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idekerlab / dot-app

Cytoscape application for exporting to .dot file format
GNU General Public License v3.0
7 stars 4 forks source link

Latest source code not building #8

Closed matthiaskoenig closed 7 years ago

matthiaskoenig commented 7 years ago

Trying to build via 

mvn clean install

after cloning the repo fails. Probably some mvn dependencies missing in pom.

mkoenig@core1:~/git/dot-app$ mvn clean install
[INFO] Scanning for projects...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building dot-app 0.9.3
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ dot-app ---
[INFO] Deleting /home/mkoenig/git/dot-app/target
[INFO] 
[INFO] --- maven-resources-plugin:3.0.1:resources (default-resources) @ dot-app ---
[WARNING] Using platform encoding (UTF-8 actually) to copy filtered resources, i.e. build is platform dependent!
[INFO] Copying 2 resources
[INFO] 
[INFO] --- maven-compiler-plugin:2.0.2:compile (default-compile) @ dot-app ---
[INFO] Compiling 16 source files to /home/mkoenig/git/dot-app/target/classes
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 1.729 s
[INFO] Finished at: 2016-10-31T12:51:03+01:00
[INFO] Final Memory: 18M/263M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:2.0.2:compile (default-compile) on project dot-app: Compilation failure: Compilation failure:
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/reader/NodeReader.java:[46,36] error: package com.alexmerz.graphviz.objects does not exist
[ERROR] 
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/reader/Reader.java:[26,36] error: package com.alexmerz.graphviz.objects does not exist
[ERROR] 
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/reader/Reader.java:[27,36] error: package com.alexmerz.graphviz.objects does not exist
[ERROR] 
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/reader/NodeReader.java:[109,141] error: cannot find symbol
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Node
[ERROR] location: class NodeReader
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:33: error: package com.alexmerz.graphviz does not exist
[ERROR] import com.alexmerz.graphviz.ParseException;
[ERROR] ^
[ERROR] 
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:[34,28] error: package com.alexmerz.graphviz does not exist
[ERROR] 
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:[35,28] error: package com.alexmerz.graphviz does not exist
[ERROR] 
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:[36,36] error: package com.alexmerz.graphviz.objects does not exist
[ERROR] 
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:[37,36] error: package com.alexmerz.graphviz.objects does not exist
[ERROR] 
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:[38,36] error: package com.alexmerz.graphviz.objects does not exist
[ERROR] 
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:[39,36] error: package com.alexmerz.graphviz.objects does not exist
[ERROR] 
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:[87,13] error: cannot find symbol
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Node
[ERROR] location: class DotReaderTask
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:90: error: cannot find symbol
[ERROR] private Map<Edge, CyEdge> edgeMap;
[ERROR] ^
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Edge
[ERROR] location: class DotReaderTask
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:92: error: cannot find symbol
[ERROR] private Map<Graph, CyNetwork> graphMap;
[ERROR] ^
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Graph
[ERROR] location: class DotReaderTask
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:139: error: cannot find symbol
[ERROR] private Map<String, String> getEdgeDefaultMap(Graph graph) {
[ERROR] ^
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Graph
[ERROR] location: class DotReaderTask
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:162: error: cannot find symbol
[ERROR] private Map<String, String> getGraphDefaultMap(Graph graph) {
[ERROR] ^
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Graph
[ERROR] location: class DotReaderTask
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:182: error: cannot find symbol
[ERROR] private String getGraphName(Graph graph) {
[ERROR] ^
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Graph
[ERROR] location: class DotReaderTask
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:202: error: cannot find symbol
[ERROR] private Map<String, String> getNodeDefaultMap(Graph graph) {
[ERROR] ^
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Graph
[ERROR] location: class DotReaderTask
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:231: error: cannot find symbol
[ERROR] private String getNodeName(Node node) {
[ERROR] ^
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Node
[ERROR] location: class DotReaderTask
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:251: error: cannot find symbol
[ERROR] private void importEdge(Edge edge, CyNetwork network) {
[ERROR] ^
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Edge
[ERROR] location: class DotReaderTask
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:298: error: cannot find symbol
[ERROR] private void importNode(Node node, CyNetwork network) {
[ERROR] ^
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Node
[ERROR] location: class DotReaderTask
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/reader/NetworkReader.java:18: error: package com.alexmerz.graphviz.objects does not exist
[ERROR] import com.alexmerz.graphviz.objects.Graph;
[ERROR] ^
[ERROR] 
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/reader/NetworkReader.java:[32,9] error: cannot find symbol
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Graph
[ERROR] location: class NetworkReader
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/reader/NetworkReader.java:45: error: cannot find symbol
[ERROR] public NetworkReader(CyNetworkView networkView, VisualStyle vizStyle, Map<String, String> defaultAttrs, Graph graph, RenderingEngineManager rendEngMgr) {
[ERROR] ^
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Graph
[ERROR] location: class NetworkReader
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/reader/EdgeReader.java:40: error: package com.alexmerz.graphviz.objects does not exist
[ERROR] import com.alexmerz.graphviz.objects.Edge;
[ERROR] ^
[ERROR] 
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/reader/EdgeReader.java:[98,42] error: cannot find symbol
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Edge
[ERROR] location: class EdgeReader
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/reader/Reader.java:309: error: cannot find symbol
[ERROR] if (element instanceof Node) {
[ERROR] ^
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Node
[ERROR] location: class Reader
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/reader/Reader.java:310: error: cannot find symbol
[ERROR] return ((Node) element).getAttributes();
[ERROR] ^
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Node
[ERROR] location: class Reader
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/reader/Reader.java:312: error: cannot find symbol
[ERROR] if (element instanceof Edge) {
[ERROR] ^
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Edge
[ERROR] location: class Reader
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/reader/Reader.java:313: error: cannot find symbol
[ERROR] return ((Edge) element).getAttributes();
[ERROR] ^
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Edge
[ERROR] location: class Reader
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:127: error: cannot find symbol
[ERROR] graphMap = new HashMap<Graph, CyNetwork>();
[ERROR] ^
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Graph
[ERROR] location: class DotReaderTask
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:128: error: cannot find symbol
[ERROR] nodeMap = new HashMap<Node, CyNode>();
[ERROR] ^
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Node
[ERROR] location: class DotReaderTask
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:129: error: cannot find symbol
[ERROR] edgeMap = new HashMap<Edge, CyEdge>();
[ERROR] ^
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Edge
[ERROR] location: class DotReaderTask
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:183: error: cannot find symbol
[ERROR] Id graphId = graph.getId();
[ERROR] ^
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Id
[ERROR] location: class DotReaderTask
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:232: error: cannot find symbol
[ERROR] Id nodeId = node.getId();
[ERROR] ^
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Id
[ERROR] location: class DotReaderTask
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:254: error: cannot find symbol
[ERROR] Node source = edge.getSource().getNode();
[ERROR] ^
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Node
[ERROR] location: class DotReaderTask
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:255: error: cannot find symbol
[ERROR] Node target = edge.getTarget().getNode();
[ERROR] ^
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Node
[ERROR] location: class DotReaderTask
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:319: error: cannot find symbol
[ERROR] Graph graph = null;
[ERROR] ^
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Graph
[ERROR] location: class DotReaderTask
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:322: error: cannot find symbol
[ERROR] for (Entry<Graph, CyNetwork> entry: graphMap.entrySet()){
[ERROR] ^
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Graph
[ERROR] location: class DotReaderTask
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:405: error: cannot find symbol
[ERROR] Parser parser = new Parser();
[ERROR] ^
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Parser
[ERROR] location: class DotReaderTask
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:405: error: cannot find symbol
[ERROR] Parser parser = new Parser();
[ERROR] ^
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Parser
[ERROR] location: class DotReaderTask
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:414: error: cannot find symbol
[ERROR] ArrayList<Graph> graphList = parser.getGraphs();
[ERROR] ^
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Graph
[ERROR] location: class DotReaderTask
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:421: error: cannot find symbol
[ERROR] for (Graph graph : graphList) {
[ERROR] ^
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Graph
[ERROR] location: class DotReaderTask
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:451: error: cannot find symbol
[ERROR] ArrayList<Node> nodeList = graph.getNodes(true);
[ERROR] ^
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Node
[ERROR] location: class DotReaderTask
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:453: error: cannot find symbol
[ERROR] for (Node node : nodeList) {
[ERROR] ^
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Node
[ERROR] location: class DotReaderTask
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:464: error: cannot find symbol
[ERROR] ArrayList<Edge> edgeList = graph.getEdges();
[ERROR] ^
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Edge
[ERROR] location: class DotReaderTask
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:466: error: cannot find symbol
[ERROR] for(Edge edge : edgeList) {
[ERROR] ^
[ERROR] 
[ERROR] could not parse error message:   symbol:   class Edge
[ERROR] location: class DotReaderTask
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:495: error: cannot find symbol
[ERROR] catch(ParseException e){
[ERROR] ^
[ERROR] 
[ERROR] could not parse error message:   symbol:   class ParseException
[ERROR] location: class DotReaderTask
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:500: error: cannot find symbol
[ERROR] catch (TokenMgrError e) {
[ERROR] ^
[ERROR] -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException
bdtfitts commented 7 years ago

Source code should build correctly with latest code