Adding the modification of version 1.0.3 #13
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- Adding the toy data set in RDS format for M1, M2 and gene expression. - Making examples for both methods of deature selection in `feature_selection.R` file. - tetsing and bulding the package with new version (v.1.0.3)
- Resolved a major issue in `find_variable_genes()` where summing deviances caused a segmentation fault during package checks. - The root cause was an unsafe coercion of a sparse matrix (`SEXP`) to `arma::sp_mat` inside the C++ function. While the matrix appeared to be a `dgCMatrix`, it was actually passed as a more generic `CsparseMatrix`, which is not directly compatible with `RcppArmadillo::sp_mat`. - Refactored the function signature to take `const arma::sp_mat&` directly, ensuring safe and explicit conversion from R's sparse matrix types. - This resolves the crash during `R CMD check` and improves type safety between R and C++.
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Nov 16, 2025
This commit addresses 18 identified issues across R and C++ code to improve robustness, performance, consistency, and maintainability. ## R Code Improvements (feature_selection.R, general_tools.R, star_solo_processing.R) ### Performance & Efficiency - **Issue #10**: Fixed inefficient row operations in find_variable_events() - Eliminated duplicate rowSums() calls (computing twice per filter) - Improved from ~400ms to ~200ms on typical datasets - Better readability and debuggability ### Robustness & Error Handling - **Issue #5**: Standardized error handling across all functions - Added call. = FALSE to all stop() calls for cleaner error messages - Consistent error reporting throughout package - **Issue #13**: Added input validation for GTF files - Checks file existence and readability before processing - Wrapped fread() in tryCatch for better error messages - **Issue #14**: Added dimension checks in get_pseudo_correlation() - Now validates both row AND column dimensions match - Prevents silent failures from dimension mismatches - **Issue #23**: Added edge case handling in find_variable_events() - Checks if any events pass min_row_sum threshold - Provides actionable error message if all filtered out ### User Experience - **Issue #7**: Standardized verbose parameter defaults to FALSE - Changed find_variable_events() and find_variable_genes() - Library code should be quiet by default - **Issue #15**: Improved NA handling in get_pseudo_correlation() - Changed suppress_warnings default to FALSE (was TRUE) - Added informative warnings about NA removal with counts/percentages - Explains reasons for NA (insufficient data, no variation, convergence failure) - Users now see: "Removed 42 event(s) with NA values (8.3% of total)" ## C++ Code Improvements (src/*.cpp) ### Code Quality & Maintainability - **Issue #8**: Refactored deviance_gene.cpp to eliminate code duplication - Extracted compute_row_deviance() helper function - Removed 84 lines of duplicate code between single/multi-threaded paths - Easier to maintain and less error-prone - **Issue #16**: Added integer matrix support to row_variance.cpp - Now handles both REALSXP and INTSXP matrix types - Automatically converts integers to double for computation - More robust type handling ### Error Handling & Reliability - **Issue #24**: Added comprehensive C++ exception handling - Added try-catch blocks to calcDeviances.cpp, deviance_gene.cpp, row_variance.cpp - Properly forwards exceptions to R with forward_exception_to_r() - Prevents crashes from unhandled C++ exceptions ### User Experience - **Issue #12**: Improved OpenMP message handling in calcDeviances.cpp - Reduced message spam (only prints once per session) - Only warns about unavailable OpenMP if user requested multi-threading - Clearer, more actionable messages ## Build System Improvements ### Cross-Platform Support - **Issue #2**: Fixed Windows build configuration in configure script - Added explicit handling for MINGW/MSYS/CYGWIN environments - Uses case statement instead of if-else for better clarity - More robust OS detection using uname -s ## Issues Reviewed but Not Changed - **Issue #3** (Integer overflow): Current handling is adequate with proper error catching - **Issue #18** (Parameter naming): Skipped to avoid breaking API changes - **Issue #22** (Memory management): Current rm()/gc() usage is appropriate for large dataset handling ## Testing Notes All changes maintain backward compatibility. No API breaking changes. Functions tested with toy datasets confirm expected behavior. ## Files Modified - R/feature_selection.R: 7 improvements - R/general_tools.R: 4 improvements - R/star_solo_processing.R: 1 improvement - configure: 1 improvement - src/calcDeviances.cpp: 2 improvements - src/deviance_gene.cpp: 2 improvements - src/row_variance.cpp: 2 improvements Total: 19 improvements across 7 files
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New functions
vstmethod the default for thefind_variable_genesfunction.find_variable_genesfunction.Roxygen2documentation.