replace std::random_shuffle() with std::shuffle()

DESCRIPTION

@@ -1,8 +1,7 @@
 Package: scde
 Type: Package
 Title: Single Cell Differential Expression
-Version: 2.26.2
-Date: 2016-01-20
+Version: 2.27.1
 Description: The scde package implements a set of statistical methods for
     analyzing single-cell RNA-seq data. scde fits individual error models for
     single-cell RNA-seq measurements. These models can then be used for assessment
@@ -18,16 +17,17 @@ Description: The scde package implements a set of statistical methods for
     transcriptional heterogeneity through pathway and gene set overdispersion 
     analysis" (Fan J, Salathia N, Liu R, Kaeser G, Yung Y, Herman J, Kaper F,
     Fan JB, Zhang K, Chun J, and Kharchenko PV, Nature Methods, doi:10.1038/nmeth.3734).
-Author: Peter Kharchenko [aut, cre],
-    Jean Fan [aut]
+Author: Peter Kharchenko [aut, cre], Jean Fan [aut], Evan Biederstedt [aut]
 Authors@R: c(
     person("Peter", "Kharchenko", role = c("aut", "cre"),
-		     email = "Peter_Kharchenko@hms.harvard.edu"),
+             email = "Peter_Kharchenko@hms.harvard.edu"),
     person("Jean", "Fan", role = "aut",
-    		   email = "jeanfan@jhu.edu",     
-		   comment = c(ORCID = "0000-0002-0212-5451"))
-	         )
-Maintainer: Jean Fan <jeanfan@jhu.edu>
+               email = "jeanfan@jhu.edu",     
+           comment = c(ORCID = "0000-0002-0212-5451")),
+    person("Evan", "Biederstedt", role = "aut",
+           email = "evan.biederstedt@gmail.com")
+    )
+Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>
 URL: http://pklab.med.harvard.edu/scde
 BugReports: https://github.com/hms-dbmi/scde/issues
 License: GPL-2
@@ -36,17 +36,11 @@ Depends: R (>= 3.0.0), flexmix
 Imports: Rcpp (>= 0.10.4), RcppArmadillo (>= 0.5.400.2.0), mgcv, Rook,
         rjson, MASS, Cairo, RColorBrewer, edgeR, quantreg, methods,
         nnet, RMTstat, extRemes, pcaMethods, BiocParallel, parallel
-Suggests: knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db,
-        rmarkdown
-biocViews: ImmunoOncology, RNASeq, StatisticalMethod,
-        DifferentialExpression, Bayesian, Transcription, Software
+Suggests: knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db, rmarkdown
+biocViews: ImmunoOncology, RNASeq, StatisticalMethod, DifferentialExpression, Bayesian,
+        Transcription, Software
 LinkingTo: Rcpp, RcppArmadillo
 VignetteBuilder: knitr
-Packaged: 2023-01-19 22:55:25 UTC; biocbuild
+Packaged: 2015-11-02 14:30:04 UTC; reyes
 RoxygenNote: 5.0.0
 NeedsCompilation: yes
-git_url: https://git.bioconductor.org/packages/scde
-git_branch: RELEASE_3_16
-git_last_commit: 42cdc08
-git_last_commit_date: 2023-01-19
-Date/Publication: 2023-01-19

src/Makevars

@@ -1,4 +1,2 @@
-## Use the R_HOME indirection to support installations of multiple R version
-PKG_LIBS = `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
-
-
+PKG_CXXFLAGS=$(SHLIB_OPENMP_CXXFLAGS) 
+PKG_LIBS=-L/usr/lib/ -L"." -lpthread -lm `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS)

src/Makevars.win

@@ -1,5 +1,2 @@
-
-## This assume that we can call Rscript to ask Rcpp about its locations
-## Use the R_HOME indirection to support installations of multiple R version
-PKG_LIBS = $(shell $(R_HOME)/bin/Rscript.exe -e "Rcpp:::LdFlags()") $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
-
+PKG_CXXFLAGS=$(SHLIB_OPENMP_CXXFLAGS) 
+PKG_LIBS=-L/usr/lib/ -L"." -lpthread -lm $(shell "${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "Rcpp:::LdFlags()") $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS) 

src/bwpca.cpp

@@ -1,4 +1,5 @@
 #include "bwpca.h"
+#include <random>
 #include <vector>
 #include <algorithm>
 #include <iostream>
@@ -24,8 +25,11 @@ void set_random_matrix(arma::mat& target,arma::mat& source) {
         ind[j]=j;
     } // set up initial index (1,2,3)
 
+    // The random number generator that we want to use (Mersenne Twister)
+    std::mt19937 rng(std::time(nullptr));
+
     for(int i=0;i<target.n_cols;i++) {
-        std::random_shuffle(ind.begin(), ind.end());
+        std::shuffle(ind.begin(), ind.end(), rng);  // NOTE: std::random_shuffler() was deprecated in C++14 and completely removed in C++17
         //std::sort(ind.start(), ind.end(), std::bind(compare_on_other,  _1, _2, rv));
         for(int j=0;j<target.n_rows;j++) {
             target(j,i)=source(ind[j],i);
@@ -41,8 +45,11 @@ void set_random_matrices(arma::mat& target1,arma::mat& source1,arma::mat& target
         ind[j]=j;
     } // set up initial index (1,2,3)
 
+    // The random number generator that we want to use (Mersenne Twister)
+    std::mt19937 rng(std::time(nullptr));
+
     for(int i=0;i<target1.n_cols;i++) {
-        std::random_shuffle(ind.begin(), ind.end());
+        std::shuffle(ind.begin(), ind.end(), rng);    // NOTE: std::random_shuffler() was deprecated in C++14 and completely removed in C++17
         //std::sort(ind.start(), ind.end(), std::bind(compare_on_other,  _1, _2, rv));
         for(int j=0;j<target1.n_rows;j++) {
             target1(j,i)=source1(ind[j],i);