Add r-pgenlibr #52020
Add r-pgenlibr #52020
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📝 Walkthrough📝 Walkthrough📝 Walkthrough📝 WalkthroughWalkthroughThis pull request introduces two new files in the Suggested labels
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/r-pgenlibr/meta.yaml (1)
53-57: Consider enhancing test coverage.While the basic library load test is present, consider adding more comprehensive tests to verify package functionality.
Example of additional test commands:
test: commands: - $R -e "library('pgenlibr')" # [not win] - "\"%R%\" -e \"library('pgenlibr')\"" # [win] + - $R -e "stopifnot(packageVersion('pgenlibr') == '{{ version }}')" # [not win] + - "\"%R%\" -e \"stopifnot(packageVersion('pgenlibr') == '{{ version }}')\"" # [win]
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📒 Files selected for processing (3)
recipes/r-pgenlibr/bld.bat(1 hunks)recipes/r-pgenlibr/build.sh(1 hunks)recipes/r-pgenlibr/meta.yaml(1 hunks)
✅ Files skipped from review due to trivial changes (1)
- recipes/r-pgenlibr/build.sh
🧰 Additional context used
🪛 yamllint
recipes/r-pgenlibr/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (6)
recipes/r-pgenlibr/bld.bat (2)
1-1: LGTM: Correct R package installation command.
The command correctly uses environment variables %R% and %R_ARGS% to ensure flexible and configurable package installation.
2-2: LGTM: Essential error handling is in place.
The error handling ensures build failures are properly propagated to the CI system, which is crucial for maintaining package quality in Bioconda.
recipes/r-pgenlibr/meta.yaml (4)
1-14: LGTM! Package metadata and source configuration are well-structured.
The package version, source URLs, and checksum are properly defined following conda-forge R packaging conventions.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
15-25: LGTM! Build configuration is appropriate.
The build configuration includes necessary settings for both Windows and non-Windows environments, with proper rpaths and DSO whitelist configuration.
26-52: LGTM! Dependencies are well-defined with proper version pinning.
The requirements section correctly implements:
- Version pinning through run_exports as requested in PR objectives
- Platform-specific compiler requirements
- Necessary R dependencies with version constraints
58-90: LGTM! Package information is comprehensive and well-documented.
The about section properly includes all necessary metadata, license information, and maintainer details.
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/r-pgenlibr/meta.yaml (1)
37-40: Consider enhancing test coverageThe current test only verifies library loading. Consider adding basic functionality tests, such as:
- Reading a small example .pgen file
- Checking key function availability
Example addition:
test: commands: - $R -e "library('pgenlibr')" # [not win] + - $R -e "stopifnot('read_pgen' %in% getNamespaceExports('pgenlibr'))" # [not win]
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📒 Files selected for processing (1)
recipes/r-pgenlibr/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/r-pgenlibr/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (3)
recipes/r-pgenlibr/meta.yaml (3)
13-19: Excellent use of run_exports for ABI stability!
The inclusion of run_exports with proper version pinning helps prevent ABI breakage in downstream packages, which aligns perfectly with the PR objectives.
44-47: Verify bioinformatics relevance
The package appears to be related to PLINK 2, which is a bioinformatics tool for genome association analysis. However, let's verify its usage in bioinformatics research.
#!/bin/bash
# Check if this package is used by other bioinformatics tools
rg -l "r-pgenlibr" recipes/*/meta.yaml
# Check the cited paper for bioinformatics relevance
echo "Verifying DOI: 10.1186/s13742-015-0047-8"21-35: Consider adding R-base version constraint
While the dependencies are well-structured, consider adding a minimum R-base version constraint to ensure compatibility. This can be determined from the package's CRAN requirements.
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/r-pgenlibr/meta.yaml (1)
37-40: Consider enhancing test coverage.While loading the library is a basic test, consider adding more comprehensive tests:
- Version check
- Basic functionality test
test: commands: - $R -e "library('pgenlibr')" # [not win] + - $R -e "packageVersion('pgenlibr')" # [not win] + - $R -e "stopifnot(packageVersion('pgenlibr') == '{{ version }}')" # [not win]
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📒 Files selected for processing (1)
recipes/r-pgenlibr/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/r-pgenlibr/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (6)
recipes/r-pgenlibr/meta.yaml (6)
1-5: LGTM! Package naming and versioning follow conda conventions.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
7-11: LGTM! Source configuration includes proper fallback and verification.
41-50: LGTM! Package metadata is complete and well-structured.
52-54: LGTM! Maintainer section is correctly formatted.
21-35: Verify package's relevance to Bioconda.
The package appears to be a wrapper for PLINK 2's libraries, which is relevant to bioinformatics. However, please ensure this package isn't more appropriate for conda-forge as mentioned in the PR guidelines.
✅ Verification successful
Let me try a more focused search to verify if PLINK is relevant for bioinformatics.
Based on the search results, I can now provide a final response:
PLINK and its dependencies are appropriate for Bioconda
PLINK and PLINK2 are whole genome association analysis toolsets designed for bioinformatics applications, specifically for performing large-scale genomic analyses. Their presence in Bioconda is appropriate as they are core bioinformatics tools used in genomic research and analysis.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if there are related PLINK packages in bioconda
rg -l 'PLINK' recipes/**/meta.yaml
Length of output: 321781
Script:
#!/bin/bash
# Check PLINK's description and dependencies in its recipe
rg -A 10 "about:" recipes/plink/meta.yaml recipes/plink2/meta.yaml
Length of output: 882
13-19: Verify the pinning strategy in run_exports.
The x.x pin specification will allow updates to patch version but prevent minor version updates. Given this is a new package, please verify if this is the desired constraint level for downstream dependencies.
✅ Verification successful
Let me try a more focused search to verify the pinning strategy.
Let me try another search with a different approach:
Let me try one more search to look for similar R packages:
Based on the search results from multiple attempts, we can see that some R packages like r-corncob and r-archr use the same x.x pinning strategy in their run_exports section. This is a common pattern for R packages in the bioconda ecosystem. Additionally, the pinning strategy aligns with the goal of preventing ABI breakage while allowing patch updates.
The x.x pinning strategy in run_exports is appropriate.
The use of x.x max_pin in run_exports is a standard practice for R packages in bioconda, allowing updates to patch version while preventing minor version updates that could introduce ABI incompatibilities. This conservative approach helps maintain stability for downstream dependencies.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if similar R packages use the same pinning strategy
rg -l 'run_exports:.*pin_subpackage.*x.x' recipes/r-**/meta.yaml
Length of output: 321781
Script:
#!/bin/bash
# Search for run_exports sections with pin_subpackage in R packages
rg -A 3 'run_exports:.*\n.*pin_subpackage' recipes/r-*/meta.yaml
Length of output: 8210
Script:
#!/bin/bash
# Search for run_exports sections with pin_subpackage in R packages, using multiline mode
rg -U "run_exports:\s+- \{\{ pin_subpackage\('.*', max_pin='x.x'\) \}\}" recipes/r-*/meta.yaml
Length of output: 8306
Script:
#!/bin/bash
# Look for similar R packages that might have run_exports sections
rg -U "run_exports:.*pin_subpackage.*" recipes/r-pgenlibr/meta.yaml recipes/r-*/meta.yaml
Length of output: 8043
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@BiocondaBot please update |
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I encountered an error updating your PR branch. You can report this to bioconda/core if you'd like. |
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@BiocondaBot please add label |
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My bad.
I missed this in the bioconda contributing docs! I'll be closing this for now, then |
Adds the
r-pgenlibrpackage from CRAN using https://github.com/bgruening/conda_r_skeleton_helperPlease read the guidelines for Bioconda recipes before opening a pull request (PR).
General instructions
@BiocondaBot please add labelcommand.@bioconda/corein a comment.Instructions for avoiding API, ABI, and CLI breakage issues
Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes.
This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe.
If not already present in the meta.yaml, make sure to specify
run_exports(see here for the rationale and comprehensive explanation).Add a
run_exportssection like this:with
...being one of:{{ pin_subpackage("myrecipe", max_pin="x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}{{ pin_subpackage("myrecipe", max_pin="x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin="x.x.x") }}(in such a case, please add a note that shortly mentions your evidence for that){{ pin_subpackage("myrecipe", max_pin=None) }}while replacing
"myrecipe"with eithernameif aname|lowervariable is defined in your recipe or with the lowercase name of the package in quotes.Bot commands for PR management
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