diff --git a/DESCRIPTION b/DESCRIPTION index 030bb29..cfb3c10 100644 --- 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 index 02a4e7a..582406b 100644 --- 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 index 3234dbe..fe04e9d 100644 --- 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 index 29ac8a7..71cb692 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,11 +1,11 @@ ## 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 @@ -13,9 +13,24 @@ ## 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 index 5ef7014..68c6938 100644 --- 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 index a39b680..1c176f7 100644 --- 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 index 3388012..9dbfc26 100644 --- 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 ) ```