@@ -1,5 +1,5 @@

 Package: NetPathMiner

-Version: 1.19.4

+Version: 1.19.5

 Date: 2014 onwards

 Title: NetPathMiner for Biological Network Construction, Path Mining

     and Visualization

@@ -18,7 +18,7 @@

 #' or remove certain annotations.

 #'

 #' NetPathMiner stores all its vertex annotation attributes in a list, and stores them collectively as

-#' a single \code{attr}. This is not to interfer with \code{\link[igraph]{attributes}} from \code{igraph} package.

+#' a single \code{attr}. This is not to interfer with \code{\link[igraph]{graph_attr_names}} from \code{igraph} package.

 #' All functions here target NetPathMiner annotations only.

 #'

 #' @param graph An annotated igraph object.

@@ -261,7 +261,7 @@ fetchAttribute <- function(graph, organism="Homo sapiens", target.attr, source.a

 #' value (or \code{NA}). The default computes Pearson's correlation.

 #' @param complex.method A function, or a string indicating the name of the function to be used in weighting edges connecting complexes.

 #' If a vertex has >1 attribute value, all possible pairwise weights are first computed, and given to \code{complex.method}. The default

-#' function is \code{\link[base]{max}}.

+#' function is \code{\link[base:Extremes]{max}}.

 #' @param missing.method A function, or a string indicating the name of the function to be used in weighting edges when one of the vertices

 #' lack expression data. The function is passed all edge weights on the graph. Default is \code{\link[stats]{median}}.

 #' @param same.gene.penalty A numerical value to be assigned when 2 adjacent vertices have the same attribute value, since correlation and

@@ -220,7 +220,7 @@ plotAllNetworks <- function(paths, metabolic.net=NULL, reaction.net=NULL, gene.n

 #' @param cluster.strength A number indicating tie strengths between vertices with the same attribute.

 #' The larger it is, the closer the vertices will be.

 #' @param layout A layout function, ideally a force-directed layout fuction, such as

-#' \code{\link[igraph]{layout.fruchterman.reingold}} and \code{\link[igraph]{layout.kamada.kawai}}.

+#' \code{\link[igraph]{layout_with_fr}} and \code{\link[igraph]{layout_with_kk}}.

 #'

 #' @return A two-column matrix indicating the x and y postions of vertices.

 #'

@@ -25,7 +25,7 @@ value (or \code{NA}). The default computes Pearson's correlation.}

 \item{complex.method}{A function, or a string indicating the name of the function to be used in weighting edges connecting complexes.

 If a vertex has >1 attribute value, all possible pairwise weights are first computed, and given to \code{complex.method}. The default

-function is \code{\link[base]{max}}.}

+function is \code{\link[base:Extremes]{max}}.}

 \item{missing.method}{A function, or a string indicating the name of the function to be used in weighting edges when one of the vertices

 lack expression data. The function is passed all edge weights on the graph. Default is \code{\link[stats]{median}}.}

@@ -46,7 +46,7 @@ All annotation attributes are exracted from \code{XRefs} associated with the ver

 MIRIAM guidelines (\code{miraim.db}, where db is the database name).

 }

 \examples{

-if(require(rBiopaxParser)){

+if(requireNamespace("rBiopaxParser")){

     data(ex_biopax)

     # Process biopax as a metabolic network

     g <- biopax2igraph(ex_biopax)

@@ -45,7 +45,7 @@ or remove certain annotations.

 }

 \details{

 NetPathMiner stores all its vertex annotation attributes in a list, and stores them collectively as

-a single \code{attr}. This is not to interfer with \code{\link[igraph]{attributes}} from \code{igraph} package.

+a single \code{attr}. This is not to interfer with \code{\link[igraph]{graph_attr_names}} from \code{igraph} package.

 All functions here target NetPathMiner annotations only.

 }

 \examples{

@@ -29,7 +29,7 @@ common attributes (in the same pathway or compartment).

  # Integration with graphite package

  \dontrun{

- if(require(graphite) & require(clipper) & require(ALL)){

+ if(requireNamespace("graphite") & requireNamespace("clipper") & requireNamespace("ALL")){

 	genesetnets <- getGeneSetNetworks(ex_kgml_sig,

 						use.attr="pathway", format="pathway-class")

 	path <- convertIdentifiers(genesetnets$`Chemokine signaling pathway`,

@@ -32,7 +32,7 @@ can be specified through \code{gene.attr} argument.

 	# Write the genesets in a GMT file, and read it using GSEABase package.

  getGeneSets(ex_kgml_sig, use.attr="pathway", gene.attr="miriam.ncbigene", gmt.file="kgml.gmt")

  \dontrun{

-	if(require(GSEABase))

+	if(requireNamespace("GSEABase"))

 		toGmt("kgml.gmt")

 	}

@@ -16,7 +16,7 @@ layoutVertexByAttr(graph, attr.name, cluster.strength = 1,

 The larger it is, the closer the vertices will be.}

 \item{layout}{A layout function, ideally a force-directed layout fuction, such as

-\code{\link[igraph]{layout.fruchterman.reingold}} and \code{\link[igraph]{layout.kamada.kawai}}.}

+\code{\link[igraph]{layout_with_fr}} and \code{\link[igraph]{layout_with_kk}}.}

 }

 \value{

 A two-column matrix indicating the x and y postions of vertices.