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Hopla: bump pandoc #50978

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merged 3 commits into from
Sep 26, 2024
Merged

Hopla: bump pandoc #50978

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421965f
Hopla: bump pandoc
matthdsm Sep 26, 2024
76f9508
Update meta.yaml
matthdsm Sep 26, 2024
66166c1
Fix the package name
martin-g Sep 26, 2024
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6 changes: 4 additions & 2 deletions recipes/hopla/meta.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -10,8 +10,10 @@ source:
sha256: {{ hash }}

build:
number: 0
number: 1
noarch: generic
run_exports:
- {{ pin_subpackage("hopla", max_pin="x") }}

requirements:
run:
Expand All @@ -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

⚠️ Potential issue

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:

  1. If there are no conflicts, proceed with the update.
  2. 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


test:
commands:
Expand Down