fix issue #9 reported by @hpages

Accio · Dec 12, 2022 · 11a5723 · 11a5723
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,8 +2,8 @@ Package: KEGGgraph
 Type: Package
 Title: KEGGgraph: A graph approach to KEGG PATHWAY in R and
         Bioconductor
-Version: 1.51.2
-Date: 2021-02-01
+Version: 1.51.3
+Date: 2022-12-12
 Author: Jitao David Zhang, with inputs from Paul Shannon
 Maintainer: Jitao David Zhang <jitao_david.zhang@roche.com>
 Description: KEGGGraph is an interface between KEGG pathway and graph

diff --git a/R/annotation.R b/R/annotation.R
@@ -3,7 +3,7 @@
 ##------------------------------##
 translateKEGGID2GeneID <- function(x, organism="hsa") {
   if(organism!="hsa") {
-    stop("This function so far supports human gene only.\n To translate KEGGIDs of other species please use online service at http://www.genome.jp/kegg/genes.html")
+    stop("This function so far supports human gene only.\n To translate KEGGIDs of other species please use online service at https://www.genome.jp/kegg/genes.html")
   }
   gid <- gsub("^[a-z][a-z][a-z]:","", x)
   return(gid)

diff --git a/R/kegg2graph-functions.R b/R/kegg2graph-functions.R
@@ -315,7 +315,7 @@ setReplaceMethod("edges", "KEGGPathway", function(object, value) {
 setMethod("getKEGGgeneLink", "character", function(object) {
   if(length(object) == 1)
     suffix <- gsub(":","+",object)
-  url <- paste("http://www.genome.jp/dbget-bin/www_bget?",suffix,sep="")
+  url <- paste("https://www.genome.jp/dbget-bin/www_bget?",suffix,sep="")
   return(url)
        })
 

diff --git a/R/kgmlfile.R b/R/kgmlfile.R
@@ -4,7 +4,7 @@ kgmlNonmetabolicName2MetabolicName <- function(destfile) {
 
 getKGMLurl <- function(pathwayid, organism="hsa") {
   ## baseurl <- "ftp://ftp.genome.jp/pub/kegg/xml/kgml/non-metabolic/organisms"
-  baseurl <- "http://rest.kegg.jp/get/%s%s/kgml"
+  baseurl <- "https://rest.kegg.jp/get/%s%s/kgml"
 
   pathwayid <- gsub("path","",pathwayid)
   pathwayid <- gsub(":","",pathwayid)

diff --git a/man/KEGGEdge-class.Rd b/man/KEGGEdge-class.Rd
@@ -30,7 +30,7 @@ edge objects in a KEGG graph}
     \item{show}{\code{signature(object = "KEGGEdge")}: Show method }
 	 }
 }
-\references{ KGML Manual \url{http://www.genome.jp/kegg/docs/xml/}}
+\references{ KGML Manual \url{https://www.genome.jp/kegg/docs/xml/}}
 \author{ Jitao David Zhang \url{mailto:jitao_david.zhang@roche.com} }
 \seealso{
   \code{\link{KEGGNode-class}}

diff --git a/man/KEGGGraphics-class.Rd b/man/KEGGGraphics-class.Rd
@@ -28,7 +28,7 @@
     color}
   }
 }
-\references{ KGML Manual \url{http://www.genome.jp/kegg/docs/xml/}}
+\references{ KGML Manual \url{https://www.genome.jp/kegg/docs/xml/}}
 \author{ Jitao David Zhang \url{mailto:jitao_david.zhang@roche.com} }
 \seealso{
   \code{\link{parseGraphics}}

diff --git a/man/KEGGNode-class.Rd b/man/KEGGNode-class.Rd
@@ -49,7 +49,7 @@ and is not intended to be directly created by users.
     \item{show}{\code{signature(object = "KEGGNode")}: show method }
   }
 }
-\references{ KGML Document manual \url{http://www.genome.jp/kegg/docs/xml/} }
+\references{ KGML Document manual \url{https://www.genome.jp/kegg/docs/xml/} }
 \author{ Jitao David Zhang \url{mailto:jitao_david.zhang@roche.com} }
 
 \seealso{\code{\link{KEGGEdge-class}}, \code{\link{parseEntry}}}

diff --git a/man/KEGGPathway-class.Rd b/man/KEGGPathway-class.Rd
@@ -48,7 +48,7 @@ Objects can be created by calls of the form \code{new("KEGGPathway",
     \item{show}{\code{signature(object = "KEGGPathway")}: display method }
 	 }
 }
-\references{ KGML Document manual \url{http://www.genome.jp/kegg/docs/xml/} }
+\references{ KGML Document manual \url{https://www.genome.jp/kegg/docs/xml/} }
 \author{ Jitao David Zhang \url{mailto:jitao_david.zhang@roche.com} }
 
 \seealso{\code{\link{parseKGML}},

diff --git a/man/KEGGPathwayInfo-class.Rd b/man/KEGGPathwayInfo-class.Rd
@@ -26,7 +26,7 @@ Objects can be created by calls of the function \code{\link{parsePathwayInfo}}.
     \item{show}{\code{signature(object = "KEGGPathwayInfo")}: show method}
     }
 }
-\references{ KGML Document Manual \url{http://www.genome.jp/kegg/docs/xml/}}
+\references{ KGML Document Manual \url{https://www.genome.jp/kegg/docs/xml/}}
 \author{ Jitao David Zhang \url{mailto:jitao_david.zhang@roche.com} }
 \examples{
 sfile <- system.file("extdata/hsa04010.xml",package="KEGGgraph")

diff --git a/man/KEGGReaction-class.Rd b/man/KEGGReaction-class.Rd
@@ -42,7 +42,7 @@ Objects can be created by calls of the function \code{\link{parseReaction}}.
       name of product}
   }
 }
-\references{ KGML Document Manual \url{http://www.genome.jp/kegg/docs/xml/}}
+\references{ KGML Document Manual \url{https://www.genome.jp/kegg/docs/xml/}}
 \author{ Jitao David Zhang \url{mailto:jitao_david.zhang@roche.com} }
 \examples{
 ## We show how to extract reactions from a 'KEGGPathway' object

diff --git a/man/KEGGpathway2reactionGraph.Rd b/man/KEGGpathway2reactionGraph.Rd
@@ -40,7 +40,7 @@ KEGGpathway2reactionGraph(pathway)
   If the pathway does not contain any chemical reactions, a warning
   message will be printed and \code{NULL} is returned.
 }
-\references{ KGML Document manual \url{http://www.genome.jp/kegg/docs/xml/} }
+\references{ KGML Document manual \url{https://www.genome.jp/kegg/docs/xml/} }
 \author{ Jitao David Zhang \url{mailto:jitao_david.zhang@roche.com} }
 \seealso{\code{\link{KEGGPathway-class}}}
 \examples{

diff --git a/man/getDisplayName-methods.Rd b/man/getDisplayName-methods.Rd
@@ -18,7 +18,7 @@
     \item{object = "KEGGNode"}{ An object of \code{\link{KEGGNode-class}} }
     \item{object = "graph"}{ A KEGG graph object}
 }}
-\references{ KGML Document Manual \url{http://www.genome.jp/kegg/docs/xml/}}
+\references{ KGML Document Manual \url{https://www.genome.jp/kegg/docs/xml/}}
 \author{ Jitao David Zhang \url{mailto:jitao_david.zhang@roche.com} }
 \examples{
 sfile <- system.file("extdata/hsa04010.xml",package="KEGGgraph")

diff --git a/man/getEntryID-methods.Rd b/man/getEntryID-methods.Rd
@@ -23,7 +23,7 @@
     \item{obj = "list"}{ A wrapper for list of \code{\link{KEGGNode-class}} or
       \code{\link{KEGGEdge-class}} objects}
 }}
-\references{ KGML Document Manual \url{http://www.genome.jp/kegg/docs/xml/}}
+\references{ KGML Document Manual \url{https://www.genome.jp/kegg/docs/xml/}}
 \author{ Jitao David Zhang \url{mailto:jitao_david.zhang@roche.com} }
 \examples{
 sfile <- system.file("extdata/hsa04010.xml",package="KEGGgraph")

diff --git a/man/getKGMLurl.Rd b/man/getKGMLurl.Rd
@@ -55,15 +55,15 @@ getCategoryIndepKGMLurl(pathwayid, organism="hsa", method="wget", ...)
 }
 \author{ Jitao David Zhang \url{mailto:jitao_david.zhang@roche.com} }
 \references{
-  Plea from KEGG (available as of Aug 2011) \url{http://www.genome.jp/kegg/docs/plea.html}
+  Plea from KEGG (available as of Aug 2011) \url{https://www.genome.jp/kegg/docs/plea.html}
 }
 \note{ 
   So far the function does not check the correctness of the
   'organism' prefix, it is the responsibility of the user to garantee
   the right spelling.
 
   For Windows users, it is necessary to download and install \code{wget} program
-  (\url{http://gnuwin32.sourceforge.net/packages/wget.htm}) to use the
+  (\url{https://gnuwin32.sourceforge.net/packages/wget.htm}) to use the
   \code{wget} method to download files. Sometimes it may be necessary to
   modify searching path to add GnuWin32 folder (where \code{wget}
   execution file is located) and re-install R to make
@@ -90,11 +90,12 @@ getKGMLurl("path:hsa00020")
 getKGMLurl("00020",organism="hsa")
 getKGMLurl(c("00460", "hsa:00461", "path:hsa00453", "path:00453"))
 
-## NOT RUN
-\dontrun{
+hasConnection <- RCurl::url.exists(getKGMLurl("cel00010"))
+if(hasConnection) {
   tmp <- tempfile()
   retrieveKGML(pathwayid='00010', organism='cel', destfile=tmp, method="wget")
+} else {
+  warnings("No connection to KEGG webservice")
 }
-## END
 }
 \keyword{ IO }
diff --git a/man/getName-methods.Rd b/man/getName-methods.Rd
@@ -23,7 +23,7 @@
 
 }}
 
-\references{ KGML Document Manual \url{http://www.genome.jp/kegg/docs/xml/}}
+\references{ KGML Document Manual \url{https://www.genome.jp/kegg/docs/xml/}}
 \author{ Jitao David Zhang \url{mailto:jitao_david.zhang@roche.com} }
 \examples{
 sfile <- system.file("extdata/hsa04010.xml",package="KEGGgraph")

diff --git a/man/getReactions-methods.Rd b/man/getReactions-methods.Rd
@@ -22,7 +22,7 @@
 \describe{
 \item{object = "KEGGPathway"}{ An object of \code{\link{KEGGPathway-class}}}
 }}
-\references{ KGML Document manual \url{http://www.genome.jp/kegg/docs/xml/} }
+\references{ KGML Document manual \url{https://www.genome.jp/kegg/docs/xml/} }
 \author{ Jitao David Zhang \url{mailto:jitao_david.zhang@roche.com} }
 \seealso{\code{\link{KEGGPathway-class}}}
 \examples{

diff --git a/man/getSubtype-methods.Rd b/man/getSubtype-methods.Rd
@@ -13,7 +13,7 @@
   See \code{\link{KEGGEdge-class}} for examples. The method for graphs
   is a wrapper to extract all subtype information from one graph.
 }
-\references{ KGML Document manual \url{http://www.genome.jp/kegg/docs/xml/} }
+\references{ KGML Document manual \url{https://www.genome.jp/kegg/docs/xml/} }
 \author{ Jitao David Zhang \url{mailto:jitao_david.zhang@roche.com} }
 \section{Methods}{
 \describe{

diff --git a/man/getTitle-methods.Rd b/man/getTitle-methods.Rd
@@ -7,7 +7,7 @@
   The methods get title attribute for given KGML element, for example
   for objects of \code{\link{KEGGPathway-class}} or \code{\link{KEGGPathwayInfo-class}}
 }
-\references{ KGML Document manual \url{http://www.genome.jp/kegg/docs/xml/} }
+\references{ KGML Document manual \url{https://www.genome.jp/kegg/docs/xml/} }
 \author{ Jitao David Zhang \url{mailto:jitao_david.zhang@roche.com} }
 \section{Methods}{
 \describe{

diff --git a/man/getType-methods.Rd b/man/getType-methods.Rd
@@ -13,7 +13,7 @@
   The meanings and descriptions of the types can be found at KGML manual listed in
   the reference.
 }
-\references{ KGML Manual \url{http://www.genome.jp/kegg/docs/xml/}}
+\references{ KGML Manual \url{https://www.genome.jp/kegg/docs/xml/}}
 \author{ Jitao David Zhang \url{mailto:jitao_david.zhang@roche.com} }
 \section{Methods}{
 \describe{

diff --git a/man/parseEntry.Rd b/man/parseEntry.Rd
@@ -15,13 +15,13 @@ parseEntry(entry)
   \item{entry}{ XML node of KGML file }
 }
 \details{
-  See \url{http://www.genome.jp/kegg/docs/xml/} for more details about
+  See \url{https://www.genome.jp/kegg/docs/xml/} for more details about
   'entry' as well as other elements in KGML files.
 }
 \value{
   An object of \code{link{KEGGNode}} or (in case of a group node) \code{link{KEGGGroup}}
 }
-\references{\url{http://www.genome.jp/kegg/docs/xml/}}
+\references{\url{https://www.genome.jp/kegg/docs/xml/}}
 \author{ Jitao David Zhang <jitao_david.zhang@roche.com> }
 \seealso{ \code{\link{parseGraphics}}, \code{\link{parseKGML}},
   \code{\link{KEGGNode-class}}, \code{\link{KEGGGroup-class}} }

diff --git a/man/parseGraphics.Rd b/man/parseGraphics.Rd
@@ -20,6 +20,6 @@ parseGraphics(graphics)
 \value{
   An object of \code{\link{KEGGGraphics-class}}.
 }
-\references{ KGML Document manual \url{http://www.genome.jp/kegg/docs/xml/} }
+\references{ KGML Document manual \url{https://www.genome.jp/kegg/docs/xml/} }
 \author{ Jitao David Zhang \url{mailto:jitao_david.zhang@roche.com} }
 \seealso{\code{\link{KEGGGraphics-class}}}
diff --git a/man/parseKGML.Rd b/man/parseKGML.Rd
@@ -18,7 +18,7 @@ parseKGML(file)
 \value{
   An object of \code{\link{KEGGPathway-class}}.
 }
-\references{ KGML Manual \url{http://www.genome.jp/kegg/docs/xml/} }
+\references{ KGML Manual \url{https://www.genome.jp/kegg/docs/xml/} }
 \author{ Jitao David Zhang \url{mailto:jitao_david.zhang@roche.com} }
 \seealso{
   \code{\link{parseEntry}}, \code{\link{parseRelation}},

diff --git a/man/parseKGMLexpandMaps.Rd b/man/parseKGMLexpandMaps.Rd
@@ -25,7 +25,7 @@ parseKGMLexpandMaps(file, downloadmethod = "wget", genesOnly = TRUE, localdir,..
 \details{
   In KEGG pathways there're usually pathways contained('cross-linked')
   in other pathways, for example see
-  \url{http://www.genome.jp/kegg/pathway/hsa/hsa04115.html}, where p53
+  \url{https://www.genome.jp/kegg/pathway/hsa/hsa04115.html}, where p53
   signalling pathway contains other two pathways 'apoptosis' and 'cell
   cycle'. This function parses these pathways (refered as 'maps' in KGML
   manual), download their KGML files from KEGG FTP website, parse them
@@ -42,6 +42,6 @@ parseKGMLexpandMaps(file, downloadmethod = "wget", genesOnly = TRUE, localdir,..
 \value{
   A directed graph object
 }
-\references{KGML Document manual \url{http://www.genome.jp/kegg/docs/xml/}}
+\references{KGML Document manual \url{https://www.genome.jp/kegg/docs/xml/}}
 \author{ Jitao David Zhang \url{jitao_david.zhang@roche.com}}
 \seealso{ for most users it is enough to use \code{\link{parseKGML2Graph}} }
diff --git a/man/parsePathwayInfo.Rd b/man/parsePathwayInfo.Rd
@@ -17,6 +17,6 @@ parsePathwayInfo(root)
 \value{
   An object of \code{\link{KEGGPathwayInfo-class}}
 }
-\references{ KGML Document Manual \url{http://www.genome.jp/kegg/docs/xml/}}
+\references{ KGML Document Manual \url{https://www.genome.jp/kegg/docs/xml/}}
 \author{Jitao David Zhang \url{mailto:jitao_david.zhang@roche.com}}
 \keyword{IO}
diff --git a/man/parseReaction.Rd b/man/parseReaction.Rd
@@ -19,6 +19,6 @@ parseReaction(reaction)
 \value{
   An object of \code{\link{KEGGReaction-class}}
 }
-\references{ KGML Document Manual \url{http://www.genome.jp/kegg/docs/xml/}}
+\references{ KGML Document Manual \url{https://www.genome.jp/kegg/docs/xml/}}
 \author{ Jitao David Zhang \url{mail:jitao_david.zhang@roche.com} }
 \keyword{IO}
diff --git a/man/parseRelation.Rd b/man/parseRelation.Rd
@@ -15,13 +15,13 @@ parseRelation(relation)
   \item{relation}{ XML node of KGML file }
 }
 \details{
-  See \url{http://www.genome.jp/kegg/docs/xml/} for more details about
+  See \url{https://www.genome.jp/kegg/docs/xml/} for more details about
   'relation' as well as other elements in KGML files.
 }
 \value{
   An object of \code{link{KEGGEdge}}.
 }
-\references{\url{http://www.genome.jp/kegg/docs/xml/}}
+\references{\url{https://www.genome.jp/kegg/docs/xml/}}
 \author{ Jitao David Zhang <jitao_david.zhang@roche.com> }
 \seealso{\code{\link{KEGGEdge-class}}, \code{\link{parseEntry}}}
 \keyword{ IO }
diff --git a/man/splitKEGGgroup.Rd b/man/splitKEGGgroup.Rd
@@ -22,7 +22,7 @@ splitKEGGgroup(pathway)
 \value{
   An object of \code{\link{KEGGPathway-class}} 
 }
-\references{KGML Manual \url{http://www.genome.jp/kegg/docs/xml/}}
+\references{KGML Manual \url{https://www.genome.jp/kegg/docs/xml/}}
 \author{ Jitao David Zhang \url{mailto:jitao_david.zhang@roche.com} }
 \seealso{ \code{\link{KEGGpathway2Graph}} }
 \examples{

diff --git a/man/translateKEGGID2GeneID.Rd b/man/translateKEGGID2GeneID.Rd
@@ -16,7 +16,7 @@ translateGeneID2KEGGID(x, organism="hsa")
 \arguments{
   \item{x}{ KEGGID, e.g. 'hsa:1432', or Entrez Gene ID, e.g. '1432' }
   \item{organism}{ Three alphabet code for organisms. The mapping
-    between the orgniams and codes can be found at \url{http://www.genome.jp/kegg/kegg3.html}}
+    between the orgniams and codes can be found at \url{https://www.genome.jp/kegg/kegg3.html}}
 }
 \details{
   The KEGGID are unique identifiers used by KEGG PATHWAY to identify

diff --git a/tests/kegg2graph.R b/tests/kegg2graph.R
@@ -3,7 +3,7 @@ library(KEGGgraph)
 library(RBGL)
 
 ## retrieve
-URLbase <- "http://rest.kegg.jp/get/%s/kgml"
+URLbase <- "https://rest.kegg.jp/get/%s/kgml"
 ids <- c("00460", "hsa:00461", "path:hsa00453", "path:00453")
 expURLs <- sprintf(URLbase,
                    c("hsa00460", "hsa00461", "hsa00453", "hsa00453"))