NEWS
SpiecEasi 2.1.1
DOCUMENTATION
- Set vignette YAML
version fields to match the package version.
INFRASTRUCTURE
- Added
venv to .Rbuildignore so local Python virtualenvs are not included in package tarballs.
SpiecEasi 1.99.5
BUG FIXES
- Fixed vignette rebuild error with pulsar >= 0.3.13: resolve the estimation function before passing to
pulsar() - this avoids lazy match.fun evaluation that fails on PSOCK cluster workers.
INFRASTRUCTURE
- Removed obsolete
CXX_STD = CXX11 from src/Makevars (R >= 4.6 defaults to C++20)
- Fixed
.Rbuildignore to exclude leftover vignettes/figure directory from knitr
SpiecEasi 1.99.4
BUG FIXES
- Fixed vignette build failure caused by
makeCluster(4, type = "SOCK") requiring unavailable snow package
- Replaced broken snow cluster example with reference to
batch.pulsar with conffile='snow'
- Set batch mode vignette chunks to
eval=FALSE to avoid build failures on systems without batchtools infrastructure
SpiecEasi 1.99.3
BUG FIXES
- Fixed BugReports URL in DESCRIPTION (removed double slash)
- Replaced sapply with vapply in R/fitdistr.R for improved type stability
- Fixed incomplete final line in .Rbuildignore file
IMPROVEMENTS
- Added BiocManager installation instructions to main vignette
- Added runnable examples to man pages for getOptInd, robustPCA, stars.roc, and triu functions
- Cleaned up promotional language in NEWS entries
- Removed unused inst/extdata files to reduce package size
INFRASTRUCTURE
- Added .registration = TRUE to useDynLib in NAMESPACE
- Updated package version to 0.99.2 for Bioconductor submission
- Verified vignette runtime compliance with Bioconductor guidelines
SpiecEasi 1.99.2
NEW FEATURES
- Added comprehensive Bioconductor package infrastructure
- Added automated GitHub Actions workflow for Bioconductor continuous integration
- Added test coverage reporting and automated testing
- Added Bioconductor-style vignettes and documentation
- Added biocViews categorization: Software, Microbiome, Metagenomics, GraphAndNetwork, NetworkInference
- Added comprehensive support documentation and issue templates
- Implemented proper code of conduct and contribution guidelines
INFRASTRUCTURE IMPROVEMENTS
- Added Bioconductor-specific GitHub Actions workflow (check-bioc.yml)
- Implemented automated R CMD check with Bioconductor standards
- Added BiocCheck integration for package validation
- Enhanced test coverage with automated reporting
- Added lifecycle badge indicating stable package status
BUG FIXES
- Resolved compliance issues identified during BiocCheck
- Enhanced error handling and package robustness
SpiecEasi 1.1.3
NEW FEATURES
- Added a
NEWS.md file to track changes to the package.
SIGNIFICANT USER-VISIBLE CHANGES
- Adding other boilerplate for Bioconductor release
BUG FIXES