cran release version 0.3.8

TomKellyGenetics · May 24, 2021 · d53d1c3 · d53d1c3
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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: 0.3.7
-Date: 2021-01-26
+Version: 0.3.8
+Date: 2021-05-24
 Authors@R: c(person("S. Thomas", "Kelly", email = "tom.kelly@riken.jp", role = c("aut", "cre", "trl")),
            person("Vincent A.", "Traag", email = "v.a.traag@cwts.leidenuniv.nl", role = c("com")))
 Description: Implements the 'Python leidenalg' module to be called in R.
@@ -17,7 +17,7 @@ Imports:
     Matrix,
     igraph
 Encoding: UTF-8
-LazyData: true
+LazyData: false
 RoxygenNote: 7.1.1
 Suggests: 
     bipartite,

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# leiden 0.3.8
+
+* bug fixes for vignettes to retain on CRAN
+
 # leiden 0.3.7
 
 * remove cairo graphics from vignette to retain on CRAN

diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # Leiden Algorithm
 
-## leiden version 0.3.7
+## leiden version 0.3.8
 
 [![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)
@@ -274,16 +274,16 @@ Please cite this implementation R in if you use it:
 ```
 To cite the leiden package in publications use:
 
-  S. Thomas Kelly (2020). leiden: R implementation of the Leiden algorithm. R
-  package version 0.3.7 https://github.com/TomKellyGenetics/leiden
+  S. Thomas Kelly (2021). leiden: R implementation of the Leiden algorithm. R
+  package version 0.3.8 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 = {2020},
-    note = {R package version 0.3.7},
+    year = {2021},
+    note = {R package version 0.3.8},
     url = {https://github.com/TomKellyGenetics/leiden},
   }
  ```

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,21 +1,36 @@
 ## Test environments
-* ubuntu 14.04 (on travis-ci), R 4.0.2, 3.6.1
-* ubuntu 14.04 (on circle-ci), R 4.0.2, 3.6.1
+* ubuntu 14.04 (on travis-ci), R 4.1.0, 3.6.1
+* ubuntu 14.04 (on circle-ci), R 4.1.0, 3.6.1
 * win-builder (devel and release) Windows Server 2008 R2 SP1, R-devel, 32/64 bit
 * rhub (release) Ubuntu Linux 16.04 LTS, R-release, GCC
 * Fedora (devel) Linux, R-devel, clang, gfortran
 * MacOS 10.14.6 R 3.6.1 
-* MacOS 10.15.7 R 4.0.2
+* MacOS 10.15.7 R 4.1.0
 
 ## R CMD check results
 
 0 errors ✔ | 0 warnings ✔ | 0 notes ✔
 
 ## Updates
 
-Changes to remove cairo graphics (M1 requirement).
+Changes to vignettes to address the following issue:
 
-Soft dependency on python module to avoid install issues.
+Specifically, please see the problems for the Debian-based checks for
+r-devel.
+
+These are from
+
+      \item \code{matrix(x, n, m)} now warns in more cases where
+      \code{length(x)} differs from than \code{n * m}; suggested by Abby
+      Spurdle and Wolfgang Huber in Feb 2021 on the R-devel mailing
+      list.
+
+      This warning can be turned into an error by setting environment
+      variable \env{_R_CHECK_MATRIX_DATA_} to \samp{TRUE}: \command{R
+        CMD check --as-cran} does so unless it is already set.
+
+in current r-devel, where the Debian-based checks are now performed with
+_R_CHECK_MATRIX_DATA_=TRUE.
 
 ## Python integration
 

diff --git a/inst/CITATION b/inst/CITATION
@@ -3,12 +3,12 @@ citHeader("To cite the leiden package in publications use:")
 citEntry(entry = "Manual",
          title        = "leiden: R implementation of the Leiden algorithm",
          author       = personList(as.person("S. Thomas Kelly")),
-         year         = "2020",
-         note         = "R package version 0.3.7",
+         year         = "2021",
+         note         = "R package version 0.3.8",
          url          = "https://github.com/TomKellyGenetics/leiden",
 
          textVersion  =
-           paste("S. Thomas Kelly (2020). leiden: R implementation of the Leiden algorithm. R package version 0.3.7",
+           paste("S. Thomas Kelly (2021). leiden: R implementation of the Leiden algorithm. R package version 0.3.8",
                  "https://github.com/TomKellyGenetics/leiden")
 )
 

diff --git a/vignettes/run_igraph.Rmd b/vignettes/run_igraph.Rmd
@@ -64,15 +64,15 @@ library("leiden")
 First set up a compatible adjacency matrix:
 
 ```{r}
-adjacency_matrix <- rbind(cbind(matrix(round(rbinom(4000, 1, 0.8)), 20, 20),
-                                matrix(round(rbinom(4000, 1, 0.3)), 20, 20), 
+adjacency_matrix <- rbind(cbind(matrix(round(rbinom(400, 1, 0.8)), 20, 20),
+                                matrix(round(rbinom(400, 1, 0.3)), 20, 20), 
                                 matrix(round(rbinom(400, 1, 0.1)), 20, 20)),
                           cbind(matrix(round(rbinom(400, 1, 0.3)), 20, 20), 
                                 matrix(round(rbinom(400, 1, 0.8)), 20, 20), 
-                                matrix(round(rbinom(4000, 1, 0.2)), 20, 20)),
+                                matrix(round(rbinom(400, 1, 0.2)), 20, 20)),
                           cbind(matrix(round(rbinom(400, 1, 0.3)), 20, 20), 
-                                matrix(round(rbinom(4000, 1, 0.1)), 20, 20), 
-                                matrix(round(rbinom(4000, 1, 0.9)), 20, 20)))
+                                matrix(round(rbinom(400, 1, 0.1)), 20, 20), 
+                                matrix(round(rbinom(400, 1, 0.9)), 20, 20)))
 str(adjacency_matrix)
 dim(adjacency_matrix )
 ```

diff --git a/vignettes/run_leiden.Rmd b/vignettes/run_leiden.Rmd
@@ -64,15 +64,15 @@ library("leiden")
 First set up a compatible adjacency matrix:
 
 ```{r}
-adjacency_matrix <- rbind(cbind(matrix(round(rbinom(4000, 1, 0.8)), 20, 20),
-                                matrix(round(rbinom(4000, 1, 0.3)), 20, 20), 
+adjacency_matrix <- rbind(cbind(matrix(round(rbinom(400, 1, 0.8)), 20, 20),
+                                matrix(round(rbinom(400, 1, 0.3)), 20, 20), 
                                 matrix(round(rbinom(400, 1, 0.1)), 20, 20)),
                           cbind(matrix(round(rbinom(400, 1, 0.3)), 20, 20), 
                                 matrix(round(rbinom(400, 1, 0.8)), 20, 20), 
-                                matrix(round(rbinom(4000, 1, 0.2)), 20, 20)),
+                                matrix(round(rbinom(400, 1, 0.2)), 20, 20)),
                           cbind(matrix(round(rbinom(400, 1, 0.3)), 20, 20), 
-                                matrix(round(rbinom(4000, 1, 0.1)), 20, 20), 
-                                matrix(round(rbinom(4000, 1, 0.9)), 20, 20)))
+                                matrix(round(rbinom(400, 1, 0.1)), 20, 20), 
+                                matrix(round(rbinom(400, 1, 0.9)), 20, 20)))
 str(adjacency_matrix)
 dim(adjacency_matrix )
 ```