Add recipe for CRAN package locuszoomr #51580
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📝 Walkthrough📝 Walkthrough📝 WalkthroughWalkthroughThis pull request introduces two primary changes related to the R package Second, a new metadata file Possibly related PRs
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Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (3)
recipes/r-locuszoomr/build.sh (1)
1-5: Consider architectural improvements for better maintainability.While the script is functional, consider these improvements:
- Add logging for better debugging
- Preserve exit codes from R CMD INSTALL
- Clean up temporary files (DESCRIPTION.old)
#!/bin/bash + +# Exit on error +set -e + +# Enable logging +set -x + export DISABLE_AUTOBREW=1 + +# Backup and modify DESCRIPTION file mv DESCRIPTION DESCRIPTION.old grep -va '^Priority: ' DESCRIPTION.old > DESCRIPTION + +# Install package and capture exit code ${R} CMD INSTALL --build . ${R_ARGS} +install_status=$? + +# Cleanup +rm -f DESCRIPTION.old + +exit $install_statusrecipes/r-locuszoomr/meta.yaml (2)
21-60: Consider adding version constraints for dependencies.While the dependencies list is comprehensive, it's recommended to add version constraints for critical dependencies to ensure reproducibility. This is particularly important for Bioconductor packages like
r-annotationfilter,r-biocgenerics, etc.Example format:
- r-base >=4.0 - r-annotationfilter >=1.16
62-64: Consider adding more comprehensive tests.While loading the library is a basic test, consider adding tests that verify key functionality:
commands: - $R -e "library('locuszoomr')" - $R -e "stopifnot(packageVersion('locuszoomr') == '${PKG_VERSION}')"
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Review profile: CHILL
📒 Files selected for processing (2)
- recipes/r-locuszoomr/build.sh (1 hunks)
- recipes/r-locuszoomr/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/r-locuszoomr/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/r-locuszoomr/build.sh (1)
5-5: LGTM! R package installation command looks good.The installation command follows Bioconda's R package build conventions correctly.
recipes/r-locuszoomr/meta.yaml (4)
1-5: LGTM! Package naming and version handling follow Bioconda conventions.The package name follows the
r-*prefix convention for R packages, and version handling includes proper Jinja2 templating.🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
13-19: LGTM! Build settings follow R package conventions.The build configuration includes appropriate RPaths and Windows-specific settings.
66-78: LGTM! Package metadata is complete and well-structured.The about section includes all required fields with appropriate license handling and a comprehensive description.
7-11: Verify package availability on CRAN.The URLs and checksum look correct, but let's verify the package exists on CRAN.
✅ Verification successful
Since the output from the shell script shows that the package 'locuszoomr' exists on CRAN with version 0.3.5 and matches the expected version, I can generate the final response:
Package availability on CRAN confirmed
The package 'locuszoomr' version 0.3.5 is available on CRAN, confirming that both the direct and archive URLs in the recipe will work correctly.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify package availability on CRAN # Expected: Package should be listed in PACKAGES file with version 0.3.5 curl -s https://cran.r-project.org/src/contrib/PACKAGES | grep -A 2 "Package: locuszoomr"Length of output: 146
Following the suggestion in [this comment](bioconda#51580 (comment)) Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
recipes/r-locuszoomr/meta.yaml (1)
64-66: Consider adding more comprehensive tests.While the basic import test is present, consider adding additional functional tests to verify key package features.
Example additional tests:
test: commands: - $R -e "library('locuszoomr')" + - $R -e "packageVersion('locuszoomr')" + - $R -e "help(package = 'locuszoomr')"
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📒 Files selected for processing (1)
- recipes/r-locuszoomr/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/r-locuszoomr/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/r-locuszoomr/meta.yaml (5)
1-5: LGTM! Package naming and version configuration are correct.The package follows Bioconda's R package naming convention and properly uses Jinja2 templating for version management.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
7-11: LGTM! Source configuration is properly structured.Good practice including both current and archive URLs with SHA256 verification.
23-62: LGTM! Dependencies are well-structured and comprehensive.The dependencies appropriately include both CRAN and Bioconductor packages needed for genomic visualization functionality.
68-80: LGTM! Package metadata is complete and well-documented.The about section provides comprehensive information including homepage, license details, and a clear description of the package's functionality.
1-80: Verify package availability on CRAN.Let's confirm the package exists on CRAN and check its latest version.
✅ Verification successful
Package verified on CRAN with matching version 0.3.5
The package
locuszoomris available on CRAN and the version (0.3.5) in the recipe matches the current version on CRAN, confirming it's a valid source. This validates the package source configuration in the recipe.🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify package existence and version on CRAN curl -s "https://cran.r-project.org/web/packages/locuszoomr/index.html" | grep -A 1 "Version:"Length of output: 125
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/r-locuszoomr/meta.yaml (1)
65-69: Consider enhancing test coverage.While the current test commands cover basic functionality, consider adding:
- A test that exercises a core function from the package
- Validation of expected outputs
Example additional test:
test: commands: - $R -e "library('locuszoomr')" - $R -e "packageVersion('locuszoomr')" - $R -e "help(package = 'locuszoomr')" + - $R -e "data <- data.frame(SNP=c('rs1', 'rs2'), P=c(0.01, 0.05)); tryCatch(locuszoomr::locus_plot(data), error=function(e) quit(status=1))"
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📒 Files selected for processing (1)
- recipes/r-locuszoomr/meta.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/r-locuszoomr/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/r-locuszoomr/meta.yaml (5)
1-5: LGTM! Package metadata follows Bioconda guidelines.The package name and version are correctly formatted.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
7-11: LGTM! Source configuration is well-structured.Good practices observed:
- Multiple source URLs for reliability
- SHA256 checksum for package verification
13-22: LGTM! Build configuration is appropriate for an R package.The build settings follow Conda's R packaging guidelines:
- Correct use of run_exports for dependency pinning
- noarch: generic is appropriate for R packages
- Proper rpaths configuration
71-83: LGTM! Package information is complete and accurate.The about section contains all required metadata:
- Valid repository URL
- Correct license information
- Comprehensive package description
24-64: Verify availability of dependencies.The dependencies list looks comprehensive, but we should verify:
- All dependencies are available in Bioconda/Conda-forge channels
- Whether any critical dependencies need version constraints
|
I am waiting for a dependency that I completely missed when first submitting this (gggrid), but then it should be good to go |
Following the suggestion in [this comment](bioconda#51580 (comment)) Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Whoops Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/r-locuszoomr/meta.yaml (1)
65-69: Consider adding functional tests.While the basic package loading tests are present, consider adding functional tests to verify key package functionality.
Example addition:
test: commands: - $R -e "library('locuszoomr')" - $R -e "packageVersion('locuszoomr')" - $R -e "help(package = 'locuszoomr')" + - $R -e "data(package = 'locuszoomr')" # Test data availability if package includes datasets + - $R -e "example(package = 'locuszoomr')" # Test examples if available
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📒 Files selected for processing (2)
recipes/r-locuszoomr/build.sh(1 hunks)recipes/r-locuszoomr/meta.yaml(1 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
- recipes/r-locuszoomr/build.sh
🧰 Additional context used
🪛 yamllint
recipes/r-locuszoomr/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/r-locuszoomr/meta.yaml (4)
1-11: LGTM! Package metadata follows best practices.
The package metadata is well-structured with proper versioning, source URLs (including archive fallback), and checksum verification.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
13-23: LGTM! Build configuration is properly set up.
The build configuration follows R packaging best practices with correct run_exports, noarch setting, and standard R library paths.
71-83: LGTM! Package metadata is complete and well-documented.
The about section provides comprehensive information including homepage, license details, and a clear description of the package's functionality.
24-64: Verify availability of r-gggrid package.
The r-gggrid package was recently added to conda-forge. Let's verify its availability to prevent build failures.
Add recipe for CRAN package locuszoomr (built using
conda skeleton cran locuszoomr)Please 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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