devtools::document() changed this

vwtlin · Mar 4, 2019 · a714f67 · a714f67
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Showing 4 changed files with 34 additions and 33 deletions.
diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -1,10 +1,6 @@
 # Generated by using Rcpp::compileAttributes() -> do not edit by hand
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
-RunModularityClusteringCpp <- function(SNN, modularityFunction, resolution, algorithm, nRandomStarts, nIterations, randomSeed, printOutput, edgefilename) {
-    .Call('_Seurat_RunModularityClusteringCpp', PACKAGE = 'Seurat', SNN, modularityFunction, resolution, algorithm, nRandomStarts, nIterations, randomSeed, printOutput, edgefilename)
-}
-
 RunUMISampling <- function(data, sample_val, upsample = FALSE, display_progress = TRUE) {
     .Call('_Seurat_RunUMISampling', PACKAGE = 'Seurat', data, sample_val, upsample, display_progress)
 }
@@ -93,6 +89,10 @@ SNNAnchor <- function(k_matrix, anchor_only) {
     .Call('_Seurat_SNNAnchor', PACKAGE = 'Seurat', k_matrix, anchor_only)
 }
 
+RunModularityClusteringCpp <- function(SNN, modularityFunction, resolution, algorithm, nRandomStarts, nIterations, randomSeed, printOutput, edgefilename) {
+    .Call('_Seurat_RunModularityClusteringCpp', PACKAGE = 'Seurat', SNN, modularityFunction, resolution, algorithm, nRandomStarts, nIterations, randomSeed, printOutput, edgefilename)
+}
+
 ComputeSNN <- function(nn_ranked, prune) {
     .Call('_Seurat_ComputeSNN', PACKAGE = 'Seurat', nn_ranked, prune)
 }

diff --git a/man/AddMetaData.Rd b/man/AddMetaData.Rd
diff --git a/man/RegressRegNB.Rd b/man/RegressRegNB.Rd
diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
@@ -6,25 +6,6 @@
 
 using namespace Rcpp;
 
-// RunModularityClusteringCpp
-IntegerVector RunModularityClusteringCpp(Eigen::SparseMatrix<double> SNN, int modularityFunction, double resolution, int algorithm, int nRandomStarts, int nIterations, int randomSeed, bool printOutput, std::string edgefilename);
-RcppExport SEXP _Seurat_RunModularityClusteringCpp(SEXP SNNSEXP, SEXP modularityFunctionSEXP, SEXP resolutionSEXP, SEXP algorithmSEXP, SEXP nRandomStartsSEXP, SEXP nIterationsSEXP, SEXP randomSeedSEXP, SEXP printOutputSEXP, SEXP edgefilenameSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< Eigen::SparseMatrix<double> >::type SNN(SNNSEXP);
-    Rcpp::traits::input_parameter< int >::type modularityFunction(modularityFunctionSEXP);
-    Rcpp::traits::input_parameter< double >::type resolution(resolutionSEXP);
-    Rcpp::traits::input_parameter< int >::type algorithm(algorithmSEXP);
-    Rcpp::traits::input_parameter< int >::type nRandomStarts(nRandomStartsSEXP);
-    Rcpp::traits::input_parameter< int >::type nIterations(nIterationsSEXP);
-    Rcpp::traits::input_parameter< int >::type randomSeed(randomSeedSEXP);
-    Rcpp::traits::input_parameter< bool >::type printOutput(printOutputSEXP);
-    Rcpp::traits::input_parameter< std::string >::type edgefilename(edgefilenameSEXP);
-    rcpp_result_gen = Rcpp::wrap(RunModularityClusteringCpp(SNN, modularityFunction, resolution, algorithm, nRandomStarts, nIterations, randomSeed, printOutput, edgefilename));
-    return rcpp_result_gen;
-END_RCPP
-}
 // RunUMISampling
 Eigen::SparseMatrix<double> RunUMISampling(Eigen::SparseMatrix<double> data, int sample_val, bool upsample, bool display_progress);
 RcppExport SEXP _Seurat_RunUMISampling(SEXP dataSEXP, SEXP sample_valSEXP, SEXP upsampleSEXP, SEXP display_progressSEXP) {
@@ -322,6 +303,25 @@ BEGIN_RCPP
     return rcpp_result_gen;
 END_RCPP
 }
+// RunModularityClusteringCpp
+IntegerVector RunModularityClusteringCpp(Eigen::SparseMatrix<double> SNN, int modularityFunction, double resolution, int algorithm, int nRandomStarts, int nIterations, int randomSeed, bool printOutput, std::string edgefilename);
+RcppExport SEXP _Seurat_RunModularityClusteringCpp(SEXP SNNSEXP, SEXP modularityFunctionSEXP, SEXP resolutionSEXP, SEXP algorithmSEXP, SEXP nRandomStartsSEXP, SEXP nIterationsSEXP, SEXP randomSeedSEXP, SEXP printOutputSEXP, SEXP edgefilenameSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< Eigen::SparseMatrix<double> >::type SNN(SNNSEXP);
+    Rcpp::traits::input_parameter< int >::type modularityFunction(modularityFunctionSEXP);
+    Rcpp::traits::input_parameter< double >::type resolution(resolutionSEXP);
+    Rcpp::traits::input_parameter< int >::type algorithm(algorithmSEXP);
+    Rcpp::traits::input_parameter< int >::type nRandomStarts(nRandomStartsSEXP);
+    Rcpp::traits::input_parameter< int >::type nIterations(nIterationsSEXP);
+    Rcpp::traits::input_parameter< int >::type randomSeed(randomSeedSEXP);
+    Rcpp::traits::input_parameter< bool >::type printOutput(printOutputSEXP);
+    Rcpp::traits::input_parameter< std::string >::type edgefilename(edgefilenameSEXP);
+    rcpp_result_gen = Rcpp::wrap(RunModularityClusteringCpp(SNN, modularityFunction, resolution, algorithm, nRandomStarts, nIterations, randomSeed, printOutput, edgefilename));
+    return rcpp_result_gen;
+END_RCPP
+}
 // ComputeSNN
 Eigen::SparseMatrix<double> ComputeSNN(Eigen::MatrixXd nn_ranked, double prune);
 RcppExport SEXP _Seurat_ComputeSNN(SEXP nn_rankedSEXP, SEXP pruneSEXP) {
@@ -362,7 +362,6 @@ END_RCPP
 }
 
 static const R_CallMethodDef CallEntries[] = {
-    {"_Seurat_RunModularityClusteringCpp", (DL_FUNC) &_Seurat_RunModularityClusteringCpp, 9},
     {"_Seurat_RunUMISampling", (DL_FUNC) &_Seurat_RunUMISampling, 4},
     {"_Seurat_RunUMISamplingPerCell", (DL_FUNC) &_Seurat_RunUMISamplingPerCell, 4},
     {"_Seurat_RowMergeMatrices", (DL_FUNC) &_Seurat_RowMergeMatrices, 5},
@@ -385,6 +384,7 @@ static const R_CallMethodDef CallEntries[] = {
     {"_Seurat_FindWeightsC", (DL_FUNC) &_Seurat_FindWeightsC, 10},
     {"_Seurat_IntegrateDataC", (DL_FUNC) &_Seurat_IntegrateDataC, 3},
     {"_Seurat_SNNAnchor", (DL_FUNC) &_Seurat_SNNAnchor, 2},
+    {"_Seurat_RunModularityClusteringCpp", (DL_FUNC) &_Seurat_RunModularityClusteringCpp, 9},
     {"_Seurat_ComputeSNN", (DL_FUNC) &_Seurat_ComputeSNN, 2},
     {"_Seurat_WriteEdgeFile", (DL_FUNC) &_Seurat_WriteEdgeFile, 3},
     {"_Seurat_DirectSNNToFile", (DL_FUNC) &_Seurat_DirectSNNToFile, 4},