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Source: NEWS.md

evanverse 0.3.7

CRAN release: 2025-10-21

Released: October 16, 2025 Published on CRAN: October 21, 2025 🎉

CRAN Compliance Release - Fixed file system operation policy violations.

CRAN Publication

CRAN Compliance Fixes

  • File operation policy compliance: Removed all default file paths that write to user’s home directory or working directory
  • Updated function signatures (Breaking Changes - Path Parameters Now Required):
  • Enhanced parameter validation: All affected functions now provide clear error messages when required paths are missing
    • Error messages guide users to use tempdir() for examples and tests
    • Documentation updated to reflect required parameters

Migration Guide

For users upgrading from 0.3.6:

# OLD (0.3.6) - No longer works in 0.3.7
create_palette("my_palette", "sequential", colors)

# NEW (0.3.7) - Explicit path required
temp_dir <- file.path(tempdir(), "palettes")
create_palette("my_palette", "sequential", colors, color_dir = temp_dir)

# For production use, specify your desired directory
create_palette("my_palette", "sequential", colors,
               color_dir = "path/to/your/palette/directory")

Technical Details

  • Reviewer: Addressed feedback from Benjamin Altmann (CRAN)
  • Policy Reference: CRAN File Writing Policy
  • Functions modified: 9 functions updated for CRAN compliance
  • Documentation: All man pages regenerated with updated parameter descriptions
  • Backward compatibility: This is a breaking change for functions that previously had default file paths

evanverse 0.3.6

Released: October 8, 2025

Maintenance Release - Minor improvements and bug fixes.

Bug Fixes

  • Fixed plot_venn function to properly handle void values in list inputs
  • Improved namespace consistency across package functions
  • Minor documentation updates for clarity

Technical Details

  • Updated package version to 0.3.6
  • All R CMD check tests passing (0 errors, 0 warnings, 0 notes)
  • Maintained CRAN compliance standards

evanverse 0.3.5

Released: October 7, 2025

CRAN Resubmission - Addressed all reviewer feedback with improved examples and file operation handling.

CRAN Compliance Fixes

  • Fixed function examples: Updated 10 functions with properly working examples per CRAN reviewer feedback
    • Replaced \donttest{} with \dontrun{} for network-dependent operations
    • Added \donttest{} with quick demos for appropriate functions
    • Fixed all commented examples in @examples sections
  • File operation improvements: All examples now use tempdir() for temporary file creation
  • Network operation handling: Properly wrapped all network-dependent examples
  • GMT file examples: Enhanced examples for gmt2df() and gmt2list() functions
  • Palette management: Fixed examples for compile_palettes() and remove_palette()

Technical Details

  • Reviewer: Addressed feedback from Benjamin Altmann (CRAN)
  • Functions updated: 10 functions with improved examples and documentation
  • Files modified: 24 R and man files for consistency
  • Compliance: All examples now follow CRAN policies for file operations and network access

evanverse 0.3.4

Released: September 28, 2025

CRAN Submission Ready - Enhanced version with dependency optimization and improved documentation quality.

Major Improvements

  • Dependency optimization: Moved bioinformatics packages (GSEABase, Biobase, GEOquery, biomaRt) from Imports to Suggests for lighter base installation
  • Enhanced documentation: Streamlined function documentation for improved readability and consistency across all 55+ functions
  • Test suite improvements: Enhanced test reliability with better isolation and parameter validation (1358 tests passing)
  • Vignette optimizations: Improved graphics parameter handling and execution speed with proper cleanup
  • Code style improvements: Consistent formatting and improved maintainability across all functions

CRAN Compliance Enhancements

  • Perfect clean check: 0 errors ✔ | 0 warnings ✔ | 0 notes ✔
  • Package size optimization: Reduced from 6.5MB to 1.5MB through dependency restructuring
  • Cross-platform validation: Confirmed compatibility across Windows, macOS, and Linux
  • Installation time improvement: Optimized to 5 seconds with reduced mandatory dependencies
  • Check time optimization: Streamlined to 133 seconds through better test organization

Documentation & Quality

  • Streamlined roxygen2 documentation: Updated across 17 core R functions for clarity
  • Enhanced function examples: All examples verified and optimized for CRAN compliance
  • Improved cross-references: Validated all internal links and references
  • Better error handling: Enhanced user-friendly error messages and validation

Technical Details

  • R CMD check status: All checks passing with perfect results across multiple platforms
  • Test coverage: 1358 tests with 25 network-dependent tests properly skipped on CRAN
  • Documentation completeness: All exported functions have comprehensive documentation
  • Dependency management: Strategic use of Imports vs Suggests for optimal installation experience

evanverse 0.3.3

Released: September 19, 2025

CRAN Submission Ready - Passed CRAN automatic checks; under manual review.

CRAN Compliance Fixes

  • Resolved all R CMD check issues: Eliminated remaining warnings and notes for full CRAN compliance
  • Enhanced documentation consistency: Fixed all argument mismatches and improved parameter descriptions
  • Optimized package dependencies: Streamlined imports and resolved namespace conflicts
  • Cross-platform validation: Confirmed compatibility across Windows, macOS, and Linux environments
  • Test suite refinement: Updated test conditions and skip logic for CRAN environment compatibility

CRAN Check Results

  • Windows (R-release): ✅ PASS - 0 errors, 0 warnings, 0 notes
  • Debian (R-devel): ✅ PASS - 0 errors, 0 warnings, 0 notes
  • All test environments: Successfully validated across multiple R versions and platforms

What’s New

  • Final CRAN submission preparations completed
  • Enhanced package robustness and reliability
  • Improved documentation quality and consistency
  • Streamlined codebase for production readiness

Technical Details

  • R CMD check status: All checks passing with clean results
  • Test coverage: 1336+ tests with appropriate CRAN skip conditions
  • Documentation: All man pages updated with proper formatting and examples
  • Vignettes: Network-dependent code properly handled with eval=FALSE

Next Steps

  • CRAN manual review: Package submitted and awaiting final approval
  • Expected timeline: Approval anticipated within 10 working days
  • Installation: Will be available via install.packages("evanverse") upon approval

evanverse 0.3.2

A maintenance release focusing on CRAN check compliance and package quality improvements.

CRAN Compliance Fixes

  • Fixed namespace imports: Added proper package::function prefixes for all base R functions
  • Removed Unicode characters: Cleaned up emoji characters from R code files for better compatibility
  • Updated documentation: Fixed argument mismatches in function documentation (e.g., %nin% operator)
  • Network dependency handling: Ensured all network-dependent code in vignettes uses eval=FALSE
  • Enhanced examples: Wrapped network-dependent examples in \dontrun{} blocks

Code Quality Improvements

  • Improved function documentation with accurate parameter descriptions
  • Standardized error messages and validation patterns
  • Enhanced CRAN submission readiness with better compliance checks
  • Updated package structure for optimal build and check processes

evanverse 0.3.1

A patch release focusing on CRAN submission preparation and cross-platform compatibility validation.

Documentation & Release Preparation

  • CRAN Submission Checklist: Added comprehensive checklist covering all policy requirements and compliance checks
  • Test Environment Documentation: Created detailed cran-comments.md with test environments and submission documentation
  • Cross-Platform Compatibility: Generated validation report confirming Windows/macOS/Linux support
  • Documentation Updates: Updated package documentation with improved man pages and examples
  • Test Suite Validation: Verified all 1336 tests pass with proper skip conditions for CRAN/CI environments

Internal Improvements

  • File Path Handling: Enhanced validation across all platforms with robust error handling
  • Platform-Specific Code: Confirmed minimal platform dependencies with proper error handling
  • Dependency Validation: Verified all dependencies are cross-platform compatible
  • Package Structure: Cleaned up package structure by removing unnecessary .here file

evanverse 0.3.0

A focused refactor release: unified CLI messaging, CRAN-safe startup, tighter parameter validation, stronger tests, and several new utilities.

New Functions

  • plot_forest() — Forest plots with publication-style defaults (forestploter), significance bolding, color recycling, and alignment options.

  • plot_bar() — Bar charts with optional fill grouping, sorting, vertical/horizontal layout, and clean defaults.

  • read_excel_flex() — Enhanced Excel reader (readxl) with optional name cleaning (janitor), range/col_types controls, and CLI feedback.

  • write_xlsx_flex() — Flexible Excel writer (openxlsx) with header styling, auto column width, overwrite/timestamp options.

  • view() — Quick interactive data viewer (reactable) for exploration/QC.

  • set_mirror() — Switch CRAN/Bioconductor mirrors with predefined, named endpoints.

  • pkg_functions() — List exported functions from any installed package, with optional keyword filtering.

Enhancements & Refactors

  • read_table_flex()
    • Inlined, robust delimiter detection for .csv/.tsv/.txt and .gz files
    • Stricter parameter checks and clearer CLI error messages
    • Enhanced encoding guardrails for better file handling
  • update_pkg()
    • Source normalization via strict match() function
    • Supports only “CRAN”, “GitHub”, “Bioconductor” sources
    • Clearer messages and mirror handling aligned with set_mirror()
  • pkg_version()
    • More robust CRAN/Bioconductor database retrieval
    • Helpful suggestions for GitHub package installations
    • Optional preview printing with clearer CLI output
  • Diagnostic Operators
    • %is% and %near% messages standardized (no emoji)
    • Tighter type/shape checks with cleaner examples
    • %nin% implemented as Negate(%in%) with simple, predictable NA semantics
  • Data Utilities
    • map_column() uses unified cli output and counts unmatched keys
    • Skips numeric columns by design, removes emoji, adds modular separators
    • with_timer() simplified using tictoc timing and cli output
    • remind() rendering fixed for cli braces with partial/case-insensitive matches
    • rgb2hex() input validation tightened with concise CLI feedback
    • rows_with_void() header streamlined, delegates detection to is_void()
  • Startup and Documentation
    • .onAttach switched to plain cli::cli_text() messages (no emoji), CRAN-safe
    • Roxygen examples trimmed for non-interactive/CRAN environments
    • Consistent headers and separators throughout documentation

Testing & QA

Internal Changes

  • Namespace and Data Access
    • Fixed internal data access during package load to avoid namespace lookup errors
    • Removed direct pkg::object dependency for bundled data
  • Code Style and Standards
    • Consistent CLI style implementation across all functions
    • Removed all emoji from code, comments, and roxygen documentation
    • Enhanced code readability and maintainability

evanverse 0.2.0

A comprehensive upgrade with expanded tools for R developers and bioinformaticians.

New Functions (by Category)

File & Data Management
Package Management Tools
Bioinformatics Color Palettes
Data Processing Tools
Development Helper Functions
Void Value Handling
Vector & Logic Operations
Visualization Tools

Internal Changes

  • Removed GitHub Actions auto-deployment logic (pkgdown.yaml)
  • Switched to local builds with docs/ deployment to GitHub Pages
  • Refactored documentation structure to improve package documentation readability

Documentation

  • Online Documentation: evanbio.github.io/evanverse
  • Comprehensive function reference with examples
  • Getting started guides and tutorials

evanverse 0.1.0

First Release

  • Introduced %p% operator for expressive string concatenation
  • Built modular structure with dev/00_setup.R, tests, and MIT license
  • Added GitHub integration and install instructions