release 0.4.3

removed deprecated method to create sparse matrices
TomKellyGenetics · Sep 12, 2022 · 95672f6 · 95672f6
1 parent 855e801
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: leiden
 Type: Package
 Title: R Implementation of Leiden Clustering Algorithm
-Version: 0.4.2
-Date: 2022-05-01
+Version: 0.4.3
+Date: 2022-09-10
 Authors@R: c(person("S. Thomas", "Kelly", email = "[email protected]", role = c("aut", "cre", "trl")),
            person("Vincent A.", "Traag", email = "[email protected]", role = c("com")))
 Description: Implements the 'Python leidenalg' module to be called in R.

diff --git a/Meta/vignette.rds b/Meta/vignette.rds
diff --git a/NAMESPACE b/NAMESPACE
@@ -7,8 +7,11 @@ S3method(leiden,igraph)
 S3method(leiden,list)
 S3method(leiden,matrix)
 export(leiden)
+importClassesFrom(Matrix,CsparseMatrix)
+importClassesFrom(Matrix,dMatrix)
 importClassesFrom(Matrix,dgCMatrix)
 importClassesFrom(Matrix,dgeMatrix)
+importClassesFrom(Matrix,generalMatrix)
 importFrom(igraph,E)
 importFrom(igraph,V)
 importFrom(igraph,as.undirected)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,11 @@
+# leiden 0.4.3
+
+Minor update to pass CRAN checks
+
+- removed deprecated method to create sparse matrices
+
+- correct links in citations and vignettes
+
 # leiden 0.4.2
 
 * migrates bug fixes to conda environment and limit on total cells to refactored package

diff --git a/R/leiden.R b/R/leiden.R
@@ -182,7 +182,7 @@ leiden.data.frame <- leiden.matrix
 
 ##' @importFrom igraph graph_from_adjacency_matrix edge_attr set_edge_attr E
 ##' @importFrom methods as
-##' @importClassesFrom Matrix dgCMatrix dgeMatrix
+##' @importClassesFrom Matrix dgCMatrix dgeMatrix CsparseMatrix generalMatrix dMatrix
 ##' @export
 leiden.Matrix <- function(object,
                           partition_type = c(
@@ -216,7 +216,7 @@ leiden.Matrix <- function(object,
     on.exit(options(oo))
 
     #cast to sparse matrix
-    object <- as(object, "dgCMatrix")
+    object <- as(as(as(object, "CsparseMatrix"), "generalMatrix"), "dMatrix")
     #run as igraph object (passes to reticulate)
     if(is.null(weights)){
         object <- graph_from_adjacency_matrix(adjmatrix = object, weighted = TRUE)

diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # Leiden Algorithm
 
-## leiden version 0.4.2
+## leiden version 0.4.3
 
 [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/leiden)](https://cran.r-project.org/package=leiden)
 [![Travis Build Status](https://travis-ci.com/TomKellyGenetics/leiden.svg?branch=master)](https://travis-ci.com/TomKellyGenetics/leiden)
@@ -284,15 +284,15 @@ Please cite this implementation R in if you use it:
 To cite the leiden package in publications use:
 
   S. Thomas Kelly (2022). leiden: R implementation of the Leiden algorithm. R
-  package version 0.4.2 https://github.com/TomKellyGenetics/leiden
+  package version 0.4.3 https://github.com/TomKellyGenetics/leiden
 
 A BibTeX entry for LaTeX users is
 
   @Manual{,
     title = {leiden: R implementation of the Leiden algorithm},
     author = {S. Thomas Kelly},
     year = {2022},
-    note = {R package version 0.4.2},
+    note = {R package version 0.4.3},
     url = {https://github.com/TomKellyGenetics/leiden},
   }
  ```

diff --git a/doc/benchmarking.html b/doc/benchmarking.html
diff --git a/doc/run_bipartite.html b/doc/run_bipartite.html
diff --git a/doc/run_igraph.html b/doc/run_igraph.html
diff --git a/doc/run_leiden.html b/doc/run_leiden.html
diff --git a/inst/CITATION b/inst/CITATION
@@ -4,13 +4,13 @@ citEntry(entry = "Manual",
          title        = "leiden: R implementation of the Leiden algorithm",
          author       = personList(as.person("S. Thomas Kelly")),
          year         = "2022",
-         note         = "R package version 0.4.2",
+         note         = "R package version 0.4.3",
          url          = "https://github.com/TomKellyGenetics/leiden",
 
          textVersion  =
-           paste("S. Thomas Kelly (2020). leiden: R implementation of the Leiden algorithm. R package version 0.4.2",
+           paste("S. Thomas Kelly (2020). leiden: R implementation of the Leiden algorithm. R package version 0.4.3",
          year         = "2022",
-         note         = "R package version 0.4.2",
+         note         = "R package version 0.4.3",
          url          = "https://github.com/TomKellyGenetics/leiden",
                  "https://github.com/TomKellyGenetics/leiden")
 )

diff --git a/vignettes/benchmarking.Rmd b/vignettes/benchmarking.Rmd
@@ -800,7 +800,7 @@ Matrix methods in R are significantly slower than the updated igraph version.
 
 ```{r, eval=module}
 library("Matrix")
-adj_mat <- as(as_adjacency_matrix(G), Class = "dgCMatrix")
+adj_mat <- as(as(as(as_adjacency_matrix(G), Class = "CsparseMatrix"), "generalMatrix"), "dMatrix")
 time15 <- Sys.time()
 partition <- leiden(adj_mat, "ModularityVertexPartition", legacy = TRUE)
 partition