CRAN release 1.0.3

TomKellyGenetics · Sep 12, 2022 · a562ca8 · a562ca8
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -57,3 +57,4 @@ import_pathcommons.R
 paxtoolsr.R
 plots_directed.html
 ^Meta$
+^CRAN-SUBMISSION$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: graphsim
 Type: Package
 Title: Simulate Expression Data from 'igraph' Networks
-Version: 1.0.2
-Date: 2021-07-27
+Version: 1.0.3
+Date: 2022-09-10
 Authors@R: c(person("S. Thomas", "Kelly",email = "tomkellygenetics@gmail.com", role = c("aut", "cre")),
              person("Michael A.", "Black", email = "mik.black@otago.ac.nz", role = c("aut", "ths")),
              person("Robrecht", "Cannoodt", role = c("ctb")),
@@ -12,7 +12,7 @@ License: GPL-3
 URL: https://github.com/TomKellyGenetics/graphsim/
 BugReports: https://github.com/TomKellyGenetics/graphsim/issues/
 Depends: R (>= 2.10)
-Imports: utils, gplots, igraph, mvtnorm, Matrix, matrixcalc, graphics
+Imports: gplots, igraph, mvtnorm, matrixcalc, Matrix, graphics
 Suggests: devtools, knitr (>= 1.5), markdown, prettydoc, R.rsp,
         rmarkdown, testthat, scales, vdiffr
 LazyData: TRUE

diff --git a/NAMESPACE b/NAMESPACE
@@ -21,8 +21,6 @@ export(make_state_matrix)
 export(plot_directed)
 import(graphics)
 import(igraph)
-importClassesFrom(Matrix,dgCMatrix)
-importFrom(Matrix,Matrix)
 importFrom(Matrix,nearPD)
 importFrom(gplots,heatmap.2)
 importFrom(igraph,E)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,13 @@
+# graphsim 1.0.3
+
+Minor update to pass CRAN checks
+
+- removed imports for unused packages
+
+- removed dependency on deprecated sparse matrices
+
+- correct links in citations and vignettes
+
 # graphsim 1.0.2
 
 Updates maintainer contact details.

diff --git a/R/graphsim-package.R b/R/graphsim-package.R
@@ -522,7 +522,7 @@
 #' }
 #' 
 #' This plotting function is demonstrated in more detail
-#' in the \href{https://CRAN.R-project.org/package=graphsim/vignettes/plots_directed.html}{plotting} vignette.
+#' in the plots_directed.Rmd plotting vignette.
 #'
 #' @section Further information:
 #'   The graphsim package is published in the \emph{Journal of Open Source Software}.

diff --git a/R/laplacian.R b/R/laplacian.R
@@ -13,8 +13,6 @@
 ##' @keywords graph network igraph Laplacian
 ##' @importFrom igraph laplacian_matrix graph.edgelist as.undirected graph_from_adjacency_matrix
 ##' @import igraph
-##' @importFrom Matrix Matrix
-##' @importClassesFrom Matrix dgCMatrix
 ##' 
 ##' @family graphsim functions
 ##' @family graph conversion functions

diff --git a/README.md b/README.md
@@ -1,5 +1,5 @@
-[![Travis-CI Build Status](https://travis-ci.com/TomKellyGenetics/graphsim.svg?branch=master)](https://travis-ci.com/TomKellyGenetics/graphsim)
-[![CircleCI build status](https://circleci.com/gh/TomKellyGenetics/graphsim.svg?style=svg)](https://circleci.com/gh/TomKellyGenetics/graphsim)
+[![Travis-CI Build Status](https://www.travis-ci.com/TomKellyGenetics/graphsim.svg?branch=master)](https://app.travis-ci.com/github/mikblacklab/graphsim)
+[![CircleCI build status](https://app.circleci.com/pipelines/github/TomKellyGenetics/graphsim.svg?style=svg)](https://app.circleci.com/pipelines/github/TomKellyGenetics/graphsim)
 [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/TomKellyGenetics/graphsim?branch=master&svg=true)](https://ci.appveyor.com/project/TomKellyGenetics/graphsim)
 [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 
@@ -16,7 +16,7 @@
 
 # graphsim
 
-## Version 1.0.2
+## Version 1.0.3
 
 
 ###  Simulate Expression Data from 'igraph' Networks 
@@ -109,7 +109,7 @@ This will display a help page and link to documentation for each function.
 To cite package 'graphsim' in publications use:
 
 >S. Thomas Kelly and Michael A. Black (2020). graphsim: Simulate Expression Data from
->'igraph' Networks. R package version 1.0.2.
+>'igraph' Networks. R package version 1.0.3.
 >https://github.com/TomKellyGenetics/graphsim doi:10.5281/zenodo.3931288
 
 A BibTeX entry for LaTeX users is:
@@ -119,7 +119,7 @@ A BibTeX entry for LaTeX users is:
     title = {{graphsim}: Simulate Expression Data from 'igraph' Networks },
     author = {S. Thomas Kelly and Michael A. Black},
     year = {2020},
-    note = {R package version R package version 1.0.2.},
+    note = {R package version R package version 1.0.3.},
     url = {https://github.com/TomKellyGenetics/graphsim},
     doi = {10.5281/zenodo.3931288},
   }

diff --git a/cran-comments.md b/cran-comments.md
@@ -7,12 +7,12 @@
 * Fedora (devel) Linux, R-devel, clang, gfortran
 * MacOS 8.6.0 R R 3.6.2
 * MacOS Mojave 10.14.6 R 3.6.1, R 3.6.2, R 4.0.2
-* MacOS Catalina 10.15.5 R 4.0.2
+* MacOS Catalina 10.15.7 R 4.2.0
 
 ## Local R CMD check results
 
-── R CMD check results ───────────────────────────────────── graphsim 1.0.2 ────
-Duration: 57.9s
+── R CMD check results ───────────────────────────────────── graphsim 1.0.3 ────
+Duration: 1m 55.4s
 
 0 errors ✓ | 0 warnings ✓ | 0 notes ✓
 

diff --git a/inst/CITATION b/inst/CITATION
@@ -4,7 +4,7 @@ citHeader("To cite package 'graphsim' in publications use:")
      desc <- packageDescription("graphsim")
      if(is.na(desc[1])){
              year <- "2020"
-             vers  <- "1.0.2"
+             vers  <- "1.0.3"
      } else {
              year <- sub(".*(2[[:digit:]]{3})-.*", "\\1", desc$Date)
             vers <- paste("R package version", desc$Version)

diff --git a/man/graphsim-package.Rd b/man/graphsim-package.Rd
diff --git a/vignettes/simulate_expression.Rmd b/vignettes/simulate_expression.Rmd
@@ -49,7 +49,7 @@ If you have problems or feedback, sumbmitting an issue to the the GitHub reposit
 
 Pathway and graph structures have a wide array of applications. Here we consider the simulation of (log-normalised) gene expression data from a biological pathway. If you have another use for this software you are welcome to apply it to your problem but please bear in mind that it was designed with this application in mind. In principle, normally-distributed continuous data can be generated based on any defined relationships. This package uses the graph structure to define a ∑ covariance matrix and generate simulated data by sampling from a multivariate normal distribution.
 
-Crucially, this allows the simulation of negative correlations based on inhibitory or repressive relationships, as commonly occur in biology <span class="citation">(Barabási and Oltvai 2004)</span>. A custom plotting function `plot_directed` is provided to visualise these relationships using the "state" parameter. This plotting function has a [dedicated vignette](https://CRAN.R-project.org/package=graphsim/vignettes/plots_directed.html).
+Crucially, this allows the simulation of negative correlations based on inhibitory or repressive relationships, as commonly occur in biology <span class="citation">(Barabási and Oltvai 2004)</span>. A custom plotting function `plot_directed` is provided to visualise these relationships using the "state" parameter. This plotting function has a dedicated vignette: plots_directed.Rmd.
 
 For more details on the background of this package, see the [paper](https://github.com/TomKellyGenetics/graphsim/blob/master/paper/paper.Rmd) included with the package on GitHub. This vignette provides more detail on the code needed to reproduce the figures presented in the manuscript.
 

diff --git a/vignettes/simulate_expression.html b/vignettes/simulate_expression.html
@@ -227,7 +227,7 @@ <h1 number="1"><span class="header-section-number">1</span> Overview of graphsim
 <div id="motivations" class="section level2" number="1.1">
 <h2 number="1.1"><span class="header-section-number">1.1</span> Motivations</h2>
 <p>Pathway and graph structures have a wide array of applications. Here we consider the simulation of (log-normalised) gene expression data from a biological pathway. If you have another use for this software you are welcome to apply it to your problem but please bear in mind that it was designed with this application in mind. In principle, normally-distributed continuous data can be generated based on any defined relationships. This package uses the graph structure to define a ∑ covariance matrix and generate simulated data by sampling from a multivariate normal distribution.</p>
-<p>Crucially, this allows the simulation of negative correlations based on inhibitory or repressive relationships, as commonly occur in biology <span class="citation">(Barabási and Oltvai 2004)</span>. A custom plotting function <code>plot_directed</code> is provided to visualise these relationships using the “state” parameter. This plotting function has a <a href="https://CRAN.R-project.org/package=graphsim/vignettes/plots_directed.html">dedicated vignette</a>.</p>
+<p>Crucially, this allows the simulation of negative correlations based on inhibitory or repressive relationships, as commonly occur in biology <span class="citation">(Barabási and Oltvai 2004)</span>. A custom plotting function <code>plot_directed</code> is provided to visualise these relationships using the “state” parameter. This plotting function has a dedicated vignette: plots_directed.Rmd.</a>.</p>
 <p>For more details on the background of this package, see the <a href="https://github.com/TomKellyGenetics/graphsim/blob/master/paper/paper.Rmd">paper</a> included with the package on GitHub. This vignette provides more detail on the code needed to reproduce the figures presented in the manuscript.</p>
 </div>
 </div>