Merge branch 'dev'

Author: evanbiederstedt

CHANGELOG.md

@@ -1,5 +1,7 @@
 # Changelog
 
+## [1.0.4] - 2022 September 25
+* Remove 'Matrix.utils' as dependency
 
 ## [1.0.3] - 2022 April 08
 * Install rigraph directly in `/src`. Remove previous linking to `igraph` R package in Makevars.

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: leidenAlg
 Type: Package
 Title: Implements the Leiden Algorithm via an R Interface
-Version: 1.0.3
+Version: 1.0.4
 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("V.A.", "Traag", email = "v.a.traag@cwts.leidenuniv.nl", role = c("ctb")), person("Gábor", "Csárdi", email = "sardi.gabor@gmail.com", role = c("ctb")), person("Tamás", "Nepusz", email = "ntamas@gmail.com", role = c("ctb")), person("Minh Van", "Nguyen", email = "nguyenminh2@gmail.com", role = c("ctb")), person("Evan", "Biederstedt", email = "evan.biederstedt@gmail.com", role=c("cre", "aut")))
 Description: An R interface to the Leiden algorithm, an iterative community detection algorithm on networks. The algorithm is designed to converge to a partition in which all subsets of all communities are locally optimally assigned, yielding communities guaranteed to be connected. The implementation proves to be fast, scales well, and can be run on graphs of millions of nodes (as long as they can fit in memory). The original implementation was constructed as a python interface "leidenalg" found here: <https://github.com/vtraag/leidenalg>. The algorithm was originally described in Traag, V.A., Waltman, L. & van Eck, N.J. "From Louvain to Leiden: guaranteeing well-connected communities". Sci Rep 9, 5233 (2019) <doi:10.1038/s41598-019-41695-z>.
 License: GPL-3 
@@ -13,7 +13,6 @@ Imports:
     graphics,
     grDevices,
     igraph,
-    Matrix.utils,
     parallel, 
     Rcpp (>= 1.0.5), 
     sccore,
@@ -23,7 +22,7 @@ Suggests:
     testthat (>= 3.1.0)
 LinkingTo: Rcpp, RcppArmadillo, RcppEigen
 SystemRequirements: C++11, GNU make (optional), libxml2 (optional), glpk (>= 4.57, optional)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.1
 URL: https://github.com/kharchenkolab/leidenAlg
 BugReports: https://github.com/kharchenkolab/leidenAlg/issues
 NeedsCompilation: yes

NAMESPACE

@@ -7,7 +7,6 @@ export(leiden.community)
 export(rleiden.community)
 exportPattern("^[[:alpha:]]+")
 import(Matrix)
-import(Matrix.utils)
 import(Rcpp)
 import(parallel)
 import(sccore)

R/communities.R

@@ -13,7 +13,6 @@
 #' @importFrom graphics par
 #' @importFrom grDevices adjustcolor
 #' @importFrom stats as.dendrogram is.leaf dendrapply as.hclust
-#' @import Matrix.utils
 #' @import Matrix
 NULL
 

man/exampleGraph.Rd

@@ -12,6 +12,11 @@ using namespace std;
 using namespace Rcpp;
 
 
+// Debug Mode implies checking assertions.
+#if defined(_GLIBCXX_ASSERTIONS)
+# define _GLIBCXX_ASSERTIONS 0
+#endif
+
 // a wrapper for the Leidgen algorithm implementation (https://github.com/vtraag/leidenalg)
 
 int R_SEXP_to_vector(SEXP sv, igraph_vector_t *v) {

src/leiden.cpp

@@ -1,6 +1,11 @@
 #include "RBConfigurationVertexPartition.h"
 #include "igraph.h"
 
+// Debug Mode implies checking assertions.
+#if defined(_GLIBCXX_ASSERTIONS)
+# define _GLIBCXX_ASSERTIONS 0
+#endif
+
 
 RBConfigurationVertexPartition::RBConfigurationVertexPartition(Graph* graph,
       vector<size_t> const& membership, double resolution_parameter) :