Cran release patch fixes

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: clustur
 Type: Package
 Title: Clustering
-Version: 0.1.0
-Date: 2024-10-18
+Version: 0.1.1
+Date: 2024-11-25
 Authors@R: c(
     person("Gregory", "Johnson", , "[email protected]", role = c("aut"),
             comment = c(ORCID = "0009-0008-3890-0297")),

R/cluster.R

@@ -156,7 +156,7 @@ validate_count_table <- function(count_table_df) {
 #' This function was created as a helper function to generate file paths to our
 #' internal data. You should use this function if you
 #' want to follow along with the example, or interact with the data
-#' @param file The file name of the data; leave as NULL (default) to get full
+#' @param The file name of the data; leave as NULL (default) to get full
 #' list of example files
 #' @examples
 #' example_path("amazon_phylip.dist")

cran-comments.md

@@ -2,6 +2,5 @@
 
 0 errors | 0 warnings | 1 note
 
-* This is a new release.
-* All of our projects use C++ 11 so we can continue to support older architectures. 
+* This should be the patch for clustur's build error on debian.
 * Build checks for macos-latest (devel), ubuntu-lastest (devel), windows-latest (devel), windows latest (4.1), ubuntu-latest (release), ubuntu-latest (oldrel-1), ubuntu-latest (oldrel-2), and ubuntu-latest (oldrel-3) are currently passing via GitHub Actions.

src/ClusterCommand.cpp

@@ -83,7 +83,6 @@ ClusterExport* ClusterCommand::runOptiCluster(OptiMatrix *optiMatrix, const doub
             clusterMetrics += (std::to_string(result) + ",");
         }
         util.AddRowToDataFrameMap(dataframeMapClusterMetrics, clusterMetrics, clusterMetricsHeaders);
-        std::chrono::time_point<std::chrono::system_clock> start, end;
 
         while ((delta > stableMetric) && (iters < maxIters)) {
             //long start = std::time(nullptr);

src/main.cpp

@@ -26,7 +26,7 @@ Rcpp::DataFrame CreateSharedDataFrame(const CountTableAdapter& countTable, const
 
 //[[Rcpp::export]]
 bool DetermineIfPhylipOrColumnFile(const std::string& filePath) {
-    std::fstream data(filePath);
+    std::ifstream data(filePath);
 
     if(!data.is_open()) {
         Rcpp::Rcout << "Please enter a valid file path\n";
@@ -96,17 +96,17 @@ Rcpp::List Cluster(const SEXP& DistanceData,const std::string& method, const std
     ClusterCommand command;
     const auto lastCutoff = distanceData.get()->GetCutoff();
     const auto listVector = distanceData.get()->GetListVector(); // Going to have to make a copy of list vector, this two values are definitely being changed
-    auto sparseMatix = distanceData.get()->GetSparseMatrix(); // Going to have to make a copy of sparse matrix
+    auto sparseMatrix = distanceData.get()->GetSparseMatrix(); // Going to have to make a copy of sparse matrix
     if(cutoff < lastCutoff)
-        sparseMatix->FilterSparseMatrix(cutoff);
-    const auto result = command.runMothurCluster(method, sparseMatix, cutoff, listVector);
+        sparseMatrix->FilterSparseMatrix(cutoff);
+    const auto result = command.runMothurCluster(method, sparseMatrix, cutoff, listVector);
     const auto label = result->GetListVector().label;
     const Rcpp::DataFrame clusterDataFrame = result->GetListVector().listVector->CreateDataFrameFromList(
         featureColumnName, binColumnName);
     const Rcpp::DataFrame tidySharedDataFrame = CreateSharedDataFrame(countTableAdapter, result);
     delete(result);
     delete(listVector);
-    delete(sparseMatix);
+    delete(sparseMatrix);
     return Rcpp::List::create(Rcpp::Named("label") = std::stod(label),
     Rcpp::Named("abundance") = tidySharedDataFrame,
     Rcpp::Named("cluster") = clusterDataFrame);