NEWS
PubMatrixR 1.0.0 (2026-03-12)
Core functionality
- Refactored
PubMatrix() to use XML parsing via xml2::read_xml() with
internal helpers for count extraction, retry handling, and date-range
validation.
- Added stricter input validation and clearer error messages for missing terms,
malformed input files, invalid database values, invalid date ranges, and
export arguments.
- Standardized result assembly as a matrix-like data frame with rows from
B
and columns from A, with safer URL encoding for API queries and exported
hyperlinks.
Heatmap helpers
- Updated heatmap documentation and behavior to display overlap percentages and
use Euclidean clustering terminology consistently.
- Improved heatmap robustness for character inputs, NA handling, and automatic
font scaling when saving plots.
Tests and vignettes
- Replaced network-dependent tests with deterministic mocked tests for
PubMatrix() and offline fixture-based XML parser tests.
- Expanded heatmap tests to cover file output and avoid creating
Rplots.pdf
during checks.
- Simplified the main vignette to an offline, CRAN-safe workflow with
non-evaluated live-query examples.
- Removed legacy vignette/test files that depended on live web access or large
examples.
Packaging and documentation
- Updated package metadata for a CRAN-oriented release (
Version: 1.0.0,
removed biocViews, cleaned imports/suggests, and refreshed LICENSE).
- Added package-level documentation and updated
README.md, Rd files, and
inst/CITATION to match current behavior and examples.
- Expanded
.Rbuildignore to exclude local development and check artifacts.
Repository cleanup
- Removed pkgdown configuration/generated
doc/ artifacts and the bundled
pubmatrix-app Shiny subproject files from the package source tree.
PubMatrixR 0.9.0
- Finalized the pre-CRAN/Bioconductor-oriented package line after iterative
"BioC optimization" updates and namespace fixes.
- Added/updated the main
PubMatrix.R implementation and related packaging
files during refactoring.
- Added a bundled Shiny app subproject (
pubmatrix-app) and deployment
metadata.
- Added OpenDocument Spreadsheet (
.ods) export support for result output.
Relevant commits include 5618668, 3c10f5d, fbc4846, 1c52679,
26e6597, 591d458, and 80699aa.