Feat/cran submission #22
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Convert all cat() calls to message() in gedi_progress.R helper functions (log_start, log_complete, log_info, log_cached, log_stage, create_progress_bar). This allows users to suppress informational output via suppressMessages() as required by CRAN policy. All helpers already check verbose >= 1 before emitting messages.
Remove fragile cat()+sink()+tempfile() progress bar pattern from the train() method. Use txtProgressBar(file=stderr()) instead, which writes to stderr and can be suppressed. This eliminates stdout capture issues and follows CRAN best practices for console output.
Use txtProgressBar(file=stderr()) instead of manual cat()-based progress bar in get_imputed_Y(). Output is now suppressible via CRAN-compliant mechanisms.
Convert manual cat()-based progress bars to txtProgressBar(file=stderr()) in compute_Y_variance() and compute_dispersion(). Gate unconditional message() calls behind verbose check in compute_Y_variance().
Add verbose=TRUE parameter to seurat_to_gedi() and gedi_to_seurat(). Gate all message() calls behind if(verbose) checks so users can suppress informational output. Follows CRAN policy for console output control.
Replace slow utils::installed.packages() calls with requireNamespace() in install_optional_dependencies() and check_optional_dependencies(). Add verbose=TRUE parameter to both functions and gate all message() calls behind if(verbose). Remove installed.packages from importFrom directive.
Convert rasterization not-implemented messages from message() to warning() in .plot_embedding_base() and plot_embedding(). This is appropriate since the user explicitly requested raster=TRUE but the feature is unavailable.
Convert informational cat() calls to message() in list_h5_structure() so output can be suppressed with suppressMessages(). The print() call for the data.frame is retained as it is standard for display functions.
Convert all cat() calls to message() in compute_dense_A() and compute_sparse_A(). Messages are already gated behind verbose level checks. Also replace non-ASCII multiplication sign with ASCII 'x'.
- Bump version from 2.3.0 to 2.3.1 - Move hdf5r from Imports to Suggests (optional dependency) - Add ggplot2 and scales to Imports (used via :: throughout) - Add uwot and digest to Suggests (optional dependencies) - Remove redundant Maintainer field (extracted from Authors@R) - Remove NeedsCompilation/Packaged/Author (auto-generated by R CMD build) - Remove Eigen3 from SystemRequirements (bundled via RcppEigen) - Clean up Description text to avoid trade names
- Remove @importFrom hdf5r directives from h5_readers.R and h5_writers.R - Add hdf5r:: prefix to bare h5attr() calls in h5_writers.R - Replace non-ASCII checkmark with ASCII in h5_writers.R message - All hdf5r functions already guarded by requireNamespace() checks
Replace full MIT license text with the two-line format required by CRAN for 'MIT + file LICENSE' declaration in DESCRIPTION.
Add @return roxygen tags to: - print.gedi_imputation, print.gedi_dynamics, print.gedi_dynamics_svd, print.gedi_pathway_associations (all return invisible(x)) - theme_gedi, scale_color_gedi_diverging, scale_fill_gedi_diverging, scale_color_gedi_discrete, compute_color_limits (internal utilities) Required by CRAN: all exported and documented functions must have \value sections in their .Rd files.
Replace Unicode symbols with ASCII equivalents in all .cpp files: - Multiplication sign (x) -> 'x' in output strings and comments - Checkmark -> '[OK]' in progress output - Kronecker product -> '(x)' in comments - Superscript T -> '^T' in comments - Y-hat -> 'Y_hat' in comments - Fix mojibake sequences in gedi_projections.cpp Prevents CRAN NOTE about non-ASCII characters in compiled code.
- Add NEWS.md documenting v2.3.1 CRAN compliance changes and v2.3.0 release - Add cran-comments.md template for CRAN submission - Add Benchmark/, gedi.Rcheck/, cran-comments.md to .Rbuildignore
- Remove hdf5r and installed.packages importFrom directives from NAMESPACE - Add \value sections to all .Rd files missing them - Update RcppExports.R from recompilation
Update URL and BugReports to point to the new repository location at https://github.com/csglab/gedi2 (old Arshammik/gedi redirects).
- Add glmnet to Suggests (used via glmnet::cv.glmnet) - Add missing @importFrom for stats (coef, median, var) and utils (object.size, setTxtProgressBar, txtProgressBar) - Add globalVariables() for ggplot2 NSE variables (Dim1, Dim2, Color, etc.) - Remove non-portable -Wno-* flags from Makevars and Makevars.win - Add @method tags to S3 print methods (NAMESPACE now uses S3method) - Fix broken \link{GEDI} cross-reference in gedi-package.Rd - Escape [gene1,] brackets in plot_feature_ratio roxygen to prevent \link parsing - Add Logo.svg to .Rbuildignore - Regenerate NAMESPACE and man pages
- Badge SVGs: Arshammik/gedi -> csglab/gedi2 (301 redirect) - MIT license URL: /licenses/MIT -> /license/MIT (301 redirect) - Fix typo in issues link: caglab -> csglab - Add CRAN status badge - Add check_output.txt to .Rbuildignore - Update cran-comments.md with accurate results
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