remove /usr/lib

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: leidenAlg
 Type: Package
 Title: Implements the Leiden Algorithm via an R Interface
-Version: 1.1.2
+Version: 1.1.3
 Authors@R: c(person("Peter", "Kharchenko", email = "Peter_Kharchenko@hms.harvard.edu", role = c("aut")), 
              person("Viktor", "Petukhov", email = "viktor.s.petukhov@ya.ru", role = c("aut")), 
              person("Yichen", "Wang", email = "wayichen@umich.edu", role=c("aut")),

README.md

@@ -89,5 +89,5 @@ If you find `leidenAlg` useful for your publication, please cite:
 ```
 Peter Kharchenko, Viktor Petukhov, Yichen Wang, and Evan Biederstedt (2023).
 leidenAlg: Implements the Leiden Algorithm via an R Interface. R
-package version 1.1.2. https://github.com/kharchenkolab/leidenAlg
+package version 1.1.3. https://github.com/kharchenkolab/leidenAlg
 ```

src/Makevars

@@ -1,15 +1,14 @@
 
 ## include OpenMP
 
-PKG_CXXFLAGS= -I"../inst/include"  -I"./rigraph/include" -I"./leidenalg/include" $(SHLIB_OPENMP_CXXFLAGS) 
+PKG_CXXFLAGS = -I"../inst/include"  -I"./rigraph/include" -I"./leidenalg/include" $(SHLIB_OPENMP_CXXFLAGS) 
 
 
-PKG_CFLAGS = -pthread 
-PKG_CFLAGS += -I"./include"  -I"../rigraph/include"
-LDFLAGS += -lpthread
+PKG_CFLAGS = -pthread -I"./include"  -I"../rigraph/include"
+LDFLAGS = -lpthread
 
 
-PKG_LIBS=-L/usr/lib/ -L"." -lpthread -lstdc++ -lleidenalg -lrigraph -lm `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS) 
+PKG_LIBS = -L"." -lpthread -lleidenalg -lrigraph -lm `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS) 
 MkInclude = $(R_HOME)/etc${R_ARCH}/Makeconf
 
 #.PHONY: all sublibs

src/Makevars.win

@@ -1,15 +1,14 @@
 
 ## include OpenMP
 
-PKG_CXXFLAGS= -I"../inst/include"  -I"./rigraph/include" -I"./leidenalg/include" $(SHLIB_OPENMP_CXXFLAGS) 
+PKG_CXXFLAGS = -I"../inst/include"  -I"./rigraph/include" -I"./leidenalg/include" $(SHLIB_OPENMP_CXXFLAGS) 
 
 
-PKG_CFLAGS = -pthread 
-PKG_CFLAGS += -I"./include"  -I"../rigraph/include"
-LDFLAGS += -lpthread
+PKG_CFLAGS = -pthread -I"./include"  -I"../rigraph/include"
+LDFLAGS = -lpthread
 
 
-PKG_LIBS=-L/usr/lib/ -L"." -lpthread -lstdc++ -lleidenalg -lrigraph -lm `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS) 
+PKG_LIBS = -L"." -lpthread -lleidenalg -lrigraph -lm `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS) 
 MkInclude = $(R_HOME)/etc${R_ARCH}/Makeconf
 
 #.PHONY: all sublibs

src/leiden.cpp

@@ -131,7 +131,7 @@ std::vector<size_t> find_partition_with_rep_rcpp(std::vector<int>& edgelist, int
   std::vector<size_t> best_cluster;
   for(int i=0; i<nrep; i++) {
     Rcpp::checkUserInterrupt();
-    int seed = R::runif(0,1)*(double)RAND_MAX;
+    // unused variable, int seed = R::runif(0,1)*(double)RAND_MAX;
     Optimiser o( (int) (R::runif(0,1)*(double)RAND_MAX) );
     RBConfigurationVertexPartition p(&og,resolution);
     double val=1;

src/leidenalg/Makefile

@@ -1,6 +1,5 @@
 CXX ?= g++
-PKG_CXXFLAGS = -O3 -pthread -fPIC $(SHLIB_OPENMP_CXXFLAGS)
-PKG_CXXFLAGS += -I"./include" -I"../rigraph/include"
+PKG_CXXFLAGS = -O3 -pthread -fPIC $(SHLIB_OPENMP_CXXFLAGS) -I"./include" -I"../rigraph/include"
 LDFLAGS += -lpthread
 
 

src/rigraph/Makefile

@@ -1,14 +1,12 @@
 C ?= gcc 
 CFLAGS = -O3 
-PKG_CFLAGS = -O3 -pthread -fPIC 
-PKG_CFLAGS += -I"./include"  -I"../rigraph/include"
-LDFLAGS += -lpthread
+PKG_CFLAGS = -O3 -pthread -fPIC -I"./include" -I"../rigraph/include"
+LDFLAGS = -lpthread
 
 
 CXX ?= g++
-PKG_CXXFLAGS = -O3 -pthread -fPIC $(SHLIB_OPENMP_CXXFLAGS)
-PKG_CXXFLAGS += -I"./include" -I"../rigraph/include"
-LDFLAGS += -lpthread
+PKG_CXXFLAGS = -O3 -pthread -fPIC $(SHLIB_OPENMP_CXXFLAGS) -I"./include" -I"../rigraph/include" 
+LDFLAGS = -lpthread
 
 
 LIB=../librigraph.a

src/rigraph/Makefile.win

@@ -1,13 +1,11 @@
 C ?= gcc 
 CFLAGS = -O3 
-PKG_CFLAGS = -O3  -pthread -fPIC 
-PKG_CFLAGS += -I"./include"  -I"../rigraph/include"
-LDFLAGS += -lpthread
+PKG_CFLAGS = -O3 -pthread -fPIC -I"./include"  -I"../rigraph/include"
+LDFLAGS = -lpthread
 
 CXX ?= g++
-PKG_CXXFLAGS = -O3 -pthread -fPIC $(SHLIB_OPENMP_CXXFLAGS)
-PKG_CXXFLAGS += -I"./include" -I"../rigraph/include"
-LDFLAGS += -lpthread
+PKG_CXXFLAGS = -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" $(SHLIB_OPENMP_CXXFLAGS)
+LDFLAGS = -lpthread
 
 LIB=../librigraph.a
 lib: $(LIB)