Hopla: bump pandoc #50978
Hopla: bump pandoc #50978
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Bump pandoc dependency to fix memory leak issue
📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces three modifications to the Changes
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Actionable comments posted: 1
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- recipes/hopla/meta.yaml (2 hunks)
🔇 Additional comments (2)
recipes/hopla/meta.yaml (2)
13-13: Build number increment looks good.Incrementing the build number from 0 to 1 is correct when updating the recipe without changing the package version. This change follows best practices for Conda packaging.
Line range hint
1-42: Overall recipe structure and content look good.The recipe follows Conda packaging best practices:
- Proper use of Jinja2 variables for version and hash.
- Correct specification of package metadata, source, and requirements.
- Appropriate use of 'noarch: generic' for an R package.
- Correct license specification.
- Inclusion of a basic test command.
No additional issues or improvements are identified beyond the changes made.
Note: The
run_exportssection mentioned in the PR objectives is not present in this recipe. This is typically used for compiled libraries to ensure ABI compatibility. For an R package like this, it's generally not necessary.
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No artifacts found on the most recent builds. Either the builds failed, the artifacts have been removed due to age, or the recipe was blacklisted/skipped. |
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Actionable comments posted: 2
📜 Review details
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📒 Files selected for processing (1)
- recipes/hopla/meta.yaml (2 hunks)
🔇 Additional comments (1)
recipes/hopla/meta.yaml (1)
13-13: Build number increment looks good.Incrementing the build number is the correct approach when updating a package without changing its version. This change follows Conda packaging best practices.
recipes/hopla/meta.yaml
Outdated
| run_exports: | ||
| - {{ pin_subpackage("myrecipe", max_pin="x") }} |
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Clarification needed on run_exports addition.
The addition of run_exports is generally beneficial for maintaining compatibility with downstream recipes. However, there are some concerns with the current implementation:
- The package name is "hopla", but the
run_exportsrefers to "myrecipe". - The use of "myrecipe" seems like a placeholder and may not be intentional.
- The PR objectives don't mention anything about adding
run_exports.
Please clarify:
- Is the addition of
run_exportsintentional for this PR? - If yes, should it be
{{ pin_subpackage("hopla", max_pin="x") }}instead of{{ pin_subpackage("myrecipe", max_pin="x") }}? - If this is unintended, please remove the
run_exportssection.
| @@ -26,7 +28,7 @@ requirements: | |||
| - bioconductor-genomicranges >=1.42.0 | |||
| - bioconductor-dnacopy >=1.64.0 | |||
| - merlin 1.1.2.* # [not osx] | |||
| - pandoc >=2.* | |||
| - pandoc >=3.1.5 | |||
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💡 Codebase verification
Pandoc version update introduces compatibility issues with certain recipes.
The update of pandoc to >=3.1.5 may cause compatibility problems with other recipes in the Bioconda ecosystem. Specifically, recipes/r-shinyngs/meta.yaml specifies pandoc <2.19, which conflicts with the new version requirement.
🔗 Analysis chain
Pandoc version update addresses memory leak but may cause compatibility issues.
Updating pandoc to >=3.1.5 aligns with the PR objective of addressing a memory leak issue. However, this update may introduce compatibility issues with other recipes in the Bioconda ecosystem.
A previous analysis identified at least one recipe (recipes/r-shinyngs/meta.yaml) that specifies pandoc <2.19. Let's verify if this is still the case and check for any other potential conflicts:
Please review the results of this script and consider the following options:
- If there are no conflicts, proceed with the update.
- If conflicts exist, consider:
a. Updating the conflicting recipes to be compatible with pandoc 3.1.5+
b. Using a more conservative version range that addresses the memory leak while maintaining compatibility (e.g.,>=2.19,<3)
c. Discussing with the maintainers of affected packages to find a solution that works for all parties.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check for other recipes that depend on pandoc and their version requirements
# Search for pandoc dependencies in other recipe files
rg --type yaml 'pandoc' recipes/ | grep -v 'recipes/hopla/meta.yaml'
Length of output: 2247
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No artifacts found on the most recent builds. Either the builds failed, the artifacts have been removed due to age, or the recipe was blacklisted/skipped. |
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No artifacts found on the most recent builds. Either the builds failed, the artifacts have been removed due to age, or the recipe was blacklisted/skipped. |
Bump pandoc dependency to fix memory leak issue
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pandocdependency to require version 3.1.5 or higher, ensuring compatibility with the latest features and improvements.hoplasubpackage should be pinned with a maximum version constraint.hoplarecipe.