Fix Bioconductor packaging gaps, live-API bugs, and rename to camelCa… - #1
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jananiravi wants to merge 4 commits into
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Fix Bioconductor packaging gaps, live-API bugs, and rename to camelCa…#1jananiravi wants to merge 4 commits into
jananiravi wants to merge 4 commits into
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…se API Packaging (R CMD check --as-cran: 4 notes -> 0): - Fix LICENSE to the 2-line DCF stub required by "MIT + file LICENSE"; move full text to LICENSE.md and .Rbuildignore it - Drop unused Imports (jsonlite, stringr) - Add @importFrom rlang .data to resolve undefined-global NOTE - Add vignettes/coiCheckR.Rmd (Bioconductor requires at least one) Bug fixes (found via live PubMed/NIH RePORTER calls): - buildCoauthorEdges(): normalize PubMed's inconsistently-abbreviated ForeName field to initials before matching, fixing silent false negatives in direct co-authorship detection - Replace ifelse() with dplyr::if_else() in 3 spots (coauthor_network.R, coi_report.R) to fix a type-instability crash when an author's co-authorship edges are empty - reporterSearchPi(): parse "Last, First" into first_name/last_name fields instead of any_name, which silently returns zero rows for the comma format on the live RePORTER API (also more precise than the any_name substring fallback for bare surnames) API rename (Bioconductor coding style: lowerCamelCase functions): - Rename all exported functions (checkCoi, buildCoauthorEdges, pmSearchAuthor, etc.); S3 class coi_report -> coiReport; variables stay snake_case; NAMESPACE/man regenerated Cleanup: - Remove real third-party names from docs/tests/vignette; use generic placeholders or the author's own consented example (Ravi J / Krishnan A) as live ground truth - Apply styler::style_pkg(); fix all lintr line-length findings (lint_package() now clean) Verified: 20/20 offline tests, 7/7 live-API tests, R CMD check 0 errors/0 warnings/0 notes Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
This update adds roxygen examples and regenerated man pages across the public API, makes the second-degree COI check accept an optional affiliation filter to reduce same-name false positives, and updates the live API test/vignette guidance to use placeholder names behind explicit opt-in. It also bumps the package version and refreshes the Bioc metadata.
- Introduced robust handling for upstream API failures and tidy internal/API changes. - Added utils.R (.markSourceFailed, .sourceFailed, .classifyCoiStatus) to tag and classify failed evidence sources; propagate failure flags from PubMed (pmSearchAuthor/pmFetchAuthors) and NIH RePORTER (reporterSearchPI) calls so checkCoi/checkCoiBatch return a status and sources_failed. - Standardized column names (PMID/DOI), renamed functions (setNCBIKey, reporterSearchPI), refactored parsing helpers, updated NAMESPACE, docs, NEWS, and tests (including new status tests). - Also added stringr/rlang usage and an `.Rproj` file.
This commit adds pkgdown site configuration and GitHub Pages publishing, updates the package URLs, and ensures live API examples are gated behind \donttest. It also hardens PubMed/NIH matching by canonicalizing names, tolerating full forenames and middle-initial variation, supporting affiliation/org-name filtering for common surnames, and validating the new behavior with regression tests and precompiled vignettes. @eboyer221 @amcim still need help with vignette + gh pages set-up. running into issues.
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Fixed Bioconductor packaging gaps, live-API bugs, and rename to camelCase API
📦 Packaging (R CMD check --as-cran: 4 notes -> 0):
🐞 Bug fixes (found via live PubMed/NIH RePORTER calls):
API rename (Bioconductor coding style: lowerCamelCase functions):
🧹 Cleanup:
Verified: 20/20 offline tests, 7/7 live-API tests, R CMD check 0 errors/0 warnings/0 notes