initial

.Rbuildignore

@@ -0,0 +1,14 @@
+^LICENSE\.md$
+^.*\.Rproj$
+^\.Rproj\.user$
+^\.travis\.yml$
+^README\.*Rmd$
+^README\.*html$
+^NOTES\.*Rmd$
+^NOTES\.*html$
+^\.codecov\.yml$
+^README_files$
+^docs$
+^CONDUCT\.md$
+^\.bash_profile$
+^java$

.gitignore

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+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

DESCRIPTION

@@ -0,0 +1,24 @@
+Package: graphstreamjars
+Type: Package
+Title: Java Archive Wrapper Supporting the 'graphstream' Package
+Version: 1.3.0
+Date: 2019-12-30
+Authors@R: c(
+    person("Bob", "Rudis", role = c("aut", "cre"), email = "bob@rud.is")
+  )
+Maintainer: Bob Rudis <bob@rud.is>
+SystemRequirements: Java
+Description: Contains all supporting JARs for working with the GraphStream Java APIs.
+    (<http://graphstream-project.org/>) Version number matches version number of included
+    'graphstreamjars' libraries.
+URL: https://gitlab.com/hrbrmstr/graphstreamjars
+BugReports: https://gitlab.com/hrbrmstr/graphstreamjars/issues
+License: LGPL
+Encoding: UTF-8
+Suggests:
+    testthat,
+    covr
+Depends:
+    R (>= 3.2.0),
+    rJava
+RoxygenNote: 7.0.2

NAMESPACE

@@ -0,0 +1,3 @@
+# Generated by roxygen2: do not edit by hand
+
+import(rJava)

NEWS.md

@@ -0,0 +1,2 @@
+1.3.0
+* Initial release

R/graphstreamjars-package.R

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+#' Java Archive Wrapper Supporting the 'graphstream' Package
+#'
+#' Contains all supporting JARs for working with the GraphStream Java APIs.
+#' (<http://graphstream-project.org/>)Version number matches version number of included
+#' 'graphstreamjars' libraries.
+#'
+#' @md
+#' @name graphstreamjars
+#' @docType package
+#' @author Bob Rudis (bob@@rud.is)
+#' @import rJava
+NULL

R/logging.r

@@ -0,0 +1,21 @@
+#' @title rJava logging
+#' @description Toggle verbose rJava logging
+#' @details This function turns off the somewhat verbose rJava logging, most of which is
+#'          uninformative. It is called automatically when tabulizer is attached via
+#'          \code{library()}, \code{require}, etc. To keep logging on, load the package
+#'          namespace using \code{requireNamespace("tabulizer")} and reference functions
+#'          in using fully qualified references (e.g., \code{tabulizer::extract_tables()}.
+#' @note This resets a global Java setting and may affect logging of other rJava operations,
+#'       requiring a restart of R.
+#' @return `NULL`, invisibly.
+#' @author Thomas J. Leeper <thosjleeper@@gmail.com>
+#' @noRd
+#' @md
+#' @examples
+#' \dontrun{
+#' stop_logging()
+#' }
+stop_logging <- function() {
+  rJava::J("java.util.logging.LogManager")$getLogManager()$reset()
+  invisible(NULL)
+}

R/zzz.r

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+.onLoad <- function(libname, pkgname) {
+  rJava::.jpackage(pkgname, jars = "*", lib.loc = libname)
+  rJava::.jaddClassPath(dir(file.path(getwd(), "inst/java"), full.names = TRUE))
+  stop_logging()
+}

README.Rmd

@@ -0,0 +1,76 @@
+---
+output: rmarkdown::github_document
+editor_options: 
+  chunk_output_type: console
+---
+```{r pkg-knitr-opts, include=FALSE}
+hrbrpkghelpr::global_opts()
+```
+
+```{r badges, results='asis', echo=FALSE, cache=FALSE}
+hrbrpkghelpr::stinking_badges(repo_status = "WIP")
+```
+
+```{r description, results='asis', echo=FALSE, cache=FALSE}
+hrbrpkghelpr::yank_title_and_description()
+```
+
+## What's Inside The Tin
+
+The following functions are implemented:
+
+```{r ingredients, results='asis', echo=FALSE, cache=FALSE}
+hrbrpkghelpr::describe_ingredients()
+```
+
+## Installation
+
+```{r install-ex, results='asis', echo=FALSE, cache=FALSE}
+hrbrpkghelpr::install_block()
+```
+
+## Usage
+
+```{r use-1}
+library(rJava)
+library(graphstreamjars)
+
+packageVersion("graphstreamjars")
+```
+
+```{r use-2}
+library(graphstreamjars)
+
+SingleGraph <- J("org.graphstream.graph.implementations.SingleGraph")
+
+(graph <- .jnew(SingleGraph, "Tutorial 1"))
+
+graph$addNode("A")
+graph$addNode("B")
+graph$addNode("C")
+graph$addEdge("AB", "A", "B")
+graph$addEdge("BC", "B", "C")
+graph$addEdge("CA", "C", "A")
+
+graph$setStrict(FALSE)
+graph$setAutoCreate(TRUE)
+graph$addEdge("AB", "A", "B")
+graph$addEdge("BC", "B", "C")
+graph$addEdge("CA", "C", "A")
+
+(A <- graph$getNode("A"))
+
+(AB <- graph$getEdge("AB"))
+
+ni <- graph$getNodeIterator()
+
+while(ni$hasNext()) {
+  print(.jrcall(ni, "next"))
+}
+```
+
+## `graphstreamjars` Metrics
+
+```{r cloc, echo=FALSE}
+cloc::cloc_pkg_md()
+```

README.md

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+
+# graphstreamjars
+
+Java Archive Wrapper Supporting the ‘awsathena’ Package
+
+## Description
+
+Contains all supporting JARs for working with the GraphStream Java APIs.
+(<http://graphstream-project.org/>). Version number matches version
+number of included ‘graphstreamjars’ libraries.
+
+## Installation
+
+``` r
+devtools::install_git("git@git.sr.ht:~hrbrmstr/graphstreamjars")
+# OR
+devtools::install_gitlab("hrbrmstr/graphstreamjars")
+# OR
+devtools::install_github("hrbrmstr/graphstreamjars")
+```
+
+## Usage
+
+``` r
+library(rJava)
+```
+
+    ## 
+    ## Attaching package: 'rJava'
+
+    ## The following object is masked from 'package:bit':
+    ## 
+    ##     clone
+
+``` r
+library(graphstreamjars)
+
+packageVersion("graphstreamjars")
+```
+
+    ## [1] '1.3.0'
+
+``` r
+library(graphstreamjars)
+
+SingleGraph <- J("org.graphstream.graph.implementations.SingleGraph")
+
+(graph <- .jnew(SingleGraph, "Tutorial 1"))
+```
+
+    ## [1] "Java-Object{Tutorial 1}"
+
+``` r
+graph$addNode("A")
+```
+
+    ## [1] "Java-Object{A}"
+
+``` r
+graph$addNode("B")
+```
+
+    ## [1] "Java-Object{B}"
+
+``` r
+graph$addNode("C")
+```
+
+    ## [1] "Java-Object{C}"
+
+``` r
+graph$addEdge("AB", "A", "B")
+```
+
+    ## [1] "Java-Object{AB[A--B]}"
+
+``` r
+graph$addEdge("BC", "B", "C")
+```
+
+    ## [1] "Java-Object{BC[B--C]}"
+
+``` r
+graph$addEdge("CA", "C", "A")
+```
+
+    ## [1] "Java-Object{CA[C--A]}"
+
+``` r
+graph$setStrict(FALSE)
+graph$setAutoCreate(TRUE)
+graph$addEdge("AB", "A", "B")
+```
+
+    ## [1] "Java-Object{AB[A--B]}"
+
+``` r
+graph$addEdge("BC", "B", "C")
+```
+
+    ## [1] "Java-Object{BC[B--C]}"
+
+``` r
+graph$addEdge("CA", "C", "A")
+```
+
+    ## [1] "Java-Object{CA[C--A]}"
+
+``` r
+(A <- graph$getNode("A"))
+```
+
+    ## [1] "Java-Object{A}"
+
+``` r
+(AB <- graph$getEdge("AB"))
+```
+
+    ## [1] "Java-Object{AB[A--B]}"
+
+``` r
+ni <- graph$getNodeIterator()
+
+while(ni$hasNext()) {
+  print(.jrcall(ni, "next"))
+}
+```
+
+    ## [1] "Java-Object{A}"
+    ## [1] "Java-Object{B}"
+    ## [1] "Java-Object{C}"
+
+## `graphstreamjars` Metrics
+
+| Lang  | \# Files |  (%) | LoC |  (%) | Blank lines |  (%) | \# Lines |  (%) |
+| :---- | -------: | ---: | --: | ---: | ----------: | ---: | -------: | ---: |
+| XML   |        1 | 0.08 |  66 | 0.32 |           0 | 0.00 |        0 | 0.00 |
+| Maven |        2 | 0.17 |  58 | 0.28 |           9 | 0.23 |        6 | 0.08 |
+| Java  |        2 | 0.17 |  28 | 0.14 |           5 | 0.13 |       18 | 0.24 |
+| Rmd   |        1 | 0.08 |  27 | 0.13 |          20 | 0.51 |       24 | 0.32 |
+| R     |        5 | 0.42 |  15 | 0.07 |           1 | 0.03 |       28 | 0.37 |
+| make  |        1 | 0.08 |  13 | 0.06 |           4 | 0.10 |        0 | 0.00 |

graphstreamjars.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageBuildArgs: --resave-data
+PackageRoxygenize: rd,collate,namespace

java/graphstreamjars/Makefile

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+.PHONY: clean pkg deps run
+
+pkg:
+	mvn --quiet package
+	cp target/graphstreamjars-1.0-SNAPSHOT.jar ../../inst/java
+	cp deps/*.jar ../../inst/java
+
+clean:
+	mvn clean
+
+deps:
+	mvn dependency:copy-dependencies -DoutputDirectory=deps
+
+new:
+	mv pom.xml /tmp
+	mvn archetype:generate -DgroupId=is.rud.graphstreamjars -DartifactId=graphstreamjars -DarchetypeArtifactId=maven-archetype-quickstart -DinteractiveMode=false
+	mv /tmp/pom.xml .

java/graphstreamjars/pom.xml

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+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+  xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>is.rud.graphstreamjars</groupId>
+  <artifactId>graphstreamjars</artifactId>
+  <packaging>jar</packaging>
+  <version>1.0-SNAPSHOT</version>
+  <name>graphstreamjars</name>
+  <url>http://maven.apache.org</url>
+    <properties>
+    <maven.compiler.source>1.6</maven.compiler.source>
+    <maven.compiler.target>1.6</maven.compiler.target>
+  </properties>
+  <dependencies>
+
+
+    <!-- https://mvnrepository.com/artifact/org.graphstream/gs-core -->
+    <dependency>
+        <groupId>org.graphstream</groupId>
+        <artifactId>gs-core</artifactId>
+        <version>1.3</version>
+    </dependency>
+
+    <!-- https://mvnrepository.com/artifact/org.graphstream/gs-ui -->
+    <dependency>
+        <groupId>org.graphstream</groupId>
+        <artifactId>gs-ui</artifactId>
+        <version>1.3</version>
+    </dependency>
+
+    <!-- https://mvnrepository.com/artifact/org.graphstream/gs-algo -->
+    <dependency>
+        <groupId>org.graphstream</groupId>
+        <artifactId>gs-algo</artifactId>
+        <version>1.3</version>
+    </dependency>
+
+  </dependencies>
+</project>

java/graphstreamjars/src/main/java/is/rud/graphstreamjars/App.java

@@ -0,0 +1,13 @@
+package is.rud.graphstreamjars;
+
+/**
+ * Hello world!
+ *
+ */
+public class App 
+{
+    public static void main( String[] args )
+    {
+        System.out.println( "Hello World!" );
+    }
+}

java/graphstreamjars/src/test/java/is/rud/graphstreamjars/AppTest.java

@@ -0,0 +1,38 @@
+package is.rud.graphstreamjars;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+/**
+ * Unit test for simple App.
+ */
+public class AppTest 
+    extends TestCase
+{
+    /**
+     * Create the test case
+     *
+     * @param testName name of the test case
+     */
+    public AppTest( String testName )
+    {
+        super( testName );
+    }
+
+    /**
+     * @return the suite of tests being tested
+     */
+    public static Test suite()
+    {
+        return new TestSuite( AppTest.class );
+    }
+
+    /**
+     * Rigourous Test :-)
+     */
+    public void testApp()
+    {
+        assertTrue( true );
+    }
+}

java/graphstreamjars/target/maven-archiver/pom.properties

@@ -0,0 +1,5 @@
+#Generated by Maven
+#Mon Dec 30 08:00:21 EST 2019
+groupId=is.rud.graphstreamjars
+artifactId=graphstreamjars
+version=1.0-SNAPSHOT

java/graphstreamjars/target/maven-status/maven-compiler-plugin/compile/default-compile/createdFiles.lst

@@ -0,0 +1 @@
+is/rud/graphstreamjars/App.class

java/graphstreamjars/target/maven-status/maven-compiler-plugin/compile/default-compile/inputFiles.lst

@@ -0,0 +1 @@
+/Users/hrbrmstr/packages/graphstreamjars/java/graphstreamjars/src/main/java/is/rud/graphstreamjars/App.java

java/graphstreamjars/target/maven-status/maven-compiler-plugin/testCompile/default-testCompile/createdFiles.lst

@@ -0,0 +1 @@
+is/rud/graphstreamjars/AppTest.class

java/graphstreamjars/target/maven-status/maven-compiler-plugin/testCompile/default-testCompile/inputFiles.lst

@@ -0,0 +1 @@
+/Users/hrbrmstr/packages/graphstreamjars/java/graphstreamjars/src/test/java/is/rud/graphstreamjars/AppTest.java

java/graphstreamjars/target/surefire-reports/TEST-is.rud.graphstreamjars.AppTest.xml

@@ -0,0 +1,66 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+<testsuite tests="1" failures="0" name="is.rud.graphstreamjars.AppTest" time="0.002" errors="0" skipped="0">
+  <properties>
+    <property name="java.runtime.name" value="Java(TM) SE Runtime Environment"/>
+    <property name="java.vm.version" value="11.0.3+12-LTS"/>
+    <property name="sun.boot.library.path" value="/Library/Java/JavaVirtualMachines/jdk-11.0.3.jdk/Contents/Home/lib"/>
+    <property name="gopherProxySet" value="false"/>
+    <property name="maven.multiModuleProjectDirectory" value="/Users/hrbrmstr/packages/graphstreamjars/java/graphstreamjars"/>
+    <property name="java.vm.vendor" value="Oracle Corporation"/>
+    <property name="java.vendor.url" value="http://java.oracle.com/"/>
+    <property name="guice.disable.misplaced.annotation.check" value="true"/>
+    <property name="path.separator" value=":"/>
+    <property name="java.vm.name" value="Java HotSpot(TM) 64-Bit Server VM"/>
+    <property name="sun.os.patch.level" value="unknown"/>
+    <property name="user.country" value="US"/>
+    <property name="sun.java.launcher" value="SUN_STANDARD"/>
+    <property name="java.vm.specification.name" value="Java Virtual Machine Specification"/>
+    <property name="user.dir" value="/Users/hrbrmstr/packages/graphstreamjars/java/graphstreamjars"/>
+    <property name="java.vm.compressedOopsMode" value="Zero based"/>
+    <property name="java.runtime.version" value="11.0.3+12-LTS"/>
+    <property name="java.awt.graphicsenv" value="sun.awt.CGraphicsEnvironment"/>
+    <property name="os.arch" value="x86_64"/>
+    <property name="java.io.tmpdir" value="/var/folders/4j/w_crq_vn0x5d512w08g2j_640000gn/T/"/>
+    <property name="line.separator" value="
+"/>
+    <property name="java.vm.specification.vendor" value="Oracle Corporation"/>
+    <property name="os.name" value="Mac OS X"/>
+    <property name="classworlds.conf" value="/usr/local/Cellar/maven/3.6.3/libexec/bin/m2.conf"/>
+    <property name="sun.jnu.encoding" value="UTF-8"/>
+    <property name="java.library.path" value="/Users/hrbrmstr/Library/Java/Extensions:/Library/Java/Extensions:/Network/Library/Java/Extensions:/System/Library/Java/Extensions:/usr/lib/java:."/>
+    <property name="maven.conf" value="/usr/local/Cellar/maven/3.6.3/libexec/conf"/>
+    <property name="jdk.debug" value="release"/>
+    <property name="java.class.version" value="55.0"/>
+    <property name="java.specification.name" value="Java Platform API Specification"/>
+    <property name="sun.management.compiler" value="HotSpot 64-Bit Tiered Compilers"/>
+    <property name="os.version" value="10.15.3"/>
+    <property name="library.jansi.path" value="/usr/local/Cellar/maven/3.6.3/libexec/lib/jansi-native"/>
+    <property name="user.home" value="/Users/hrbrmstr"/>
+    <property name="user.timezone" value="America/New_York"/>
+    <property name="java.awt.printerjob" value="sun.lwawt.macosx.CPrinterJob"/>
+    <property name="file.encoding" value="UTF-8"/>
+    <property name="java.specification.version" value="11"/>
+    <property name="user.name" value="hrbrmstr"/>
+    <property name="java.class.path" value="/usr/local/Cellar/maven/3.6.3/libexec/boot/plexus-classworlds-2.6.0.jar"/>
+    <property name="org.slf4j.simpleLogger.defaultLogLevel" value="error"/>
+    <property name="java.vm.specification.version" value="11"/>
+    <property name="sun.arch.data.model" value="64"/>
+    <property name="sun.java.command" value="org.codehaus.plexus.classworlds.launcher.Launcher --quiet package"/>
+    <property name="java.home" value="/Library/Java/JavaVirtualMachines/jdk-11.0.3.jdk/Contents/Home"/>
+    <property name="user.language" value="en"/>
+    <property name="java.specification.vendor" value="Oracle Corporation"/>
+    <property name="awt.toolkit" value="sun.lwawt.macosx.LWCToolkit"/>
+    <property name="java.vm.info" value="mixed mode"/>
+    <property name="java.version" value="11.0.3"/>
+    <property name="java.vendor" value="Oracle Corporation"/>
+    <property name="maven.home" value="/usr/local/Cellar/maven/3.6.3/libexec"/>
+    <property name="file.separator" value="/"/>
+    <property name="java.version.date" value="2019-04-16"/>
+    <property name="java.vendor.url.bug" value="http://bugreport.java.com/bugreport/"/>
+    <property name="sun.io.unicode.encoding" value="UnicodeBig"/>
+    <property name="sun.cpu.endian" value="little"/>
+    <property name="java.vendor.version" value="18.9"/>
+    <property name="sun.cpu.isalist" value=""/>
+  </properties>
+  <testcase classname="is.rud.graphstreamjars.AppTest" name="testApp" time="0.002"/>
+</testsuite>

java/graphstreamjars/target/surefire-reports/is.rud.graphstreamjars.AppTest.txt

@@ -0,0 +1,4 @@
+-------------------------------------------------------------------------------
+Test set: is.rud.graphstreamjars.AppTest
+-------------------------------------------------------------------------------
+Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec

java/pom.xml

@@ -0,0 +1,34 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+  xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>is.rud.graphstreamjars</groupId>
+  <artifactId>graphstreamjars</artifactId>
+  <packaging>jar</packaging>
+  <version>1.0-SNAPSHOT</version>
+  <name>graphstreamjars</name>
+  <url>http://maven.apache.org</url>
+  <dependencies>
+
+    <!-- https://mvnrepository.com/artifact/org.graphstream/gs-core -->
+    <dependency>
+        <groupId>org.graphstream</groupId>
+        <artifactId>gs-core</artifactId>
+        <version>1.3</version>
+    </dependency>
+
+    <!-- https://mvnrepository.com/artifact/org.graphstream/gs-ui -->
+    <dependency>
+        <groupId>org.graphstream</groupId>
+        <artifactId>gs-ui</artifactId>
+        <version>1.3</version>
+    </dependency>
+
+    <!-- https://mvnrepository.com/artifact/org.graphstream/gs-algo -->
+    <dependency>
+        <groupId>org.graphstream</groupId>
+        <artifactId>gs-algo</artifactId>
+        <version>1.3</version>
+    </dependency>
+
+  </dependencies>
+</project>

man/graphstreamjars.Rd

@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/graphstreamjars-package.R
+\docType{package}
+\name{graphstreamjars}
+\alias{graphstreamjars}
+\title{Java Archive Wrapper Supporting the 'graphstream' Package}
+\description{
+Contains all supporting JARs for working with the GraphStream Java APIs.
+(\url{http://graphstream-project.org/})Version number matches version number of included
+'graphstreamjars' libraries.
+}
+\author{
+Bob Rudis (bob@rud.is)
+}

tests/test-all.R

@@ -0,0 +1,2 @@
+library(testthat)
+test_check("graphstreamjars")

tests/testthat/test-graphstreamjars.R

@@ -0,0 +1,4 @@
+context("basic functionality")
+test_that("we can do something", {
+
+})