This pull request addresses an error encountered in R-CMD check due to improperly formatted example data within the reverseOperonSeq function. The primary motivation for this change was to ensure that the function operates without errors and meets R-CMD check requirements.
Motivation
The R-CMD check error was raised when running the function due to issues in the example data, which did not meet required standards. This PR aims to resolve that issue by refactoring the example data and adjusting the function to handle potential edge cases within genomic contexts.
Adjustments Made
Refactored reverseOperonSeq to handle diverse genomic contexts, specifically to handle cases with >, <, and =.
Added test cases in test-reverse_operons.R to verify that the function handles various genomic context formats without errors.
Configured a .lintr file for consistent linting and used styler to format the R scripts, ensuring compliance with style guidelines.
Related Issues
This pull request resolves issue #118 and provides additional unit tests to prevent similar issues in the future.
Also, if you haven't already, please use pre-commit run --all-files to help check your files using this project's pre-commit configuration.
Pre-commit checks will automatically run as part of opening this pull request and we seek to ensure all checks pass before merging changes.
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What kind of change(s) are included?
[ ] Feature (adds or updates new capabilities)
[x ] Bug fix (fixes an issue).
[ ] Enhancement (adds functionality).
[ ] Breaking change (these changes would cause existing functionality to not work as expected).
Checklist
Please ensure that all boxes are checked before indicating that this pull request is ready for review.
[x ] I have read and followed the CONTRIBUTING.md guidelines.
[x ] I have searched for existing content to ensure this is not a duplicate.
[x ] I have performed a self-review of these additions (including spelling, grammar, and related).
[x ] I have added comments to my code to help provide understanding.
[x ] I have added a test which covers the code changes found within this PR.
[x ] I have deleted all non-relevant text in this pull request template.
[x ] Reviewer assignment: Tag a relevant team member to review and approve the changes.
Pull Request Description:
Summary
This pull request addresses an error encountered in
R-CMD checkdue to improperly formatted example data within thereverseOperonSeqfunction. The primary motivation for this change was to ensure that the function operates without errors and meetsR-CMD checkrequirements.Motivation
The
R-CMD checkerror was raised when running the function due to issues in the example data, which did not meet required standards. This PR aims to resolve that issue by refactoring the example data and adjusting the function to handle potential edge cases within genomic contexts.Adjustments Made
reverseOperonSeqto handle diverse genomic contexts, specifically to handle cases with>,<, and=.test-reverse_operons.Rto verify that the function handles various genomic context formats without errors..lintrfile for consistent linting and usedstylerto format the R scripts, ensuring compliance with style guidelines.Related Issues
This pull request resolves issue #118 and provides additional unit tests to prevent similar issues in the future. Also, if you haven't already, please use
pre-commit run --all-filesto help check your files using this project's pre-commit configuration. Pre-commit checks will automatically run as part of opening this pull request and we seek to ensure all checks pass before merging changes. -->What kind of change(s) are included?
Checklist
Please ensure that all boxes are checked before indicating that this pull request is ready for review.