Merge pull request #4 from bedapub/devel

Upating ribiosGraph to make it ready for CRAN submission

Author: Accio

.github/workflows/standard-ci-workflow.yml

@@ -40,6 +40,14 @@ jobs:
           r-version: ${{ matrix.config.r }}
           use-public-rspm: true
 
+      - name: Install macOS system dependencies
+        if: runner.os == 'macOS'
+        run: |
+          brew install gettext
+          mkdir -p ~/.R
+          echo "CPPFLAGS += -I$(brew --prefix gettext)/include" >> ~/.R/Makevars
+          echo "LDFLAGS += -L$(brew --prefix gettext)/lib" >> ~/.R/Makevars
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rcmdcheck

.gitignore

@@ -2,4 +2,5 @@
 *.so
 *.o
 *.pdf
-*.Rhistory
+*.Rhistory*.tar.gz
+*.tar.gz

DESCRIPTION

@@ -1,18 +1,15 @@
 Package: ribiosGraph
 Type: Package
-Title: Manipulate and Visualize Graphs in the Ribios Software Suite
+Title: Manipulate and Visualize Graphs in the 'ribios' Software Suite
 Version: 1.1.0
 Date: 2026-01-24
 Authors@R:
   c(person(given = "Jitao David",
            family = "Zhang",
            role = c("aut", "cre"),
            email = "jitao_david.zhang@roche.com",
-           comment = c(ORCID="0000-0002-3085-0909")),
-    person("F.Hoffmann-La Roche AG", role="cph"))
-Description: Tools to manipulate and visualize graphs (networks) for
-    computational biology in drug discovery. Provides functions for creating
-    bipartite graphs and interactive visualizations using plotly.
+           comment = c(ORCID="0000-0002-3085-0909")))
+Description: The package implements tools to manipulate and visualize graphs (networks) for computational biology in drug discovery, for instance functions for creating bipartite graphs and for interactive visualizations. Zhang (2025) <https://github.com/bedapub/ribiosGraph>.
 Depends:
     R (>= 3.4.0),
     igraph

R/exportGML.R

@@ -10,7 +10,8 @@ fixNodeLabel <- function(name) {
 #' 
 #' @param igraph An \code{igraph} object
 #' @param filename Filename
-#'
+#' @return Invisible NULL
+#' @description
 #'   \code{exportGML} exports an \code{igraph} object to GML files
 #' complying with specifications defined by Cytoscape and yEd. Compared
 #'  to the native \code{write.graph} function provided by the
@@ -86,4 +87,5 @@ exportGML <- function(igraph, filename) {
   }
   cat("]\n", file=file)
   close(file)
+  return(invisible(NULL))
 }

R/incidence2bipartite.R

@@ -6,11 +6,9 @@
 #'   in rows and in columns
 #' @param label.color A vector of length 2, color of labels of nodes
 #'   in rows and in columns
-#' @param V A named list of other node styles, each item of length 1 or 2.
-#'   In the latter case, the first value is used for nodes in rows and the 
-#'   second for nodes in columns
+#' @param V A named list of other node styles, each item of length 1 or 2.  In the latter case, the first value is used for nodes in rows and the second for nodes in columns
 #' @param E A named list of edge styles. Each item must be length of 1.
-#' @return A graph
+#' @return An instance of \code{igraph} graph
 #' @importFrom igraph graph_from_incidence_matrix V E `V<-` `E<-`
 #' @examples
 #' myIncMat <- matrix(c(0, 0, 1,