Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Hopla: bump pandoc #50978

Merged
merged 3 commits into from
Sep 26, 2024
Merged

Hopla: bump pandoc #50978

Changes from 2 commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 4 additions & 2 deletions recipes/hopla/meta.yaml
View file
Open in desktop
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("myrecipe", max_pin="x") }}
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

⚠️ Potential issue

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:

  1. The package name is "hopla", but the run_exports refers to "myrecipe".
  2. The use of "myrecipe" seems like a placeholder and may not be intentional.
  3. The PR objectives don't mention anything about adding run_exports.

Please clarify:

  1. Is the addition of run_exports intentional for this PR?
  2. If yes, should it be {{ pin_subpackage("hopla", max_pin="x") }} instead of {{ pin_subpackage("myrecipe", max_pin="x") }}?
  3. If this is unintended, please remove the run_exports section.

martin-g marked this conversation as resolved.
Show resolved Hide resolved

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
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

💡 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
Loading