.
The macOS-specific URL and checksum have been updated. Let's verify the checksum.
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