Fix CRAN-blocking issues for package submission

R/feature_selection.R

@@ -72,7 +72,6 @@ find_variable_events <- function(m1_matrix, m2_matrix, min_row_sum = 50, n_threa
   sum_deviances <- Reduce(`+`, deviance_results)
   rez <- data.table::data.table(events = names(sum_deviances), sum_deviance = as.numeric(sum_deviances))
   return(rez)
-  cat("All Done!\n")
 }
 
 #' Find Variable Genes Using Variance or Deviance-Based Metrics
@@ -118,7 +117,7 @@ find_variable_events <- function(m1_matrix, m2_matrix, min_row_sum = 50, n_threa
 #' @importClassesFrom Matrix dgCMatrix dsCMatrix dgTMatrix dsTMatrix
 #' @export
 find_variable_genes <- function(gene_expression_matrix, method = "vst", n_threads = 1, verbose = TRUE, ...) {
-  # addinng the vst method as the deafult
+  # adding the vst method as the default
   method <- match.arg(method, choices = c("vst", "sum_deviance"))
 
   # Verify that gene_expression_matrix is a sparse Matrix
@@ -168,7 +167,7 @@ find_variable_genes <- function(gene_expression_matrix, method = "vst", n_thread
       deviances_list <- vector("list", length(libraries))
       names(deviances_list) <- libraries
 
-      # Getting the sim devinaces fir NB model
+      # Getting the sum deviances for NB model
       deviances_list <- lapply(libraries, function(lib) {
         filter <- which(meta[, ID] == lib)
         gene_expression_matrix_sub <- gene_expression_matrix[, filter, drop = FALSE]

R/zzz.R

@@ -12,12 +12,3 @@
     "=======================================================================================================\n"
   )
 }
-
-
-.onLoad <- function(libname, pkgname) {
-  required_pkgs <- c("Rcpp", "RcppEigen", "RcppArmadillo", "Matrix", "data.table")
-  missing_pkgs  <- required_pkgs[!vapply(required_pkgs, requireNamespace, quietly = TRUE, FUN.VALUE = logical(1))]
-  if (length(missing_pkgs)) {
-    install.packages(missing_pkgs, dependencies = TRUE)
-  }
-}

README.md

@@ -6,7 +6,7 @@
 [![R-CMD-check](https://github.com/csglab/splikit/actions/workflows/R-CMD-check.yml/badge.svg)](https://github.com/csglab/splikit/actions/workflows/R-CMD-check.yml)
 [![Documentation](https://img.shields.io/badge/Docs-Learn%20More-blue.svg)](https://csglab.github.io/splikit/)
 
-## **Requirments**
+## **Requirements**
 
 -   [R version 3.5.0](http://www.r-project.org/) or later.
 -   R libraries: [Rcpp](https://cran.r-project.org/web/packages/Rcpp/index.html), [RcppArmadillo](https://cran.r-project.org/web/packages/RcppArmadillo/index.html), [Matrix](https://cran.r-project.org/web/packages/Matrix/index.html), [data.table](https://cran.r-project.org/web/packages/data.table/index.html)

src/Makevars.linux

@@ -1,4 +1,4 @@
 ## src/Makevars (Linux)
 CXX_STD = CXX14
-PKG_CXXFLAGS += -O3 -march=native -pipe -fopenmp
+PKG_CXXFLAGS += -O3 -pipe -fopenmp
 PKG_LIBS += -fopenmp $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

src/calcDeviances.cpp

@@ -1,5 +1,6 @@
 // calcDeviances_ratio.cpp
 #include <RcppArmadillo.h>
+#include <atomic>
 #ifdef _OPENMP
 #include <omp.h>
 #endif
@@ -15,9 +16,10 @@ arma::vec calcDeviances_ratio(const arma::sp_mat& M1,
   int n_cols = M1.n_cols;
   arma::vec dev(n_rows, arma::fill::zeros);
 
-  // Notify about OpenMP availability only once
-  static bool has_printed = false;
-  if (!has_printed) {
+  // Notify about OpenMP availability only once (thread-safe)
+  static std::atomic<bool> has_printed(false);
+  bool expected = false;
+  if (has_printed.compare_exchange_strong(expected, true)) {
     if (num_threads <= 1) {
 #ifdef _OPENMP
       Rcpp::Rcout << "Note: OpenMP is available. "
@@ -33,7 +35,6 @@ arma::vec calcDeviances_ratio(const arma::sp_mat& M1,
       Rcpp::Rcout << "OpenMP not detected: running in single-thread mode.\n";
 #endif
     }
-    has_printed = true;
   }
 
   // Set the number of threads if OpenMP is available

src/deviance_gene.cpp

@@ -1,4 +1,5 @@
 #include <RcppArmadillo.h>
+#include <atomic>
 #ifdef _OPENMP
 #include <omp.h>
 #endif
@@ -13,9 +14,10 @@ arma::vec calcNBDeviancesWithThetaEstimation(const arma::sp_mat& gene_expression
   int n_cols = gene_expression.n_cols;  // number of cells
   arma::vec dev(n_rows, arma::fill::zeros);
 
-  // Notify about OpenMP availability only once
-  static bool has_printed = false;
-  if (!has_printed) {
+  // Notify about OpenMP availability only once (thread-safe)
+  static std::atomic<bool> has_printed(false);
+  bool expected = false;
+  if (has_printed.compare_exchange_strong(expected, true)) {
     #ifdef _OPENMP
       if (num_threads > 1) {
         Rcpp::Rcout << "OpenMP is available. Using " << num_threads << " threads for NB deviance calculation.\n";
@@ -25,7 +27,6 @@ arma::vec calcNBDeviancesWithThetaEstimation(const arma::sp_mat& gene_expression
         Rcpp::Rcout << "OpenMP is not available. Running in single-threaded mode.\n";
       }
     #endif
-    has_printed = true;
   }
 
   #ifdef _OPENMP