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1.0 1.0 2.0 294.5 MB

License: Apache License 2.0

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ami's Introduction

petermr repositories

Many of these repos are widely used in collaborative projects and include:

code
data
projects

This special repo is to coordinate navigation and discussion

discussion lists

The "Discussions" for this repo https://github.com/petermr/petermr/discussions include discussions for the other repos and are of indicated by their name. They may replace our (private) Slack for all public-facing material (private project management will remain on Slack).

active repos

https://github.com/petermr/pygetpapers. automatic downloading of articles and preprints in bulk. Pioneered by Rik Smith-Unna and ported to Python by @ayush garg. CLI. PyPi: https://pypi.org/project/pygetpapers/
https://github.com/petermr/pyami. Port of Java https://github.com/petermr/ami3 to Python (@petermr). CLI. Includes a prototype GUI in tkinter. PyPi: https://pypi.org/project/py4ami/ (Note there is already an unrelated pyAMI in PyPi so in that namespace we are py4ami, but on Github it's pyami)
https://github.com/petermr/pyamiimage. Analysis of scientific duagrams (@petermr, @anuvc). No CLI, or PyPI yet.
https://github.com/petermr/docanalysis. Text-based analysis of scientific articles (@shweatahegde). CLI under dev. No PyPi yet.
https://github.com/petermr/cevopen. Projects, dictionaries and outreach for analysing articles in plant sciences.
https://github.com/petermr/openvirus. Projects, dictionaries and outreach for analysing articles on viral epidemics.
https://github.com/petermr/crops. NIPGR-intern projects on crops. Minicorpora and dictionaries for terpene synthases
https://github.com/petermr/opendiagram. Adaptation of pyamiimage to extract data from diagrams, especially materials science/batteries
https://github.com/petermr/dictionary. Software for distributed dictionaries and many dictionaries

active Python projects:

For context: We have 4 packages (if that's the right word). They are largely standalone but can have useful library routines. They all share a common data structure on disk (simply named directories). This means that state is less important and often held on the filesystem. It also means that data can be further manipulated by Unix tools and other utilities. This is very fluid as we are constantly adding new data substructures. (I developed much of this in Java - https://github.com/petermr/ami3/blob/master/README.md) . The top directory is a CProject and its document children are called CTrees as they are useful split into many subdirectory trees.

Each package has a maintainer. These are all volunteers. Their Python is all self-taught . There are also interns - mixture of compsci/engineers/plant_sci who have a 3-month stay. They test the tools, develop resources, explore text-mining, NLP, image analysis, machine-learning, etc. They are encouraged to use the packages, link them into Python scripts or Notebooks but don't have time for serious development. (They might add readers or exporters).

pygetpapers , Ayush Garg. https://github.com/petermr/pygetpapers . Searches and downloads articles from repositories. Standalone, but the results may be used by docanalysis or possibly imageanalysis. Can be called from other tools.
docanalysis. Shweata Hegde. https://github.com/petermr/docanalysis . Ingests CProjects and carries out text-analysis of documents, including sectioning, NLP/text-mining, vocabulary generation. Uses NLTK and other Python tools for many operations, and spaCy, scispaCy for annotation of entities. Outputs summary data, correlations, word-dictionaries. Links entities to Wikidata.
pyamiimage, Anuv Chakroborty + PMR. https://github.com/petermr/pyamiimage . Ingests Figures/images, applies many image processing techniques (erode-dilate, colour quantization, skeletons, etc.), extracts words (Tesseract) , extracts lines and symbols (uses sknw/NetworkX) and recreates semantic diagrams (not finished)
py4ami . PMR. https://github.com/petermr/pyami . Translation of ami3(J) to Python. Processes CProjects to extract and combine primitives into semantic objects. Some functionality overlaps with docanalysis and imageanalysis. Includes libraries (e.g. for Wikimedia) and includes prototype GUI in tkinter, and a complex structure of word-dictionaries covering science and related disciplines. (Note the project is called pyami locally but there is already a PyAMI project so there it is called py4ami)

All packages aim to have a common commandline approach, use config files, generate and process CProjects (e.g. iterating over CTrees and applying filters, transformers, map/reduce, etc.). All 4 packages have been uploaded to PyPI

basicTest

Checks that the Python environment works (independently of the applications) https://github.com/petermr/basicTest/blob/main/README.md

presentations

Some presentations about the software, many from collaborators/interns

pygetpapers

https://youtu.be/pUjiNzLVHLY (@ayushGarg) 5 min

notebook

https://github.com/petermr/docanalysis/blob/main/resources/docanalysis_demo.ipynb

docanalysis

docanalysis slides (MADICES): https://github.com/petermr/CEVOpen/blob/master/outreach/docanalysis_demo_madices.pdf

wikidata

WikidataCon Presentation slides and recording: https://github.com/petermr/crops/tree/main/outreach/WikidataCon2021

ami's People

Contributors

Stargazers

Watchers

Forkers

rossmounce anusharanganathan

ami's Issues

phyloanalysis under processImage needs refactoring

The processImage() stuff should be recast as a per-cmDir analysis and put inside (not outside) runAndOutput()

ami-regex matches all have xpath on first paragraph

        String testXML = "<div>"
                + "<p> lorum conducted with Q = 300 and more lorum n = 123 lorum the study n = 250 was </p>"
                + "<p> try p &lt; 0.01 </p>"
                + "<p> dummy </p>"
                + "<p> this is another Q = 23 to test </p>"
                + "</div>";

the search

<compoundRegex title="statistics">
<!--   <regex fields="bar pre number post">\s*[Pp]\s*</regex> -->
  <regex fields="foo pre number post">[nQ]\s*=\s*[0-9]+</regex>
</compoundRegex>

matches twice but only the first para is tagged with the xpath of the last para:

<?xml version="1.0" encoding="UTF-8"?>
<results title="statistics">
 <result pre=" lorum conducted with Q = 300 and more lorum n = 123 lorum the study " name0="number" value0="n = 250" post="was " xpath="/*[local-name()='html'][1]/*[local-name()='body'][1]/*[local-name()='div'][1]/*[local-name()='p'][4]"/>
 <result pre=" this is another " name0="number" value0="Q = 23" post="to test "/>
</results>

regex only selects last match in paragraph

        String testXML = "<div>"
                + "<p> lorum conducted with Q = 300 and more lorum n = 123 lorum the study n = 250 was </p>"
                + "<p> try p &lt; 0.01 </p>"
                + "<p> dummy </p>"
                + "<p> this is another Q = 23 to test </p>"
                + "</div>";

searched with

  <regex fields="foo pre number post">[nQ]\s*=\s*[0-9]+</regex>

in the first sentence only finds the last match

<results title="statistics">
 <result pre=" lorum conducted with Q = 300 and more lorum n = 123 lorum the study " 
   name0="number" value0="n = 250" post="was " 
    xpath="/*[local-name()='html'][1]/*[local-name()='body'][1]/*[local-name()='div'][1]/*[local-name()='p'][4]"/>
 <result pre=" this is another " name0="number" value0="Q = 23" post="to test "/>
</results>

The last sentence was fine.

"<" in regexes

Since regexes are defined in XML, we need to escape <.

<regex fields="foo">P\s*&lt;\s*\d?\.\d+</regex>

However I can't get this working.
Will try to create a failing test

Error compiling ami

Commit: 05887e8

[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.xml-cml:ami2:jar:0.1-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-surefire-plugin is missing. @ line 229, column 12
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING] 
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building AMI 0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ ami2 ---
[INFO] Deleting /home/anusha/Documents/DigitalNest/src/java/pmr-ami-plugin/target
[INFO] 
[INFO] --- maven-resources-plugin:2.3:resources (default-resources) @ ami2 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 102 resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.5:compile (default-compile) @ ami2 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 108 source files to /home/anusha/Documents/DigitalNest/src/java/pmr-ami-plugin/target/classes
[INFO] /home/anusha/Documents/DigitalNest/src/java/pmr-ami-plugin/src/main/java/org/xmlcml/ami2/lookups/RRIDLookup.java: Some input files use or override a deprecated API.
[INFO] /home/anusha/Documents/DigitalNest/src/java/pmr-ami-plugin/src/main/java/org/xmlcml/ami2/lookups/RRIDLookup.java: Recompile with -Xlint:deprecation for details.
[INFO] /home/anusha/Documents/DigitalNest/src/java/pmr-ami-plugin/src/main/java/org/xmlcml/ami2/plugins/AMIArgProcessor.java: /home/anusha/Documents/DigitalNest/src/java/pmr-ami-plugin/src/main/java/org/xmlcml/ami2/plugins/AMIArgProcessor.java uses unchecked or unsafe operations.
[INFO] /home/anusha/Documents/DigitalNest/src/java/pmr-ami-plugin/src/main/java/org/xmlcml/ami2/plugins/AMIArgProcessor.java: Recompile with -Xlint:unchecked for details.
[INFO] 
[INFO] --- maven-resources-plugin:2.3:testResources (default-testResources) @ ami2 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 904 resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.5:testCompile (default-testCompile) @ ami2 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 49 source files to /home/anusha/Documents/DigitalNest/src/java/pmr-ami-plugin/target/test-classes
[INFO] /home/anusha/Documents/DigitalNest/src/java/pmr-ami-plugin/src/test/java/org/xmlcml/ami2/misc/HEPTest.java: /home/anusha/Documents/DigitalNest/src/java/pmr-ami-plugin/src/test/java/org/xmlcml/ami2/misc/HEPTest.java uses or overrides a deprecated API.
[INFO] /home/anusha/Documents/DigitalNest/src/java/pmr-ami-plugin/src/test/java/org/xmlcml/ami2/misc/HEPTest.java: Recompile with -Xlint:deprecation for details.
[INFO] -------------------------------------------------------------
[ERROR] COMPILATION ERROR : 
[INFO] -------------------------------------------------------------
[ERROR] /home/anusha/Documents/DigitalNest/src/java/pmr-ami-plugin/src/test/java/org/xmlcml/ami2/TutorialTest.java:[219,17] constructor DefaultArgProcessor in class org.xmlcml.cmine.args.DefaultArgProcessor cannot be applied to given types;
  required: no arguments
  found: java.lang.String
  reason: actual and formal argument lists differ in length
[ERROR] /home/anusha/Documents/DigitalNest/src/java/pmr-ami-plugin/src/test/java/org/xmlcml/ami2/TutorialTest.java:[221,17] constructor DefaultArgProcessor in class org.xmlcml.cmine.args.DefaultArgProcessor cannot be applied to given types;
  required: no arguments
  found: java.lang.String
  reason: actual and formal argument lists differ in length
[ERROR] /home/anusha/Documents/DigitalNest/src/java/pmr-ami-plugin/src/test/java/org/xmlcml/ami2/TutorialTest.java:[223,17] constructor DefaultArgProcessor in class org.xmlcml.cmine.args.DefaultArgProcessor cannot be applied to given types;
  required: no arguments
  found: java.lang.String
  reason: actual and formal argument lists differ in length
[ERROR] /home/anusha/Documents/DigitalNest/src/java/pmr-ami-plugin/src/test/java/org/xmlcml/ami2/TutorialTest.java:[225,17] constructor DefaultArgProcessor in class org.xmlcml.cmine.args.DefaultArgProcessor cannot be applied to given types;
  required: no arguments
  found: java.lang.String
  reason: actual and formal argument lists differ in length
[ERROR] /home/anusha/Documents/DigitalNest/src/java/pmr-ami-plugin/src/test/java/org/xmlcml/ami2/TutorialTest.java:[229,17] constructor DefaultArgProcessor in class org.xmlcml.cmine.args.DefaultArgProcessor cannot be applied to given types;
  required: no arguments
  found: java.lang.String
  reason: actual and formal argument lists differ in length
[ERROR] /home/anusha/Documents/DigitalNest/src/java/pmr-ami-plugin/src/test/java/org/xmlcml/ami2/TutorialTest.java:[231,17] constructor DefaultArgProcessor in class org.xmlcml.cmine.args.DefaultArgProcessor cannot be applied to given types;
  required: no arguments
  found: java.lang.String
  reason: actual and formal argument lists differ in length
[ERROR] /home/anusha/Documents/DigitalNest/src/java/pmr-ami-plugin/src/test/java/org/xmlcml/ami2/TutorialTest.java:[233,17] constructor DefaultArgProcessor in class org.xmlcml.cmine.args.DefaultArgProcessor cannot be applied to given types;
  required: no arguments
  found: java.lang.String
  reason: actual and formal argument lists differ in length
[ERROR] /home/anusha/Documents/DigitalNest/src/java/pmr-ami-plugin/src/test/java/org/xmlcml/ami2/TutorialTest.java:[235,17] constructor DefaultArgProcessor in class org.xmlcml.cmine.args.DefaultArgProcessor cannot be applied to given types;
  required: no arguments
  found: java.lang.String
  reason: actual and formal argument lists differ in length
[ERROR] /home/anusha/Documents/DigitalNest/src/java/pmr-ami-plugin/src/test/java/org/xmlcml/ami2/TutorialTest.java:[237,17] constructor DefaultArgProcessor in class org.xmlcml.cmine.args.DefaultArgProcessor cannot be applied to given types;
  required: no arguments
  found: java.lang.String
  reason: actual and formal argument lists differ in length
[INFO] 9 errors 
[INFO] -------------------------------------------------------------
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 5.905s
[INFO] Finished at: Wed Jan 27 09:52:15 GMT 2016
[INFO] Final Memory: 24M/236M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.5:testCompile (default-testCompile) on project ami2: Compilation failure: Compilation failure:
[ERROR] /home/anusha/Documents/DigitalNest/src/java/pmr-ami-plugin/src/test/java/org/xmlcml/ami2/TutorialTest.java:[219,17] constructor DefaultArgProcessor in class org.xmlcml.cmine.args.DefaultArgProcessor cannot be applied to given types;
[ERROR] required: no arguments
[ERROR] found: java.lang.String
[ERROR] reason: actual and formal argument lists differ in length
[ERROR] /home/anusha/Documents/DigitalNest/src/java/pmr-ami-plugin/src/test/java/org/xmlcml/ami2/TutorialTest.java:[221,17] constructor DefaultArgProcessor in class org.xmlcml.cmine.args.DefaultArgProcessor cannot be applied to given types;
[ERROR] required: no arguments
[ERROR] found: java.lang.String
[ERROR] reason: actual and formal argument lists differ in length
[ERROR] /home/anusha/Documents/DigitalNest/src/java/pmr-ami-plugin/src/test/java/org/xmlcml/ami2/TutorialTest.java:[223,17] constructor DefaultArgProcessor in class org.xmlcml.cmine.args.DefaultArgProcessor cannot be applied to given types;
[ERROR] required: no arguments
[ERROR] found: java.lang.String
[ERROR] reason: actual and formal argument lists differ in length
[ERROR] /home/anusha/Documents/DigitalNest/src/java/pmr-ami-plugin/src/test/java/org/xmlcml/ami2/TutorialTest.java:[225,17] constructor DefaultArgProcessor in class org.xmlcml.cmine.args.DefaultArgProcessor cannot be applied to given types;
[ERROR] required: no arguments
[ERROR] found: java.lang.String
[ERROR] reason: actual and formal argument lists differ in length
[ERROR] /home/anusha/Documents/DigitalNest/src/java/pmr-ami-plugin/src/test/java/org/xmlcml/ami2/TutorialTest.java:[229,17] constructor DefaultArgProcessor in class org.xmlcml.cmine.args.DefaultArgProcessor cannot be applied to given types;
[ERROR] required: no arguments
[ERROR] found: java.lang.String
[ERROR] reason: actual and formal argument lists differ in length
[ERROR] /home/anusha/Documents/DigitalNest/src/java/pmr-ami-plugin/src/test/java/org/xmlcml/ami2/TutorialTest.java:[231,17] constructor DefaultArgProcessor in class org.xmlcml.cmine.args.DefaultArgProcessor cannot be applied to given types;
[ERROR] required: no arguments
[ERROR] found: java.lang.String
[ERROR] reason: actual and formal argument lists differ in length
[ERROR] /home/anusha/Documents/DigitalNest/src/java/pmr-ami-plugin/src/test/java/org/xmlcml/ami2/TutorialTest.java:[233,17] constructor DefaultArgProcessor in class org.xmlcml.cmine.args.DefaultArgProcessor cannot be applied to given types;
[ERROR] required: no arguments
[ERROR] found: java.lang.String
[ERROR] reason: actual and formal argument lists differ in length
[ERROR] /home/anusha/Documents/DigitalNest/src/java/pmr-ami-plugin/src/test/java/org/xmlcml/ami2/TutorialTest.java:[235,17] constructor DefaultArgProcessor in class org.xmlcml.cmine.args.DefaultArgProcessor cannot be applied to given types;
[ERROR] required: no arguments
[ERROR] found: java.lang.String
[ERROR] reason: actual and formal argument lists differ in length
[ERROR] /home/anusha/Documents/DigitalNest/src/java/pmr-ami-plugin/src/test/java/org/xmlcml/ami2/TutorialTest.java:[237,17] constructor DefaultArgProcessor in class org.xmlcml.cmine.args.DefaultArgProcessor cannot be applied to given types;
[ERROR] required: no arguments
[ERROR] found: java.lang.String
[ERROR] reason: actual and formal argument lists differ in length
[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

Tests in error: testEditLabels

ami(0.1.13)
ami(0.1.13)
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec

Results :

Tests in error: 
  testEditLabels(org.xmlcml.ami2.plugins.phylotree.PhyloArgProcessorTest)

Tests run: 111, Failures: 0, Errors: 1, Skipped: 32

[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 2:24.920s
[INFO] Finished at: Tue Aug 18 13:11:18 BST 2015
[INFO] Final Memory: 23M/245M

can't seem to get the new code to build. Any idea?
Full log here: https://gist.github.com/rossmounce/e0047fc0944381e3e37f

Error in tests - RegressionDemoTest

Failure on running mvn install when running tests.

23278 [main] DEBUG org.xmlcml.ami2.plugins.RegressionDemoTest - --sp.species --context 35 50 --sp.type binomial genus genussp -q target/multiple/bmc_trials_15_1_511 target/multiple/http_www.trialsjournal.com_content_16_1_1 -i scholarly.html
2.0.1
23281 [main] ERROR org.xmlcml.cmine.args.DefaultArgProcessor - File does not exist: /home/tom/src/contentmine/ami-plugin/target/multiple/bmc_trials_15_1_511
23281 [main] ERROR org.xmlcml.cmine.args.DefaultArgProcessor - File does not exist: /home/tom/src/contentmine/ami-plugin/target/multiple/http_www.trialsjournal.com_content_16_1_1
23281 [main] ERROR org.xmlcml.cmine.args.DefaultArgProcessor - Cannot create output: --project or --output must be given
2.0.1
Tests run: 6, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 0.597 sec <<< FAILURE!

error: generics are not supported in -source 1.3

Different machine with different java and different Build problems:

Apache Maven 3.0.5
Maven home: /usr/share/maven
Java version: 1.7.0_80, vendor: Oracle Corporation
Java home: /usr/lib/jvm/java-7-oracle/jre
Default locale: en_GB, platform encoding: UTF-8
OS name: "linux", version: "3.13.0-61-generic", arch: "amd64", family: "unix"
[INFO] Error stacktraces are turned on.
[DEBUG] Reading global settings from /usr/share/maven/conf/settings.xml
[DEBUG] Reading user settings from /home/ross/.m2/settings.xml
[DEBUG] Using local repository at /home/ross/.m2/repository
[DEBUG] Using manager EnhancedLocalRepositoryManager with priority 10 for /home/ross/.m2/repository
[INFO] Scanning for projects...
[DEBUG] Extension realms for project org.xml-cml:ami2:jar:0.1-SNAPSHOT: (none)
[DEBUG] Looking up lifecyle mappings for packaging jar from ClassRealm[plexus.core, parent: null]
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.xml-cml:ami2:jar:0.1-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-surefire-plugin is missing. @ line 228, column 12
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING] 
[DEBUG] === REACTOR BUILD PLAN ================================================
[DEBUG] Project: org.xml-cml:ami2:jar:0.1-SNAPSHOT
[DEBUG] Tasks:   [clean, install]
[DEBUG] Style:   Regular
[DEBUG] =======================================================================
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building AMI 0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[DEBUG] Lifecycle default -> [validate, initialize, generate-sources, process-sources, generate-resources, process-resources, compile, process-classes, generate-test-sources, process-test-sources, generate-test-resources, process-test-resources, test-compile, process-test-classes, test, prepare-package, package, pre-integration-test, integration-test, post-integration-test, verify, install, deploy]
[DEBUG] Lifecycle clean -> [pre-clean, clean, post-clean]
[DEBUG] Lifecycle site -> [pre-site, site, post-site, site-deploy]
[DEBUG] Lifecycle default -> [validate, initialize, generate-sources, process-sources, generate-resources, process-resources, compile, process-classes, generate-test-sources, process-test-sources, generate-test-resources, process-test-resources, test-compile, process-test-classes, test, prepare-package, package, pre-integration-test, integration-test, post-integration-test, verify, install, deploy]
[DEBUG] Lifecycle clean -> [pre-clean, clean, post-clean]
[DEBUG] Lifecycle site -> [pre-site, site, post-site, site-deploy]
[DEBUG] Lifecycle default -> [validate, initialize, generate-sources, process-sources, generate-resources, process-resources, compile, process-classes, generate-test-sources, process-test-sources, generate-test-resources, process-test-resources, test-compile, process-test-classes, test, prepare-package, package, pre-integration-test, integration-test, post-integration-test, verify, install, deploy]
[DEBUG] Lifecycle clean -> [pre-clean, clean, post-clean]
[DEBUG] Lifecycle site -> [pre-site, site, post-site, site-deploy]
[DEBUG] Lifecycle default -> [validate, initialize, generate-sources, process-sources, generate-resources, process-resources, compile, process-classes, generate-test-sources, process-test-sources, generate-test-resources, process-test-resources, test-compile, process-test-classes, test, prepare-package, package, pre-integration-test, integration-test, post-integration-test, verify, install, deploy]
[DEBUG] Lifecycle clean -> [pre-clean, clean, post-clean]
[DEBUG] Lifecycle site -> [pre-site, site, post-site, site-deploy]
[DEBUG] Lifecycle default -> [validate, initialize, generate-sources, process-sources, generate-resources, process-resources, compile, process-classes, generate-test-sources, process-test-sources, generate-test-resources, process-test-resources, test-compile, process-test-classes, test, prepare-package, package, pre-integration-test, integration-test, post-integration-test, verify, install, deploy]
[DEBUG] Lifecycle clean -> [pre-clean, clean, post-clean]
[DEBUG] Lifecycle site -> [pre-site, site, post-site, site-deploy]
[DEBUG] Lifecycle default -> [validate, initialize, generate-sources, process-sources, generate-resources, process-resources, compile, process-classes, generate-test-sources, process-test-sources, generate-test-resources, process-test-resources, test-compile, process-test-classes, test, prepare-package, package, pre-integration-test, integration-test, post-integration-test, verify, install, deploy]
[DEBUG] Lifecycle clean -> [pre-clean, clean, post-clean]
[DEBUG] Lifecycle site -> [pre-site, site, post-site, site-deploy]
[DEBUG] Lifecycle default -> [validate, initialize, generate-sources, process-sources, generate-resources, process-resources, compile, process-classes, generate-test-sources, process-test-sources, generate-test-resources, process-test-resources, test-compile, process-test-classes, test, prepare-package, package, pre-integration-test, integration-test, post-integration-test, verify, install, deploy]
[DEBUG] Lifecycle clean -> [pre-clean, clean, post-clean]
[DEBUG] Lifecycle site -> [pre-site, site, post-site, site-deploy]
[DEBUG] Lifecycle default -> [validate, initialize, generate-sources, process-sources, generate-resources, process-resources, compile, process-classes, generate-test-sources, process-test-sources, generate-test-resources, process-test-resources, test-compile, process-test-classes, test, prepare-package, package, pre-integration-test, integration-test, post-integration-test, verify, install, deploy]
[DEBUG] Lifecycle clean -> [pre-clean, clean, post-clean]
[DEBUG] Lifecycle site -> [pre-site, site, post-site, site-deploy]
[DEBUG] Lifecycle default -> [validate, initialize, generate-sources, process-sources, generate-resources, process-resources, compile, process-classes, generate-test-sources, process-test-sources, generate-test-resources, process-test-resources, test-compile, process-test-classes, test, prepare-package, package, pre-integration-test, integration-test, post-integration-test, verify, install, deploy]
[DEBUG] Lifecycle clean -> [pre-clean, clean, post-clean]
[DEBUG] Lifecycle site -> [pre-site, site, post-site, site-deploy]
[DEBUG] Lifecycle default -> [validate, initialize, generate-sources, process-sources, generate-resources, process-resources, compile, process-classes, generate-test-sources, process-test-sources, generate-test-resources, process-test-resources, test-compile, process-test-classes, test, prepare-package, package, pre-integration-test, integration-test, post-integration-test, verify, install, deploy]
[DEBUG] Lifecycle clean -> [pre-clean, clean, post-clean]
[DEBUG] Lifecycle site -> [pre-site, site, post-site, site-deploy]
[DEBUG] === PROJECT BUILD PLAN ================================================
[DEBUG] Project:       org.xml-cml:ami2:0.1-SNAPSHOT
[DEBUG] Dependencies (collect): []
[DEBUG] Dependencies (resolve): [compile, runtime, test]
[DEBUG] Repositories (dependencies): [ebi-repo (http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo/, releases), ebi-repo-snapshots (http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo-snapshots/, snapshots), ebi-repo-3rd (http://www.ebi.ac.uk/~maven/m2repo, releases+snapshots), ucc-repo (https://maven.ch.cam.ac.uk/m2repo, releases+snapshots), central (http://repo.maven.apache.org/maven2, releases)]
[DEBUG] Repositories (plugins)     : [central (http://repo.maven.apache.org/maven2, releases)]
[DEBUG] -----------------------------------------------------------------------
[DEBUG] Goal:          org.apache.maven.plugins:maven-clean-plugin:2.5:clean (default-clean)
[DEBUG] Style:         Regular
[DEBUG] Configuration: <?xml version="1.0" encoding="UTF-8"?>
<configuration>
  <directory default-value="${project.build.directory}"/>
  <excludeDefaultDirectories default-value="false">${clean.excludeDefaultDirectories}</excludeDefaultDirectories>
  <failOnError default-value="true">${maven.clean.failOnError}</failOnError>
  <followSymLinks default-value="false">${clean.followSymLinks}</followSymLinks>
  <outputDirectory default-value="${project.build.outputDirectory}"/>
  <reportDirectory default-value="${project.reporting.outputDirectory}"/>
  <retryOnError default-value="true">${maven.clean.retryOnError}</retryOnError>
  <skip default-value="false">${clean.skip}</skip>
  <testOutputDirectory default-value="${project.build.testOutputDirectory}"/>
  <verbose>${clean.verbose}</verbose>
</configuration>
[DEBUG] -----------------------------------------------------------------------
[DEBUG] Goal:          org.apache.maven.plugins:maven-resources-plugin:2.3:resources (default-resources)
[DEBUG] Style:         Regular
[DEBUG] Configuration: <?xml version="1.0" encoding="UTF-8"?>
<configuration>
  <encoding default-value="${project.build.sourceEncoding}">${encoding}</encoding>
  <escapeString>${maven.resources.escapeString}</escapeString>
  <filters>${project.build.filters}</filters>
  <includeEmptyDirs default-value="false">${maven.resources.includeEmptyDirs}</includeEmptyDirs>
  <outputDirectory>${project.build.outputDirectory}</outputDirectory>
  <overwrite default-value="false">${maven.resources.overwrite}</overwrite>
  <project>${project}</project>
  <resources>${project.resources}</resources>
  <session>${session}</session>
</configuration>
[DEBUG] -----------------------------------------------------------------------
[DEBUG] Goal:          org.apache.maven.plugins:maven-compiler-plugin:2.0.2:compile (default-compile)
[DEBUG] Style:         Regular
[DEBUG] Configuration: <?xml version="1.0" encoding="UTF-8"?>
<configuration>
  <basedir>${basedir}</basedir>
  <buildDirectory>${project.build.directory}</buildDirectory>
  <classpathElements>${project.compileClasspathElements}</classpathElements>
  <compileSourceRoots>${project.compileSourceRoots}</compileSourceRoots>
  <compilerId default-value="javac">${maven.compiler.compilerId}</compilerId>
  <compilerVersion>${maven.compiler.compilerVersion}</compilerVersion>
  <debug default-value="true">${maven.compiler.debug}</debug>
  <encoding>${maven.compiler.encoding}</encoding>
  <executable>${maven.compiler.executable}</executable>
  <failOnError default-value="true">${maven.compiler.failOnError}</failOnError>
  <fork default-value="false"/>
  <maxmem>${maven.compiler.maxmem}</maxmem>
  <meminitial>${maven.compiler.meminitial}</meminitial>
  <optimize default-value="false">${maven.compiler.optimize}</optimize>
  <outputDirectory>${project.build.outputDirectory}</outputDirectory>
  <outputFileName>${project.build.finalName}</outputFileName>
  <projectArtifact>${project.artifact}</projectArtifact>
  <showDeprecation default-value="false">${maven.compiler.showDeprecation}</showDeprecation>
  <showWarnings default-value="false">${maven.compiler.showWarnings}</showWarnings>
  <source>${maven.compiler.source}</source>
  <staleMillis default-value="0">${lastModGranularityMs}</staleMillis>
  <target>${maven.compiler.target}</target>
  <verbose default-value="false">${maven.compiler.verbose}</verbose>
</configuration>
[DEBUG] -----------------------------------------------------------------------
[DEBUG] Goal:          org.apache.maven.plugins:maven-resources-plugin:2.3:testResources (default-testResources)
[DEBUG] Style:         Regular
[DEBUG] Configuration: <?xml version="1.0" encoding="UTF-8"?>
<configuration>
  <encoding default-value="${project.build.sourceEncoding}">${encoding}</encoding>
  <escapeString>${maven.resources.escapeString}</escapeString>
  <filters>${project.build.filters}</filters>
  <includeEmptyDirs default-value="false">${maven.resources.includeEmptyDirs}</includeEmptyDirs>
  <outputDirectory>${project.build.testOutputDirectory}</outputDirectory>
  <overwrite default-value="false">${maven.resources.overwrite}</overwrite>
  <project>${project}</project>
  <resources>${project.testResources}</resources>
  <session>${session}</session>
</configuration>
[DEBUG] -----------------------------------------------------------------------
[DEBUG] Goal:          org.apache.maven.plugins:maven-compiler-plugin:2.0.2:testCompile (default-testCompile)
[DEBUG] Style:         Regular
[DEBUG] Configuration: <?xml version="1.0" encoding="UTF-8"?>
<configuration>
  <basedir>${basedir}</basedir>
  <buildDirectory>${project.build.directory}</buildDirectory>
  <classpathElements>${project.testClasspathElements}</classpathElements>
  <compileSourceRoots>${project.testCompileSourceRoots}</compileSourceRoots>
  <compilerId default-value="javac">${maven.compiler.compilerId}</compilerId>
  <compilerVersion>${maven.compiler.compilerVersion}</compilerVersion>
  <debug default-value="true">${maven.compiler.debug}</debug>
  <encoding>${maven.compiler.encoding}</encoding>
  <executable>${maven.compiler.executable}</executable>
  <failOnError default-value="true">${maven.compiler.failOnError}</failOnError>
  <fork default-value="false"/>
  <maxmem>${maven.compiler.maxmem}</maxmem>
  <meminitial>${maven.compiler.meminitial}</meminitial>
  <optimize default-value="false">${maven.compiler.optimize}</optimize>
  <outputDirectory>${project.build.testOutputDirectory}</outputDirectory>
  <outputFileName>${project.build.finalName}</outputFileName>
  <showDeprecation default-value="false">${maven.compiler.showDeprecation}</showDeprecation>
  <showWarnings default-value="false">${maven.compiler.showWarnings}</showWarnings>
  <skip>${maven.test.skip}</skip>
  <source>${maven.compiler.source}</source>
  <staleMillis default-value="0">${lastModGranularityMs}</staleMillis>
  <target>${maven.compiler.target}</target>
  <verbose default-value="false">${maven.compiler.verbose}</verbose>
</configuration>
[DEBUG] -----------------------------------------------------------------------
[DEBUG] Goal:          org.apache.maven.plugins:maven-surefire-plugin:2.10:test (default-test)
[DEBUG] Style:         Regular
[DEBUG] Configuration: <?xml version="1.0" encoding="UTF-8"?>
<configuration>
  <argLine>${argLine}</argLine>
  <basedir default-value="${basedir}"/>
  <childDelegation default-value="false">${childDelegation}</childDelegation>
  <classesDirectory default-value="${project.build.outputDirectory}"/>
  <debugForkedProcess>${maven.surefire.debug}</debugForkedProcess>
  <disableXmlReport default-value="false">${disableXmlReport}</disableXmlReport>
  <enableAssertions default-value="true">${enableAssertions}</enableAssertions>
  <excludedGroups>${excludedGroups}</excludedGroups>
  <failIfNoTests>${failIfNoTests}</failIfNoTests>
  <forkMode default-value="once">${forkMode}</forkMode>
  <forkedProcessTimeoutInSeconds>${surefire.timeout}</forkedProcessTimeoutInSeconds>
  <groups>${groups}</groups>
  <junitArtifactName default-value="junit:junit">${junitArtifactName}</junitArtifactName>
  <jvm>${jvm}</jvm>
  <localRepository>${localRepository}</localRepository>
  <objectFactory>${objectFactory}</objectFactory>
  <parallel>${parallel}</parallel>
  <parallelMavenExecution default-value="${session.parallel}"/>
  <perCoreThreadCount default-value="true">${perCoreThreadCount}</perCoreThreadCount>
  <pluginArtifactMap>${plugin.artifactMap}</pluginArtifactMap>
  <printSummary default-value="true">${surefire.printSummary}</printSummary>
  <project default-value="${project}"/>
  <projectArtifactMap>${project.artifactMap}</projectArtifactMap>
  <redirectTestOutputToFile default-value="false">${maven.test.redirectTestOutputToFile}</redirectTestOutputToFile>
  <remoteRepositories>${project.pluginArtifactRepositories}</remoteRepositories>
  <reportFormat default-value="brief">${surefire.reportFormat}</reportFormat>
  <reportNameSuffix default-value="">${surefire.reportNameSuffix}</reportNameSuffix>
  <reportsDirectory default-value="${project.build.directory}/surefire-reports"/>
  <runOrder default-value="filesystem"/>
  <session>${session}</session>
  <skip default-value="false">${maven.test.skip}</skip>
  <skipExec>${maven.test.skip.exec}</skipExec>
  <skipTests default-value="false">${skipTests}</skipTests>
  <test>${test}</test>
  <testClassesDirectory default-value="${project.build.testOutputDirectory}"/>
  <testFailureIgnore default-value="false">${maven.test.failure.ignore}</testFailureIgnore>
  <testNGArtifactName default-value="org.testng:testng">${testNGArtifactName}</testNGArtifactName>
  <testSourceDirectory default-value="${project.build.testSourceDirectory}"/>
  <threadCount>${threadCount}</threadCount>
  <trimStackTrace default-value="true">${trimStackTrace}</trimStackTrace>
  <useFile default-value="true">${surefire.useFile}</useFile>
  <useManifestOnlyJar default-value="true">${surefire.useManifestOnlyJar}</useManifestOnlyJar>
  <useSystemClassLoader default-value="true">${surefire.useSystemClassLoader}</useSystemClassLoader>
  <useUnlimitedThreads default-value="false">${useUnlimitedThreads}</useUnlimitedThreads>
  <workingDirectory>${basedir}</workingDirectory>
</configuration>
[DEBUG] -----------------------------------------------------------------------
[DEBUG] Goal:          org.apache.maven.plugins:maven-jar-plugin:2.2:jar (default-jar)
[DEBUG] Style:         Regular
[DEBUG] Configuration: <?xml version="1.0" encoding="UTF-8"?>
<configuration>
  <classesDirectory>${project.build.outputDirectory}</classesDirectory>
  <defaultManifestFile>${project.build.outputDirectory}/META-INF/MANIFEST.MF</defaultManifestFile>
  <finalName default-value="${project.build.finalName}">${jar.finalName}</finalName>
  <forceCreation default-value="false">${jar.forceCreation}</forceCreation>
  <outputDirectory>${project.build.directory}</outputDirectory>
  <project>${project}</project>
  <useDefaultManifestFile default-value="false">${jar.useDefaultManifestFile}</useDefaultManifestFile>
</configuration>
[DEBUG] -----------------------------------------------------------------------
[DEBUG] Goal:          org.codehaus.mojo:appassembler-maven-plugin:1.8.1:assemble (assembly)
[DEBUG] Style:         Regular
[DEBUG] Configuration: <?xml version="1.0" encoding="UTF-8"?>
<configuration>
  <artifacts default-value="${project.runtimeArtifacts}"/>
  <assembleDirectory default-value="${project.build.directory}/appassembler">${assembleDirectory}</assembleDirectory>
  <binFolder default-value="bin"/>
  <buildFilters default-value="${project.build.filters}"/>
  <configurationDirectory default-value="etc"/>
  <configurationSourceDirectory default-value="src/main/config"/>
  <copyConfigurationDirectory default-value="false"/>
  <encoding default-value="${project.build.sourceEncoding}"/>
  <filterConfigurationDirectory default-value="false"/>
  <generateRepository default-value="true"/>
  <includeConfigurationDirectoryInClasspath default-value="true"/>
  <localRepository default-value="${localRepository}"/>
  <logsDirectory>${logsDirectory}</logsDirectory>
  <mavenProject default-value="${project}"/>
  <programs>
    <program>
      <mainClass>org.xmlcml.ami2.plugins.gene.GenePlugin</mainClass>
      <id>ami2-gene</id>
    </program>
    <program>
      <mainClass>org.xmlcml.ami2.plugins.identifier.IdentifierPlugin</mainClass>
      <id>ami2-identifier</id>
    </program>
    <program>
      <mainClass>org.xmlcml.ami2.plugins.phylotree.PhyloTreePlugin</mainClass>
      <id>ami2-phylotree</id>
    </program>
    <program>
      <mainClass>org.xmlcml.ami2.plugins.regex.RegexPlugin</mainClass>
      <id>ami2-regex</id>
    </program>
    <program>
      <mainClass>org.xmlcml.ami2.plugins.sequence.SequencePlugin</mainClass>
      <id>ami2-sequence</id>
    </program>
    <program>
      <mainClass>org.xmlcml.ami2.plugins.species.SpeciesPlugin</mainClass>
      <id>ami2-species</id>
    </program>
    <program>
      <mainClass>org.xmlcml.ami2.plugins.word.WordPlugin</mainClass>
      <id>ami2-word</id>
    </program>
  </programs>
  <projectArtifact default-value="${project.artifact}"/>
  <projectArtifactFirstInClassPath default-value="false"/>
  <repositoryLayout default-value="default">flat</repositoryLayout>
  <repositoryName default-value="repo"/>
  <session default-value="${session}"/>
  <showConsoleWindow default-value="true"/>
  <tempDirectory>${tempDirectory}</tempDirectory>
  <unixScriptTemplate>${unixScriptTemplate}</unixScriptTemplate>
  <useAllProjectDependencies default-value="false"/>
  <useTimestampInSnapshotFileName default-value="true"/>
  <useWildcardClassPath default-value="false"/>
  <windowsScriptTemplate>${windowsScriptTemplate}</windowsScriptTemplate>
</configuration>
[DEBUG] -----------------------------------------------------------------------
[DEBUG] Goal:          org.vafer:jdeb:1.3:jdeb (default)
[DEBUG] Style:         Regular
[DEBUG] Configuration: <?xml version="1.0" encoding="UTF-8"?>
<configuration>
  <attach default-value="true"/>
  <baseDir default-value="${basedir}"/>
  <buildDirectory>${project.build.directory}</buildDirectory>
  <changesIn default-value="[[baseDir]]/CHANGES.txt"/>
  <changesOut default-value="[[buildDir]]/[[artifactId]]_[[version]]_all.changes"/>
  <changesSave default-value="[[baseDir]]/CHANGES.txt"/>
  <compression default-value="gzip"/>
  <controlDir default-value="[[baseDir]]/src/deb/control"/>
  <dataSet>
    <data>
      <src>/home/ross/workspace/pluto-20150818/ami-plugin/target/appassembler/</src>
      <type>directory</type>
      <mapper>
        <type>perm</type>
        <filemode>555</filemode>
        <prefix>/usr/share/ami-repo</prefix>
      </mapper>
    </data>
    <data>
      <type>link</type>
      <symlink>true</symlink>
      <linkName>/usr/bin/ami2-gene</linkName>
      <linkTarget>/usr/share/ami-repo/bin/ami2-gene</linkTarget>
    </data>
    <data>
      <type>link</type>
      <symlink>true</symlink>
      <linkName>/usr/bin/ami2-identifier</linkName>
      <linkTarget>/usr/share/ami-repo/bin/ami2-identifier</linkTarget>
    </data>
    <data>
      <type>link</type>
      <symlink>true</symlink>
      <linkName>/usr/bin/ami2-phylotree</linkName>
      <linkTarget>/usr/share/ami-repo/bin/ami2-phylotree</linkTarget>
    </data>
    <data>
      <type>link</type>
      <symlink>true</symlink>
      <linkName>/usr/bin/ami2-regex</linkName>
      <linkTarget>/usr/share/ami-repo/bin/ami2-regex</linkTarget>
    </data>
    <data>
      <type>link</type>
      <symlink>true</symlink>
      <linkName>/usr/bin/ami2-sequence</linkName>
      <linkTarget>/usr/share/ami-repo/bin/ami2-sequence</linkTarget>
    </data>
    <data>
      <type>link</type>
      <symlink>true</symlink>
      <linkName>/usr/bin/ami2-species</linkName>
      <linkTarget>/usr/share/ami-repo/bin/ami2-species</linkTarget>
    </data>
    <data>
      <type>link</type>
      <symlink>true</symlink>
      <linkName>/usr/bin/ami2-word</linkName>
      <linkTarget>/usr/share/ami-repo/bin/ami2-word</linkTarget>
    </data>
  </dataSet>
  <deb default-value="[[buildDir]]/[[artifactId]]_[[version]]_all.[[extension]]"/>
  <installDir default-value="/opt/[[artifactId]]"/>
  <project default-value="${project}"/>
  <session default-value="${session}"/>
  <settings default-value="${settings}"/>
  <signCfgPrefix default-value="jdeb."/>
  <signMethod default-value="debsig-verify"/>
  <signPackage default-value="false"/>
  <signRole default-value="origin"/>
  <skip default-value="false"/>
  <skipPOMs default-value="true"/>
  <skipSubmodules default-value="false"/>
  <snapshotEnv default-value="SNAPSHOT"/>
  <snapshotExpand default-value="false"/>
  <submodules default-value="true"/>
  <type default-value="deb"/>
  <verbose default-value="false"/>
</configuration>
[DEBUG] -----------------------------------------------------------------------
[DEBUG] Goal:          org.apache.maven.plugins:maven-assembly-plugin:2.4.1:single (default)
[DEBUG] Style:         Regular
[DEBUG] Configuration: <?xml version="1.0" encoding="UTF-8"?>
<configuration>
  <appendAssemblyId default-value="true">${assembly.appendAssemblyId}</appendAssemblyId>
  <attach default-value="true">${assembly.attach}</attach>
  <basedir default-value="${project.basedir}"/>
  <classifier>${classifier}</classifier>
  <descriptor>src/main/assembly/bin.xml</descriptor>
  <descriptorId>${descriptorId}</descriptorId>
  <dryRun default-value="false">${assembly.dryRun}</dryRun>
  <encoding default-value="${project.build.sourceEncoding}">${encoding}</encoding>
  <escapeString>${assembly.escapeString}</escapeString>
  <finalName default-value="${project.build.finalName}"/>
  <ignoreDirFormatExtensions default-value="true"/>
  <ignoreMissingDescriptor default-value="false">${assembly.ignoreMissingDescriptor}</ignoreMissingDescriptor>
  <ignorePermissions default-value="false">${assembly.ignorePermissions}</ignorePermissions>
  <includeSite default-value="false">${includeSite}</includeSite>
  <localRepository default-value="${localRepository}"/>
  <outputDirectory default-value="${project.build.directory}"/>
  <reactorProjects default-value="${reactorProjects}"/>
  <recompressZippedFiles default-value="true"/>
  <remoteRepositories default-value="${project.remoteArtifactRepositories}"/>
  <runOnlyAtExecutionRoot default-value="false">${assembly.runOnlyAtExecutionRoot}</runOnlyAtExecutionRoot>
  <siteDirectory default-value="${project.reporting.outputDirectory}"/>
  <skipAssembly default-value="false">${assembly.skipAssembly}</skipAssembly>
  <tarLongFileMode default-value="warn">${assembly.tarLongFileMode}</tarLongFileMode>
  <tempRoot default-value="${project.build.directory}/archive-tmp"/>
  <updateOnly default-value="false">${assembly.updateOnly}</updateOnly>
  <useJvmChmod default-value="false">${assembly.useJvmChmod}</useJvmChmod>
  <workDirectory default-value="${project.build.directory}/assembly/work"/>
  <mavenSession default-value="${session}"/>
  <project default-value="${project}"/>
</configuration>
[DEBUG] -----------------------------------------------------------------------
[DEBUG] Goal:          org.apache.maven.plugins:maven-install-plugin:2.3:install (default-install)
[DEBUG] Style:         Regular
[DEBUG] Configuration: <?xml version="1.0" encoding="UTF-8"?>
<configuration>
  <artifact default-value="${project.artifact}"/>
  <attachedArtifacts default-value="${project.attachedArtifacts}"/>
  <createChecksum default-value="false">${createChecksum}</createChecksum>
  <localRepository>${localRepository}</localRepository>
  <packaging default-value="${project.packaging}"/>
  <pomFile default-value="${project.file}"/>
  <updateReleaseInfo default-value="false">${updateReleaseInfo}</updateReleaseInfo>
</configuration>
[DEBUG] =======================================================================
[DEBUG] Could not find metadata org.xml-cml:norma:0.1-SNAPSHOT/maven-metadata.xml in local (/home/ross/.m2/repository)
[DEBUG] Failure to find org.xml-cml:norma:0.1-SNAPSHOT/maven-metadata.xml in http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo-snapshots/ was cached in the local repository, resolution will not be reattempted until the update interval of ebi-repo-snapshots has elapsed or updates are forced
[DEBUG] Failure to find org.xml-cml:norma:0.1-SNAPSHOT/maven-metadata.xml in http://www.ebi.ac.uk/~maven/m2repo was cached in the local repository, resolution will not be reattempted until the update interval of ebi-repo-3rd has elapsed or updates are forced
[DEBUG] Skipped remote update check for org.xml-cml:norma:0.1-SNAPSHOT/maven-metadata.xml, locally cached metadata up-to-date.
[DEBUG] Could not find metadata org.xml-cml:cmine:0.1-SNAPSHOT/maven-metadata.xml in local (/home/ross/.m2/repository)
[DEBUG] Failure to find org.xml-cml:cmine:0.1-SNAPSHOT/maven-metadata.xml in http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo-snapshots/ was cached in the local repository, resolution will not be reattempted until the update interval of ebi-repo-snapshots has elapsed or updates are forced
[DEBUG] Failure to find org.xml-cml:cmine:0.1-SNAPSHOT/maven-metadata.xml in http://www.ebi.ac.uk/~maven/m2repo was cached in the local repository, resolution will not be reattempted until the update interval of ebi-repo-3rd has elapsed or updates are forced
[DEBUG] Skipped remote update check for org.xml-cml:cmine:0.1-SNAPSHOT/maven-metadata.xml, locally cached metadata up-to-date.
[DEBUG] Could not find metadata org.xml-cml:html:0.2-SNAPSHOT/maven-metadata.xml in local (/home/ross/.m2/repository)
[DEBUG] Failure to find org.xml-cml:html:0.2-SNAPSHOT/maven-metadata.xml in http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo-snapshots/ was cached in the local repository, resolution will not be reattempted until the update interval of ebi-repo-snapshots has elapsed or updates are forced
[DEBUG] Failure to find org.xml-cml:html:0.2-SNAPSHOT/maven-metadata.xml in http://www.ebi.ac.uk/~maven/m2repo was cached in the local repository, resolution will not be reattempted until the update interval of ebi-repo-3rd has elapsed or updates are forced
[DEBUG] Skipped remote update check for org.xml-cml:html:0.2-SNAPSHOT/maven-metadata.xml, locally cached metadata up-to-date.
[DEBUG] Could not find metadata org.xml-cml:svg:0.2-SNAPSHOT/maven-metadata.xml in local (/home/ross/.m2/repository)
[DEBUG] Failure to find org.xml-cml:svg:0.2-SNAPSHOT/maven-metadata.xml in http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo-snapshots/ was cached in the local repository, resolution will not be reattempted until the update interval of ebi-repo-snapshots has elapsed or updates are forced
[DEBUG] Failure to find org.xml-cml:svg:0.2-SNAPSHOT/maven-metadata.xml in http://www.ebi.ac.uk/~maven/m2repo was cached in the local repository, resolution will not be reattempted until the update interval of ebi-repo-3rd has elapsed or updates are forced
[DEBUG] Skipped remote update check for org.xml-cml:svg:0.2-SNAPSHOT/maven-metadata.xml, locally cached metadata up-to-date.
[DEBUG] Failure to find org.xml-cml:euclid:1.1-SNAPSHOT/maven-metadata.xml in http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo-snapshots/ was cached in the local repository, resolution will not be reattempted until the update interval of ebi-repo-snapshots has elapsed or updates are forced
[DEBUG] Failure to find org.xml-cml:euclid:1.1-SNAPSHOT/maven-metadata.xml in http://www.ebi.ac.uk/~maven/m2repo was cached in the local repository, resolution will not be reattempted until the update interval of ebi-repo-3rd has elapsed or updates are forced
[DEBUG] Skipped remote update check for org.xml-cml:euclid:1.1-SNAPSHOT/maven-metadata.xml, locally cached metadata up-to-date.
[DEBUG] Could not find metadata uk.ac.cam.ch.wwmm:wwmm-parent:5-SNAPSHOT/maven-metadata.xml in local (/home/ross/.m2/repository)
[DEBUG] Failure to find uk.ac.cam.ch.wwmm:wwmm-parent:5-SNAPSHOT/maven-metadata.xml in http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo-snapshots/ was cached in the local repository, resolution will not be reattempted until the update interval of ebi-repo-snapshots has elapsed or updates are forced
[DEBUG] Failure to find uk.ac.cam.ch.wwmm:wwmm-parent:5-SNAPSHOT/maven-metadata.xml in http://www.ebi.ac.uk/~maven/m2repo was cached in the local repository, resolution will not be reattempted until the update interval of ebi-repo-3rd has elapsed or updates are forced
[DEBUG] Skipped remote update check for uk.ac.cam.ch.wwmm:wwmm-parent:5-SNAPSHOT/maven-metadata.xml, locally cached metadata up-to-date.
[DEBUG] Could not find metadata org.xml-cml:svg2xml:0.1-SNAPSHOT/maven-metadata.xml in local (/home/ross/.m2/repository)
[DEBUG] Failure to find org.xml-cml:svg2xml:0.1-SNAPSHOT/maven-metadata.xml in http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo-snapshots/ was cached in the local repository, resolution will not be reattempted until the update interval of ebi-repo-snapshots has elapsed or updates are forced
[DEBUG] Failure to find org.xml-cml:svg2xml:0.1-SNAPSHOT/maven-metadata.xml in http://www.ebi.ac.uk/~maven/m2repo was cached in the local repository, resolution will not be reattempted until the update interval of ebi-repo-3rd has elapsed or updates are forced
[DEBUG] Skipped remote update check for org.xml-cml:svg2xml:0.1-SNAPSHOT/maven-metadata.xml, locally cached metadata up-to-date.
[DEBUG] Could not find metadata org.xml-cml:pdf2svg:1.1-SNAPSHOT/maven-metadata.xml in local (/home/ross/.m2/repository)
[DEBUG] Failure to find org.xml-cml:pdf2svg:1.1-SNAPSHOT/maven-metadata.xml in http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo-snapshots/ was cached in the local repository, resolution will not be reattempted until the update interval of ebi-repo-snapshots has elapsed or updates are forced
[DEBUG] Failure to find org.xml-cml:pdf2svg:1.1-SNAPSHOT/maven-metadata.xml in http://www.ebi.ac.uk/~maven/m2repo was cached in the local repository, resolution will not be reattempted until the update interval of ebi-repo-3rd has elapsed or updates are forced
[DEBUG] Skipped remote update check for org.xml-cml:pdf2svg:1.1-SNAPSHOT/maven-metadata.xml, locally cached metadata up-to-date.
[DEBUG] Could not find metadata org.xml-cml:imageanalysis:0.1-SNAPSHOT/maven-metadata.xml in local (/home/ross/.m2/repository)
[DEBUG] Failure to find org.xml-cml:imageanalysis:0.1-SNAPSHOT/maven-metadata.xml in http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo-snapshots/ was cached in the local repository, resolution will not be reattempted until the update interval of ebi-repo-snapshots has elapsed or updates are forced
[DEBUG] Failure to find org.xml-cml:imageanalysis:0.1-SNAPSHOT/maven-metadata.xml in http://www.ebi.ac.uk/~maven/m2repo was cached in the local repository, resolution will not be reattempted until the update interval of ebi-repo-3rd has elapsed or updates are forced
[DEBUG] Skipped remote update check for org.xml-cml:imageanalysis:0.1-SNAPSHOT/maven-metadata.xml, locally cached metadata up-to-date.
[DEBUG] Could not find metadata org.xml-cml:svgbuilder:0.1-SNAPSHOT/maven-metadata.xml in local (/home/ross/.m2/repository)
[DEBUG] Failure to find org.xml-cml:svgbuilder:0.1-SNAPSHOT/maven-metadata.xml in http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo-snapshots/ was cached in the local repository, resolution will not be reattempted until the update interval of ebi-repo-snapshots has elapsed or updates are forced
[DEBUG] Failure to find org.xml-cml:svgbuilder:0.1-SNAPSHOT/maven-metadata.xml in http://www.ebi.ac.uk/~maven/m2repo was cached in the local repository, resolution will not be reattempted until the update interval of ebi-repo-3rd has elapsed or updates are forced
[DEBUG] Skipped remote update check for org.xml-cml:svgbuilder:0.1-SNAPSHOT/maven-metadata.xml, locally cached metadata up-to-date.
[DEBUG] Could not find metadata org.xml-cml:diagramanalyzer:0.1-SNAPSHOT/maven-metadata.xml in local (/home/ross/.m2/repository)
[DEBUG] Failure to find org.xml-cml:diagramanalyzer:0.1-SNAPSHOT/maven-metadata.xml in http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo-snapshots/ was cached in the local repository, resolution will not be reattempted until the update interval of ebi-repo-snapshots has elapsed or updates are forced
[DEBUG] Failure to find org.xml-cml:diagramanalyzer:0.1-SNAPSHOT/maven-metadata.xml in http://www.ebi.ac.uk/~maven/m2repo was cached in the local repository, resolution will not be reattempted until the update interval of ebi-repo-3rd has elapsed or updates are forced
[DEBUG] Skipped remote update check for org.xml-cml:diagramanalyzer:0.1-SNAPSHOT/maven-metadata.xml, locally cached metadata up-to-date.
[DEBUG] Could not find metadata org.xml-cml:javaocrnew:0.1-SNAPSHOT/maven-metadata.xml in local (/home/ross/.m2/repository)
[DEBUG] Failure to find org.xml-cml:javaocrnew:0.1-SNAPSHOT/maven-metadata.xml in http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo-snapshots/ was cached in the local repository, resolution will not be reattempted until the update interval of ebi-repo-snapshots has elapsed or updates are forced
[DEBUG] Failure to find org.xml-cml:javaocrnew:0.1-SNAPSHOT/maven-metadata.xml in http://www.ebi.ac.uk/~maven/m2repo was cached in the local repository, resolution will not be reattempted until the update interval of ebi-repo-3rd has elapsed or updates are forced
[DEBUG] Skipped remote update check for org.xml-cml:javaocrnew:0.1-SNAPSHOT/maven-metadata.xml, locally cached metadata up-to-date.
[DEBUG] org.xml-cml:ami2:jar:0.1-SNAPSHOT
[DEBUG]    org.xml-cml:norma:jar:0.1-SNAPSHOT:compile
[DEBUG]       org.xml-cml:cmine:jar:0.1-SNAPSHOT:compile
[DEBUG]          org.xml-cml:html:jar:0.2-SNAPSHOT:compile
[DEBUG]             org.xml-cml:svg:jar:0.2-SNAPSHOT:compile
[DEBUG]                org.xml-cml:euclid:jar:1.1-SNAPSHOT:compile
[DEBUG]                   log4j:log4j:jar:1.2.16:compile
[DEBUG]                   org.apache.commons:commons-math:jar:2.2:compile
[DEBUG]                   joda-time:joda-time:jar:1.6.2:compile
[DEBUG]                   xom:xom:jar:1.2.5:compile
[DEBUG]             xml-apis:xml-apis:jar:1.4.01:compile
[DEBUG]             jtidy:jtidy:jar:4aug2000r7-dev:compile
[DEBUG]             org.ccil.cowan.tagsoup:tagsoup:jar:1.2:compile
[DEBUG]             net.sourceforge.htmlunit:htmlunit:jar:2.15:compile
[DEBUG]                xalan:xalan:jar:2.7.1:compile
[DEBUG]                   xalan:serializer:jar:2.7.1:compile
[DEBUG]                commons-collections:commons-collections:jar:3.2.1:compile
[DEBUG]                org.apache.commons:commons-lang3:jar:3.3.2:compile
[DEBUG]                org.apache.httpcomponents:httpclient:jar:4.3.3:compile
[DEBUG]                   org.apache.httpcomponents:httpcore:jar:4.3.2:compile
[DEBUG]                org.apache.httpcomponents:httpmime:jar:4.3.3:compile
[DEBUG]                commons-codec:commons-codec:jar:1.9:compile
[DEBUG]                net.sourceforge.htmlunit:htmlunit-core-js:jar:2.15:compile
[DEBUG]                xerces:xercesImpl:jar:2.11.0:compile
[DEBUG]                net.sourceforge.nekohtml:nekohtml:jar:1.9.21:compile
[DEBUG]                net.sourceforge.cssparser:cssparser:jar:0.9.14:compile
[DEBUG]                   org.w3c.css:sac:jar:1.3:compile
[DEBUG]                commons-logging:commons-logging:jar:1.1.3:compile
[DEBUG]                org.eclipse.jetty:jetty-websocket:jar:8.1.15.v20140411:compile
[DEBUG]                   org.eclipse.jetty:jetty-util:jar:8.1.15.v20140411:compile
[DEBUG]                   org.eclipse.jetty:jetty-io:jar:8.1.15.v20140411:compile
[DEBUG]                   org.eclipse.jetty:jetty-http:jar:8.1.15.v20140411:compile
[DEBUG]          com.google.code.gson:gson:jar:2.3.1:compile
[DEBUG]       net.sf.saxon:Saxon-HE:jar:9.6.0-3:compile
[DEBUG]       org.xml-cml:svg2xml:jar:0.1-SNAPSHOT:compile
[DEBUG]          org.xml-cml:pdf2svg:jar:1.1-SNAPSHOT:compile
[DEBUG]             org.apache.pdfbox:pdfbox:jar:1.8.8:compile
[DEBUG]                org.apache.pdfbox:fontbox:jar:1.8.8:compile
[DEBUG]                org.apache.pdfbox:jempbox:jar:1.8.8:compile
[DEBUG]             org.bouncycastle:bcprov-jdk16:jar:1.46:compile
[DEBUG]       org.jsoup:jsoup:jar:1.8.2:compile
[DEBUG]       xmlunit:xmlunit:jar:1.4:compile
[DEBUG]    org.xml-cml:diagramanalyzer:jar:0.1-SNAPSHOT:compile
[DEBUG]       org.xml-cml:javaocrnew:jar:0.1-SNAPSHOT:compile
[DEBUG]          org.xml-cml:imageanalysis:jar:0.1-SNAPSHOT:compile
[DEBUG]             org.boofcv:io:jar:0.17:compile
[DEBUG]                org.ddogleg:ddogleg:jar:0.5:compile
[DEBUG]                org.boofcv:ip:jar:0.17:compile
[DEBUG]                com.thoughtworks.xstream:xstream:jar:1.4.7:compile
[DEBUG]                   xmlpull:xmlpull:jar:1.1.3.1:compile
[DEBUG]                   xpp3:xpp3_min:jar:1.1.4c:compile
[DEBUG]                org.georegression:georegression:jar:0.6:compile
[DEBUG]                com.googlecode.efficient-java-matrix-library:ejml:jar:0.25:compile
[DEBUG]             org.boofcv:feature:jar:0.17:compile
[DEBUG]             org.boofcv:visualize:jar:0.17:compile
[DEBUG]                org.boofcv:recognition:jar:0.17:compile
[DEBUG]                org.boofcv:sfm:jar:0.17:compile
[DEBUG]                   org.boofcv:calibration:jar:0.17:compile
[DEBUG]                org.boofcv:geo:jar:0.17:compile
[DEBUG]             org.imgscalr:imgscalr-lib:jar:4.2:compile
[DEBUG]       org.xml-cml:svgbuilder:jar:0.1-SNAPSHOT:compile
[DEBUG]          com.google.code.findbugs:jsr305:jar:2.0.2:compile
[DEBUG]    org.apache.lucene:lucene-core:jar:4.10.3:compile
[DEBUG]    org.apache.lucene:lucene-analyzers-common:jar:4.10.3:compile
[DEBUG]    com.google.guava:guava:jar:18.0:compile
[DEBUG]    junit:junit:jar:4.11:test
[DEBUG]       org.hamcrest:hamcrest-core:jar:1.3:test
[DEBUG]    blogspot.software-and-algorithms:stern-library:jar:0.1:compile
[DEBUG]    org.vafer:jdeb:jar:1.3:provided
[DEBUG]       commons-io:commons-io:jar:2.4:compile
[DEBUG]       org.apache.commons:commons-compress:jar:1.7:provided
[DEBUG]          org.tukaani:xz:jar:1.4:provided
[DEBUG]       org.apache.maven:maven-core:jar:3.2.2:provided
[DEBUG]          org.apache.maven:maven-model:jar:3.2.2:provided
[DEBUG]          org.apache.maven:maven-settings:jar:3.2.2:provided
[DEBUG]          org.apache.maven:maven-settings-builder:jar:3.2.2:provided
[DEBUG]          org.apache.maven:maven-repository-metadata:jar:3.2.2:provided
[DEBUG]          org.apache.maven:maven-artifact:jar:3.2.2:provided
[DEBUG]          org.apache.maven:maven-model-builder:jar:3.2.2:provided
[DEBUG]          org.apache.maven:maven-aether-provider:jar:3.2.2:provided
[DEBUG]             org.eclipse.aether:aether-spi:jar:0.9.0.M2:provided
[DEBUG]          org.eclipse.aether:aether-impl:jar:0.9.0.M2:provided
[DEBUG]          org.eclipse.aether:aether-api:jar:0.9.0.M2:provided
[DEBUG]          org.eclipse.aether:aether-util:jar:0.9.0.M2:provided
[DEBUG]          org.eclipse.sisu:org.eclipse.sisu.plexus:jar:0.0.0.M5:provided
[DEBUG]             javax.enterprise:cdi-api:jar:1.0:provided
[DEBUG]                javax.annotation:jsr250-api:jar:1.0:provided
[DEBUG]                javax.inject:javax.inject:jar:1:provided
[DEBUG]             org.sonatype.sisu:sisu-guice:jar:no_aop:3.1.0:provided
[DEBUG]                aopalliance:aopalliance:jar:1.0:provided
[DEBUG]             org.eclipse.sisu:org.eclipse.sisu.inject:jar:0.0.0.M5:provided
[DEBUG]          org.codehaus.plexus:plexus-interpolation:jar:1.19:provided
[DEBUG]          org.codehaus.plexus:plexus-utils:jar:3.0.17:provided
[DEBUG]          org.codehaus.plexus:plexus-classworlds:jar:2.5.1:provided
[DEBUG]          org.codehaus.plexus:plexus-component-annotations:jar:1.5.5:provided
[DEBUG]          org.sonatype.plexus:plexus-sec-dispatcher:jar:1.3:provided
[DEBUG]             org.sonatype.plexus:plexus-cipher:jar:1.4:provided
[DEBUG]       org.apache.maven:maven-plugin-api:jar:3.2.2:provided
[DEBUG]       org.apache.ant:ant:jar:1.9.3:provided
[DEBUG]          org.apache.ant:ant-launcher:jar:1.9.3:provided
[DEBUG]       org.bouncycastle:bcpg-jdk15on:jar:1.51:provided
[DEBUG]          org.bouncycastle:bcprov-jdk15on:jar:1.51:provided
[DEBUG]    com.jayway.jsonpath:json-path:jar:2.0.0:compile
[DEBUG]       org.slf4j:slf4j-api:jar:1.7.10:compile
[DEBUG]       net.minidev:json-smart:jar:2.1.1:compile
[DEBUG]          net.minidev:asm:jar:1.0.2:compile
[DEBUG]             asm:asm:jar:3.3.1:compile
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ ami2 ---
[DEBUG] Created new class realm maven.api
[DEBUG] Importing foreign packages into class realm maven.api
[DEBUG]   Imported: org.apache.maven.wagon.events < plexus.core
[DEBUG]   Imported: org.sonatype.aether.transfer < plexus.core
[DEBUG]   Imported: org.apache.maven.exception < plexus.core
[DEBUG]   Imported: org.sonatype.aether.metadata < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.util.xml.Xpp3Dom < plexus.core
[DEBUG]   Imported: org.sonatype.aether.collection < plexus.core
[DEBUG]   Imported: org.sonatype.aether.version < plexus.core
[DEBUG]   Imported: org.apache.maven.monitor < plexus.core
[DEBUG]   Imported: org.apache.maven.wagon.repository < plexus.core
[DEBUG]   Imported: org.apache.maven.repository < plexus.core
[DEBUG]   Imported: org.apache.maven.wagon.resource < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.logging < plexus.core
[DEBUG]   Imported: org.apache.maven.profiles < plexus.core
[DEBUG]   Imported: org.sonatype.aether.repository < plexus.core
[DEBUG]   Imported: org.apache.maven.classrealm < plexus.core
[DEBUG]   Imported: org.apache.maven.execution < plexus.core
[DEBUG]   Imported: org.sonatype.aether.artifact < plexus.core
[DEBUG]   Imported: org.sonatype.aether.spi < plexus.core
[DEBUG]   Imported: org.apache.maven.reporting < plexus.core
[DEBUG]   Imported: org.apache.maven.usability < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.container < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.component < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.util.xml.pull.XmlSerializer < plexus.core
[DEBUG]   Imported: org.apache.maven.wagon.authentication < plexus.core
[DEBUG]   Imported: org.apache.maven.lifecycle < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.classworlds < plexus.core
[DEBUG]   Imported: org.sonatype.aether.graph < plexus.core
[DEBUG]   Imported: org.sonatype.aether.* < plexus.core
[DEBUG]   Imported: org.apache.maven.settings < plexus.core
[DEBUG]   Imported: org.codehaus.classworlds < plexus.core
[DEBUG]   Imported: org.sonatype.aether.impl < plexus.core
[DEBUG]   Imported: org.apache.maven.wagon.* < plexus.core
[DEBUG]   Imported: org.apache.maven.toolchain < plexus.core
[DEBUG]   Imported: org.sonatype.aether.deployment < plexus.core
[DEBUG]   Imported: org.apache.maven.wagon.observers < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.util.xml.pull.XmlPullParserException < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.util.xml.pull.XmlPullParser < plexus.core
[DEBUG]   Imported: org.apache.maven.configuration < plexus.core
[DEBUG]   Imported: org.apache.maven.cli < plexus.core
[DEBUG]   Imported: org.sonatype.aether.installation < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.context < plexus.core
[DEBUG]   Imported: org.apache.maven.wagon.authorization < plexus.core
[DEBUG]   Imported: org.apache.maven.project < plexus.core
[DEBUG]   Imported: org.apache.maven.rtinfo < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.lifecycle < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.configuration < plexus.core
[DEBUG]   Imported: org.apache.maven.artifact < plexus.core
[DEBUG]   Imported: org.apache.maven.model < plexus.core
[DEBUG]   Imported: org.apache.maven.* < plexus.core
[DEBUG]   Imported: org.apache.maven.wagon.proxy < plexus.core
[DEBUG]   Imported: org.sonatype.aether.resolution < plexus.core
[DEBUG]   Imported: org.apache.maven.plugin < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.* < plexus.core
[DEBUG]   Imported: org.codehaus.plexus.personality < plexus.core
[DEBUG] Populating class realm maven.api
[DEBUG] org.apache.maven.plugins:maven-clean-plugin:jar:2.5:
[DEBUG]    org.apache.maven:maven-plugin-api:jar:2.0.6:compile
[DEBUG]    org.codehaus.plexus:plexus-utils:jar:3.0:compile
[DEBUG] Created new class realm plugin>org.apache.maven.plugins:maven-clean-plugin:2.5
[DEBUG] Importing foreign packages into class realm plugin>org.apache.maven.plugins:maven-clean-plugin:2.5
[DEBUG]   Imported:  < maven.api
[DEBUG] Populating class realm plugin>org.apache.maven.plugins:maven-clean-plugin:2.5
[DEBUG]   Included: org.apache.maven.plugins:maven-clean-plugin:jar:2.5
[DEBUG]   Included: org.codehaus.plexus:plexus-utils:jar:3.0
[DEBUG]   Excluded: org.apache.maven:maven-plugin-api:jar:2.0.6
[DEBUG] Configuring mojo org.apache.maven.plugins:maven-clean-plugin:2.5:clean from plugin realm ClassRealm[plugin>org.apache.maven.plugins:maven-clean-plugin:2.5, parent: sun.misc.Launcher$AppClassLoader@10b28f30]
[DEBUG] Configuring mojo 'org.apache.maven.plugins:maven-clean-plugin:2.5:clean' with basic configurator -->
[DEBUG]   (f) directory = /home/ross/workspace/pluto-20150818/ami-plugin/target
[DEBUG]   (f) excludeDefaultDirectories = false
[DEBUG]   (f) failOnError = true
[DEBUG]   (f) followSymLinks = false
[DEBUG]   (f) outputDirectory = /home/ross/workspace/pluto-20150818/ami-plugin/target/classes
[DEBUG]   (f) reportDirectory = /home/ross/workspace/pluto-20150818/ami-plugin/target/site
[DEBUG]   (f) retryOnError = true
[DEBUG]   (f) skip = false
[DEBUG]   (f) testOutputDirectory = /home/ross/workspace/pluto-20150818/ami-plugin/target/test-classes
[DEBUG] -- end configuration --
[INFO] Deleting /home/ross/workspace/pluto-20150818/ami-plugin/target
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/tagger/plosone/documentTagger.xml
[INFO] Deleting directory /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/tagger/plosone
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/tagger/hindawi/documentTagger.xml
[INFO] Deleting directory /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/tagger/hindawi
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/tagger/bmc/documentTagger.xml
[INFO] Deleting directory /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/tagger/bmc
[INFO] Deleting directory /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/tagger
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/am1.dot.png
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/sequence/args.xml
[INFO] Deleting directory /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/sequence
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/args.xml
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/identifier/args.xml
[INFO] Deleting directory /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/identifier
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/gene/args.xml
[INFO] Deleting directory /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/gene
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/species/args.xml
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/species/speciesFromLinnaeus.tsv
[INFO] Deleting directory /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/species
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/simple/args.xml
[INFO] Deleting directory /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/simple
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/ami.dot
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/regex/args.xml
[INFO] Deleting directory /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/regex
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/clinicaltrials.xml
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/clinicaltrials200.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stopwords.pub.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_slovak_1_sk.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_danish_1_da.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_greek_1_el.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_brazil_1_br.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_russian_1_ru.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_english_1_en.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_greek_2_el.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_czech_3_cz.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_swedish_2_sv.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_chinese_1_zh.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_swedish_1_sv.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_french_1_fr.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_portugese_1_pt.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_romanian_1_ro.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_italian_1_it.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_english_3_en.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_german_1_de.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_czech_1_cz.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_norwegian_2_no.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_persian_1_fa.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_bulgarian_1_bg.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_dutch_1_nl.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_czech_2_cz.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_dutch_2_nl.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_portugese_2_pt.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_polish_2_pl.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_turkish_1_tr.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_indonesian_1_id.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_japanese_1_ja.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_finnish_2_fi.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_turkish_2_tr.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_polish_3_pl.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_norwegian_1_no.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_polish_1_pl.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_slovak_2_sk.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_hindi_1_hi.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_hungarian_1_hu.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_english_2_en.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_spanish_1_es.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_german_2_de.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_french_2_fr.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_arabic_2_ar.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_arabic_1_ar.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_english_6_en.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_catalan_1_ca.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_finnish_1_fi.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_hungarian_2_hu.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_italian_2_it.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_spanish_2_es.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_russian_2_ru.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_latvian_1_lv.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_english_5_en.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_english_4_google_en.txt
[INFO] Deleting directory /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/project-information.txt
[INFO] Deleting directory /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stopwords.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/args.xml
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words_spanish_es.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stopwords.fr.txt
[INFO] Deleting directory /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/phylotree/genus.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/phylotree/binomial.txt
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/phylotree/args.xml
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/phylotree/ijsemNew.xml
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/phylotree/ijsemSpeciesEditor.xml
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/phylotree/ijsem.xml
[INFO] Deleting directory /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/phylotree
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/ami.dot.png
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/graphchem/args.xml
[INFO] Deleting directory /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/graphchem
[INFO] Deleting directory /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins
[INFO] Deleting directory /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2
[INFO] Deleting directory /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml
[INFO] Deleting directory /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org
[INFO] Deleting file /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/log4j.properties
[INFO] Deleting directory /home/ross/workspace/pluto-20150818/ami-plugin/target/classes
[INFO] Deleting directory /home/ross/workspace/pluto-20150818/ami-plugin/target
[DEBUG] Skipping non-existing directory /home/ross/workspace/pluto-20150818/ami-plugin/target/classes
[DEBUG] Skipping non-existing directory /home/ross/workspace/pluto-20150818/ami-plugin/target/test-classes
[DEBUG] Skipping non-existing directory /home/ross/workspace/pluto-20150818/ami-plugin/target/site
[INFO] 
[INFO] --- maven-resources-plugin:2.3:resources (default-resources) @ ami2 ---
[DEBUG] org.apache.maven.plugins:maven-resources-plugin:jar:2.3:
[DEBUG]    org.apache.maven:maven-plugin-api:jar:2.0.6:compile
[DEBUG]    org.apache.maven:maven-project:jar:2.0.6:compile
[DEBUG]       org.apache.maven:maven-settings:jar:2.0.6:compile
[DEBUG]       org.apache.maven:maven-profile:jar:2.0.6:compile
[DEBUG]       org.apache.maven:maven-model:jar:2.0.6:compile
[DEBUG]       org.apache.maven:maven-artifact-manager:jar:2.0.6:compile
[DEBUG]          org.apache.maven:maven-repository-metadata:jar:2.0.6:compile
[DEBUG]       org.apache.maven:maven-plugin-registry:jar:2.0.6:compile
[DEBUG]       org.apache.maven:maven-artifact:jar:2.0.6:compile
[DEBUG]       org.codehaus.plexus:plexus-container-default:jar:1.0-alpha-9-stable-1:compile
[DEBUG]          junit:junit:jar:3.8.1:compile
[DEBUG]          classworlds:classworlds:jar:1.1-alpha-2:compile
[DEBUG]    org.codehaus.plexus:plexus-utils:jar:1.5.6:compile
[DEBUG]    org.apache.maven.shared:maven-filtering:jar:1.0-beta-2:compile
[DEBUG]       org.apache.maven:maven-core:jar:2.0.6:compile
[DEBUG]          org.apache.maven:maven-plugin-parameter-documenter:jar:2.0.6:compile
[DEBUG]          org.apache.maven.reporting:maven-reporting-api:jar:2.0.6:compile
[DEBUG]             org.apache.maven.doxia:doxia-sink-api:jar:1.0-alpha-7:compile
[DEBUG]          org.apache.maven:maven-error-diagnostics:jar:2.0.6:compile
[DEBUG]          commons-cli:commons-cli:jar:1.0:compile
[DEBUG]          org.apache.maven:maven-plugin-descriptor:jar:2.0.6:compile
[DEBUG]          org.codehaus.plexus:plexus-interactivity-api:jar:1.0-alpha-4:compile
[DEBUG]       org.apache.maven:maven-monitor:jar:2.0.6:compile
[DEBUG]       org.codehaus.plexus:plexus-interpolation:jar:1.6:compile
[DEBUG] Created new class realm plugin>org.apache.maven.plugins:maven-resources-plugin:2.3
[DEBUG] Importing foreign packages into class realm plugin>org.apache.maven.plugins:maven-resources-plugin:2.3
[DEBUG]   Imported:  < maven.api
[DEBUG] Populating class realm plugin>org.apache.maven.plugins:maven-resources-plugin:2.3
[DEBUG]   Included: org.apache.maven.plugins:maven-resources-plugin:jar:2.3
[DEBUG]   Included: junit:junit:jar:3.8.1
[DEBUG]   Included: org.codehaus.plexus:plexus-utils:jar:1.5.6
[DEBUG]   Included: org.apache.maven.shared:maven-filtering:jar:1.0-beta-2
[DEBUG]   Included: org.apache.maven.reporting:maven-reporting-api:jar:2.0.6
[DEBUG]   Included: org.apache.maven.doxia:doxia-sink-api:jar:1.0-alpha-7
[DEBUG]   Included: commons-cli:commons-cli:jar:1.0
[DEBUG]   Included: org.codehaus.plexus:plexus-interactivity-api:jar:1.0-alpha-4
[DEBUG]   Included: org.codehaus.plexus:plexus-interpolation:jar:1.6
[DEBUG]   Excluded: org.apache.maven:maven-plugin-api:jar:2.0.6
[DEBUG]   Excluded: org.apache.maven:maven-project:jar:2.0.6
[DEBUG]   Excluded: org.apache.maven:maven-settings:jar:2.0.6
[DEBUG]   Excluded: org.apache.maven:maven-profile:jar:2.0.6
[DEBUG]   Excluded: org.apache.maven:maven-model:jar:2.0.6
[DEBUG]   Excluded: org.apache.maven:maven-artifact-manager:jar:2.0.6
[DEBUG]   Excluded: org.apache.maven:maven-repository-metadata:jar:2.0.6
[DEBUG]   Excluded: org.apache.maven:maven-plugin-registry:jar:2.0.6
[DEBUG]   Excluded: org.apache.maven:maven-artifact:jar:2.0.6
[DEBUG]   Excluded: org.codehaus.plexus:plexus-container-default:jar:1.0-alpha-9-stable-1
[DEBUG]   Excluded: classworlds:classworlds:jar:1.1-alpha-2
[DEBUG]   Excluded: org.apache.maven:maven-core:jar:2.0.6
[DEBUG]   Excluded: org.apache.maven:maven-plugin-parameter-documenter:jar:2.0.6
[DEBUG]   Excluded: org.apache.maven:maven-error-diagnostics:jar:2.0.6
[DEBUG]   Excluded: org.apache.maven:maven-plugin-descriptor:jar:2.0.6
[DEBUG]   Excluded: org.apache.maven:maven-monitor:jar:2.0.6
[DEBUG] Configuring mojo org.apache.maven.plugins:maven-resources-plugin:2.3:resources from plugin realm ClassRealm[plugin>org.apache.maven.plugins:maven-resources-plugin:2.3, parent: sun.misc.Launcher$AppClassLoader@10b28f30]
[DEBUG] Configuring mojo 'org.apache.maven.plugins:maven-resources-plugin:2.3:resources' with basic configurator -->
[DEBUG]   (f) filters = []
[DEBUG]   (s) includeEmptyDirs = false
[DEBUG]   (s) outputDirectory = /home/ross/workspace/pluto-20150818/ami-plugin/target/classes
[DEBUG]   (s) overwrite = false
[DEBUG]   (f) project = MavenProject: org.xml-cml:ami2:0.1-SNAPSHOT @ /home/ross/workspace/pluto-20150818/ami-plugin/pom.xml
[DEBUG]   (s) resources = [Resource {targetPath: null, filtering: false, FileSet {directory: /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources, PatternSet [includes: {}, excludes: {}]}}]
[DEBUG]   (f) session = org.apache.maven.execution.MavenSession@723e7e4c
[DEBUG] -- end configuration --
[DEBUG] properties used {java.vendor=Oracle Corporation, env.IM_CONFIG_PHASE=1, env.PVM_ROOT=/usr/lib/pvm3, env.LESSOPEN=| /usr/bin/lesspipe %s, env.NVM_BIN=/home/ross/.nvm/v0.10.38/bin, env._LXSESSION_PID=1678, sun.java.launcher=SUN_STANDARD, env.QT_IM_MODULE=xim, sun.management.compiler=HotSpot 64-Bit Tiered Compilers, os.name=Linux, env.UPSTART_SESSION=unix:abstract=/com/ubuntu/upstart-session/1000/1518, sun.boot.class.path=/usr/lib/jvm/java-7-oracle/jre/lib/resources.jar:/usr/lib/jvm/java-7-oracle/jre/lib/rt.jar:/usr/lib/jvm/java-7-oracle/jre/lib/sunrsasign.jar:/usr/lib/jvm/java-7-oracle/jre/lib/jsse.jar:/usr/lib/jvm/java-7-oracle/jre/lib/jce.jar:/usr/lib/jvm/java-7-oracle/jre/lib/charsets.jar:/usr/lib/jvm/java-7-oracle/jre/lib/jfr.jar:/usr/lib/jvm/java-7-oracle/jre/classes, env.PWD=/home/ross/workspace/pluto-20150818/ami-plugin, env.LANG=en_GB.UTF-8, java.vm.specification.vendor=Oracle Corporation, env.XDG_MENU_PREFIX=lxde-, java.runtime.version=1.7.0_80-b15, env.GTK_IM_MODULE=xim, env.DEFAULTS_PATH=/usr/share/gconf/Lubuntu.default.path, env.UPSTART_EVENTS=started xsession, env.XDG_VTNR=7, env.DISPLAY=:0.0, user.name=ross, env.QT4_IM_MODULE=xim, env._=/usr/bin/mvn, maven.build.version=Apache Maven 3.0.5, env.USER=ross, env.SHELL=/bin/bash, env.DESKTOP_SESSION=Lubuntu, env.XDG_DATA_DIRS=/etc/xdg/lubuntu:/usr/local/share:/usr/share:/usr/share/gdm:/var/lib/menu-xdg:/usr/share/Lubuntu:/usr/local/share/:/usr/share/, env.NLSPATH=/usr/dt/lib/nls/msg/%L/%N.cat, env.NODE_PATH=/usr/lib/nodejs:/usr/lib/node_modules:/usr/share/javascript, env.PATH=/home/ross/.nvm/v0.10.38/bin:/home/ross/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/ross/.rvm/bin:/home/ross/.rvm/bin, env.XDG_CURRENT_DESKTOP=LXDE, user.language=en, sun.boot.library.path=/usr/lib/jvm/java-7-oracle/jre/lib/amd64, classworlds.conf=/usr/share/maven/bin/m2.conf, env.TEXTDOMAIN=im-config, env.UPSTART_JOB=lxsession, env.SELINUX_INIT=YES, java.version=1.7.0_80, user.timezone=, env.DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-sNPBztzgwX, sun.arch.data.model=64, java.endorsed.dirs=/usr/lib/jvm/java-7-oracle/jre/lib/endorsed, sun.cpu.isalist=, sun.jnu.encoding=UTF-8, file.encoding.pkg=sun.io, env.SHLVL=1, file.separator=/, java.specification.name=Java Platform API Specification, java.class.version=51.0, env.GDMSESSION=Lubuntu, user.country=GB, env.GNOME_KEYRING_PID=, java.home=/usr/lib/jvm/java-7-oracle/jre, java.vm.info=mixed mode, env.LOGNAME=ross, os.version=3.13.0-61-generic, env.SAL_USE_VCLPLUGIN=gtk, env.NVM_IOJS_ORG_VERSION_LISTING=https://iojs.org/dist/index.tab, path.separator=:, java.vm.version=24.80-b11, env.UPSTART_INSTANCE=, env.LANGUAGE=en_GB:en, env.TEXTDOMAINDIR=/usr/share/locale/, env.XDG_SESSION_PATH=/org/freedesktop/DisplayManager/Session0, env.NVM_NODEJS_ORG_MIRROR=https://nodejs.org/dist, env.SESSIONTYPE=lxsession, env.JAVA_HOME=/usr/lib/jvm/java-7-oracle/jre/, env.TERM=xterm, java.awt.printerjob=sun.print.PSPrinterJob, sun.io.unicode.encoding=UnicodeLittle, awt.toolkit=sun.awt.X11.XToolkit, env.XMODIFIERS=@im=ibus, env.MANPATH=/home/ross/.nvm/v0.10.38/share/man:/home/ross/share/man:/usr/local/man:/usr/local/share/man:/usr/share/man:/home/ross/.rvm/man, env.GDM_LANG=en_GB, user.home=/home/ross, env.JOB=dbus, env.OLDPWD=/home/ross/workspace/pluto-20150818/ami-plugin, java.specification.vendor=Oracle Corporation, guava.version=18.0, java.vendor.url=http://java.oracle.com/, java.library.path=/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib, env.XDG_SEAT=seat0, java.vm.vendor=Oracle Corporation, java.runtime.name=Java(TM) SE Runtime Environment, maven.home=/usr/share/maven, java.class.path=/usr/share/maven/boot/plexus-classworlds-2.x.jar, sun.java.command=org.codehaus.plexus.classworlds.launcher.Launcher clean install -X, env.XDG_SESSION_ID=c1, maven.version=3.0.5, env.XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt, java.vm.specification.name=Java Virtual Machine Specification, java.vm.specification.version=1.7, sun.os.patch.level=unknown, sun.cpu.endian=little, env.HOME=/home/ross, env.XDG_SEAT_PATH=/org/freedesktop/DisplayManager/Seat0, env.LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lz=01;31:*.xz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.axa=00;36:*.oga=00;36:*.spx=00;36:*.xspf=00;36:, java.io.tmpdir=/tmp, env.NVM_PATH=/home/ross/.nvm/v0.10.38/lib/node, java.vendor.url.bug=http://bugreport.sun.com/bugreport/, env.SSH_AUTH_SOCK=/run/user/1000/keyring-PRHk5f/ssh, env.XDG_CONFIG_HOME=/home/ross/.config, env.CLUTTER_IM_MODULE=xim, java.awt.graphicsenv=sun.awt.X11GraphicsEnvironment, os.arch=amd64, env.INSTANCE=, env.XDG_RUNTIME_DIR=/run/user/1000, java.ext.dirs=/usr/lib/jvm/java-7-oracle/jre/lib/ext:/usr/java/packages/lib/ext, env.XAUTHORITY=/home/ross/.Xauthority, env.SESSION=Lubuntu, user.dir=/home/ross/workspace/pluto-20150818/ami-plugin, env.MANDATORY_PATH=/usr/share/gconf/Lubuntu.mandatory.path, line.separator=
, java.vm.name=Java HotSpot(TM) 64-Bit Server VM, env.NVM_IOJS_ORG_MIRROR=https://iojs.org/dist, env.XDG_GREETER_DATA_DIR=/var/lib/lightdm-data/ross, file.encoding=UTF-8, env.NVM_DIR=/home/ross/.nvm, env.GPG_AGENT_INFO=/run/user/1000/keyring-PRHk5f/gpg:0:1, java.specification.version=1.7, env.GNOME_KEYRING_CONTROL=/run/user/1000/keyring-PRHk5f, env.XDG_CONFIG_DIRS=/etc/xdg/lubuntu:/etc/xdg/xdg-Lubuntu:/usr/share/upstart/xdg:/etc/xdg, env.LESSCLOSE=/usr/bin/lesspipe %s %s}
[WARNING] Using platform encoding (UTF-8 actually) to copy filtered resources, i.e. build is platform dependent!
[DEBUG] resource with targetPath null
directory /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources
excludes []
includes []
[INFO] Copying 83 resources
[DEBUG] file log4j.properties has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/log4j.properties to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/log4j.properties
[DEBUG] file args.xml has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/graphchem/args.xml to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/graphchem/args.xml
[DEBUG] file ami.dot.png has a non filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/ami.dot.png to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/ami.dot.png
[DEBUG] file ijsem.xml has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/phylotree/ijsem.xml to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/phylotree/ijsem.xml
[DEBUG] file ijsemSpeciesEditor.xml has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/phylotree/ijsemSpeciesEditor.xml to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/phylotree/ijsemSpeciesEditor.xml
[DEBUG] file ijsemNew.xml has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/phylotree/ijsemNew.xml to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/phylotree/ijsemNew.xml
[DEBUG] file args.xml has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/phylotree/args.xml to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/phylotree/args.xml
[DEBUG] file binomial.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/phylotree/binomial.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/phylotree/binomial.txt
[DEBUG] file genus.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/phylotree/genus.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/phylotree/genus.txt
[DEBUG] file stopwords.fr.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stopwords.fr.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stopwords.fr.txt
[DEBUG] file stop-words_spanish_es.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words_spanish_es.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words_spanish_es.txt
[DEBUG] file args.xml has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/args.xml to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/args.xml
[DEBUG] file stopwords.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stopwords.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stopwords.txt
[DEBUG] file project-information.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/project-information.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/project-information.txt
[DEBUG] file stop-words_english_4_google_en.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_english_4_google_en.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_english_4_google_en.txt
[DEBUG] file stop-words_english_5_en.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_english_5_en.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_english_5_en.txt
[DEBUG] file stop-words_latvian_1_lv.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_latvian_1_lv.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_latvian_1_lv.txt
[DEBUG] file stop-words_russian_2_ru.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_russian_2_ru.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_russian_2_ru.txt
[DEBUG] file stop-words_spanish_2_es.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_spanish_2_es.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_spanish_2_es.txt
[DEBUG] file stop-words_italian_2_it.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_italian_2_it.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_italian_2_it.txt
[DEBUG] file stop-words_hungarian_2_hu.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_hungarian_2_hu.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_hungarian_2_hu.txt
[DEBUG] file stop-words_finnish_1_fi.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_finnish_1_fi.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_finnish_1_fi.txt
[DEBUG] file stop-words_catalan_1_ca.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_catalan_1_ca.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_catalan_1_ca.txt
[DEBUG] file stop-words_english_6_en.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_english_6_en.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_english_6_en.txt
[DEBUG] file stop-words_arabic_1_ar.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_arabic_1_ar.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_arabic_1_ar.txt
[DEBUG] file stop-words_arabic_2_ar.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_arabic_2_ar.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_arabic_2_ar.txt
[DEBUG] file stop-words_french_2_fr.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_french_2_fr.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_french_2_fr.txt
[DEBUG] file stop-words_german_2_de.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_german_2_de.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_german_2_de.txt
[DEBUG] file stop-words_spanish_1_es.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_spanish_1_es.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_spanish_1_es.txt
[DEBUG] file stop-words_english_2_en.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_english_2_en.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_english_2_en.txt
[DEBUG] file stop-words_hungarian_1_hu.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_hungarian_1_hu.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_hungarian_1_hu.txt
[DEBUG] file stop-words_hindi_1_hi.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_hindi_1_hi.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_hindi_1_hi.txt
[DEBUG] file stop-words_slovak_2_sk.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_slovak_2_sk.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_slovak_2_sk.txt
[DEBUG] file stop-words_polish_1_pl.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_polish_1_pl.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_polish_1_pl.txt
[DEBUG] file stop-words_norwegian_1_no.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_norwegian_1_no.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_norwegian_1_no.txt
[DEBUG] file stop-words_polish_3_pl.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_polish_3_pl.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_polish_3_pl.txt
[DEBUG] file stop-words_turkish_2_tr.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_turkish_2_tr.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_turkish_2_tr.txt
[DEBUG] file stop-words_finnish_2_fi.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_finnish_2_fi.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_finnish_2_fi.txt
[DEBUG] file stop-words_japanese_1_ja.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_japanese_1_ja.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_japanese_1_ja.txt
[DEBUG] file stop-words_indonesian_1_id.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_indonesian_1_id.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_indonesian_1_id.txt
[DEBUG] file stop-words_turkish_1_tr.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_turkish_1_tr.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_turkish_1_tr.txt
[DEBUG] file stop-words_polish_2_pl.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_polish_2_pl.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_polish_2_pl.txt
[DEBUG] file stop-words_portugese_2_pt.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_portugese_2_pt.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_portugese_2_pt.txt
[DEBUG] file stop-words_dutch_2_nl.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_dutch_2_nl.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_dutch_2_nl.txt
[DEBUG] file stop-words_czech_2_cz.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_czech_2_cz.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_czech_2_cz.txt
[DEBUG] file stop-words_dutch_1_nl.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_dutch_1_nl.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_dutch_1_nl.txt
[DEBUG] file stop-words_bulgarian_1_bg.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_bulgarian_1_bg.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_bulgarian_1_bg.txt
[DEBUG] file stop-words_persian_1_fa.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_persian_1_fa.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_persian_1_fa.txt
[DEBUG] file stop-words_norwegian_2_no.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_norwegian_2_no.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_norwegian_2_no.txt
[DEBUG] file stop-words_czech_1_cz.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_czech_1_cz.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_czech_1_cz.txt
[DEBUG] file stop-words_german_1_de.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_german_1_de.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_german_1_de.txt
[DEBUG] file stop-words_english_3_en.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_english_3_en.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_english_3_en.txt
[DEBUG] file stop-words_italian_1_it.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_italian_1_it.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_italian_1_it.txt
[DEBUG] file stop-words_romanian_1_ro.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_romanian_1_ro.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_romanian_1_ro.txt
[DEBUG] file stop-words_portugese_1_pt.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_portugese_1_pt.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_portugese_1_pt.txt
[DEBUG] file stop-words_french_1_fr.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_french_1_fr.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_french_1_fr.txt
[DEBUG] file stop-words_swedish_1_sv.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_swedish_1_sv.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_swedish_1_sv.txt
[DEBUG] file stop-words_chinese_1_zh.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_chinese_1_zh.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_chinese_1_zh.txt
[DEBUG] file stop-words_swedish_2_sv.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_swedish_2_sv.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_swedish_2_sv.txt
[DEBUG] file stop-words_czech_3_cz.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_czech_3_cz.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_czech_3_cz.txt
[DEBUG] file stop-words_greek_2_el.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_greek_2_el.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_greek_2_el.txt
[DEBUG] file stop-words_english_1_en.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_english_1_en.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_english_1_en.txt
[DEBUG] file stop-words_russian_1_ru.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_russian_1_ru.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_russian_1_ru.txt
[DEBUG] file stop-words_brazil_1_br.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_brazil_1_br.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_brazil_1_br.txt
[DEBUG] file stop-words_greek_1_el.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_greek_1_el.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_greek_1_el.txt
[DEBUG] file stop-words_danish_1_da.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_danish_1_da.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_danish_1_da.txt
[DEBUG] file stop-words_slovak_1_sk.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_slovak_1_sk.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stop-words-collection-2014-02-24/stop-words/stop-words_slovak_1_sk.txt
[DEBUG] file stopwords.pub.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/stopwords.pub.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/stopwords.pub.txt
[DEBUG] file clinicaltrials200.txt has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/clinicaltrials200.txt to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/clinicaltrials200.txt
[DEBUG] file clinicaltrials.xml has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/word/clinicaltrials.xml to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/word/clinicaltrials.xml
[DEBUG] file args.xml has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/regex/args.xml to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/regex/args.xml
[DEBUG] file ami.dot has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/ami.dot to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/ami.dot
[DEBUG] file args.xml has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/simple/args.xml to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/simple/args.xml
[DEBUG] file speciesFromLinnaeus.tsv has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/species/speciesFromLinnaeus.tsv to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/species/speciesFromLinnaeus.tsv
[DEBUG] file args.xml has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/species/args.xml to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/species/args.xml
[DEBUG] file args.xml has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/gene/args.xml to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/gene/args.xml
[DEBUG] file args.xml has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/identifier/args.xml to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/identifier/args.xml
[DEBUG] file args.xml has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/args.xml to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/args.xml
[DEBUG] file args.xml has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/sequence/args.xml to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/sequence/args.xml
[DEBUG] file am1.dot.png has a non filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/plugins/am1.dot.png to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/plugins/am1.dot.png
[DEBUG] file documentTagger.xml has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/tagger/bmc/documentTagger.xml to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/tagger/bmc/documentTagger.xml
[DEBUG] file documentTagger.xml has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/tagger/hindawi/documentTagger.xml to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/tagger/hindawi/documentTagger.xml
[DEBUG] file documentTagger.xml has a filtered file extension
[DEBUG] copy /home/ross/workspace/pluto-20150818/ami-plugin/src/main/resources/org/xmlcml/ami2/tagger/plosone/documentTagger.xml to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes/org/xmlcml/ami2/tagger/plosone/documentTagger.xml
[INFO] 
[INFO] --- maven-compiler-plugin:2.0.2:compile (default-compile) @ ami2 ---
[DEBUG] org.apache.maven.plugins:maven-compiler-plugin:jar:2.0.2:
[DEBUG]    org.apache.maven:maven-plugin-api:jar:2.0:compile
[DEBUG]    org.codehaus.plexus:plexus-utils:jar:1.0.4:compile
[DEBUG]    org.codehaus.plexus:plexus-compiler-api:jar:1.5.3:compile
[DEBUG]       org.codehaus.plexus:plexus-container-default:jar:1.0-alpha-8:compile
[DEBUG]          junit:junit:jar:3.8.1:compile
[DEBUG]          classworlds:classworlds:jar:1.1-alpha-2:compile
[DEBUG]    org.codehaus.plexus:plexus-compiler-manager:jar:1.5.3:compile
[DEBUG]    org.codehaus.plexus:plexus-compiler-javac:jar:1.5.3:runtime
[DEBUG]    org.apache.maven:maven-artifact:jar:2.0:compile
[DEBUG] Created new class realm plugin>org.apache.maven.plugins:maven-compiler-plugin:2.0.2
[DEBUG] Importing foreign packages into class realm plugin>org.apache.maven.plugins:maven-compiler-plugin:2.0.2
[DEBUG]   Imported:  < maven.api
[DEBUG] Populating class realm plugin>org.apache.maven.plugins:maven-compiler-plugin:2.0.2
[DEBUG]   Included: org.apache.maven.plugins:maven-compiler-plugin:jar:2.0.2
[DEBUG]   Included: org.codehaus.plexus:plexus-utils:jar:1.0.4
[DEBUG]   Included: org.codehaus.plexus:plexus-compiler-api:jar:1.5.3
[DEBUG]   Included: junit:junit:jar:3.8.1
[DEBUG]   Included: org.codehaus.plexus:plexus-compiler-manager:jar:1.5.3
[DEBUG]   Included: org.codehaus.plexus:plexus-compiler-javac:jar:1.5.3
[DEBUG]   Excluded: org.apache.maven:maven-plugin-api:jar:2.0
[DEBUG]   Excluded: org.codehaus.plexus:plexus-container-default:jar:1.0-alpha-8
[DEBUG]   Excluded: classworlds:classworlds:jar:1.1-alpha-2
[DEBUG]   Excluded: org.apache.maven:maven-artifact:jar:2.0
[DEBUG] Configuring mojo org.apache.maven.plugins:maven-compiler-plugin:2.0.2:compile from plugin realm ClassRealm[plugin>org.apache.maven.plugins:maven-compiler-plugin:2.0.2, parent: sun.misc.Launcher$AppClassLoader@10b28f30]
[DEBUG] Configuring mojo 'org.apache.maven.plugins:maven-compiler-plugin:2.0.2:compile' with basic configurator -->
[DEBUG]   (f) basedir = /home/ross/workspace/pluto-20150818/ami-plugin
[DEBUG]   (f) buildDirectory = /home/ross/workspace/pluto-20150818/ami-plugin/target
[DEBUG]   (f) classpathElements = [/home/ross/workspace/pluto-20150818/ami-plugin/target/classes, /home/ross/.m2/repository/org/xml-cml/norma/0.1-SNAPSHOT/norma-0.1-SNAPSHOT.jar, /home/ross/.m2/repository/org/xml-cml/cmine/0.1-SNAPSHOT/cmine-0.1-SNAPSHOT.jar, /home/ross/.m2/repository/org/xml-cml/html/0.2-SNAPSHOT/html-0.2-SNAPSHOT.jar, /home/ross/.m2/repository/org/xml-cml/svg/0.2-SNAPSHOT/svg-0.2-SNAPSHOT.jar, /home/ross/.m2/repository/org/xml-cml/euclid/1.1-SNAPSHOT/euclid-1.1-SNAPSHOT.jar, /home/ross/.m2/repository/log4j/log4j/1.2.16/log4j-1.2.16.jar, /home/ross/.m2/repository/org/apache/commons/commons-math/2.2/commons-math-2.2.jar, /home/ross/.m2/repository/joda-time/joda-time/1.6.2/joda-time-1.6.2.jar, /home/ross/.m2/repository/xom/xom/1.2.5/xom-1.2.5.jar, /home/ross/.m2/repository/xml-apis/xml-apis/1.4.01/xml-apis-1.4.01.jar, /home/ross/.m2/repository/jtidy/jtidy/4aug2000r7-dev/jtidy-4aug2000r7-dev.jar, /home/ross/.m2/repository/org/ccil/cowan/tagsoup/tagsoup/1.2/tagsoup-1.2.jar, /home/ross/.m2/repository/net/sourceforge/htmlunit/htmlunit/2.15/htmlunit-2.15.jar, /home/ross/.m2/repository/xalan/xalan/2.7.1/xalan-2.7.1.jar, /home/ross/.m2/repository/xalan/serializer/2.7.1/serializer-2.7.1.jar, /home/ross/.m2/repository/commons-collections/commons-collections/3.2.1/commons-collections-3.2.1.jar, /home/ross/.m2/repository/org/apache/commons/commons-lang3/3.3.2/commons-lang3-3.3.2.jar, /home/ross/.m2/repository/org/apache/httpcomponents/httpclient/4.3.3/httpclient-4.3.3.jar, /home/ross/.m2/repository/org/apache/httpcomponents/httpcore/4.3.2/httpcore-4.3.2.jar, /home/ross/.m2/repository/org/apache/httpcomponents/httpmime/4.3.3/httpmime-4.3.3.jar, /home/ross/.m2/repository/commons-codec/commons-codec/1.9/commons-codec-1.9.jar, /home/ross/.m2/repository/net/sourceforge/htmlunit/htmlunit-core-js/2.15/htmlunit-core-js-2.15.jar, /home/ross/.m2/repository/xerces/xercesImpl/2.11.0/xercesImpl-2.11.0.jar, /home/ross/.m2/repository/net/sourceforge/nekohtml/nekohtml/1.9.21/nekohtml-1.9.21.jar, /home/ross/.m2/repository/net/sourceforge/cssparser/cssparser/0.9.14/cssparser-0.9.14.jar, /home/ross/.m2/repository/org/w3c/css/sac/1.3/sac-1.3.jar, /home/ross/.m2/repository/commons-logging/commons-logging/1.1.3/commons-logging-1.1.3.jar, /home/ross/.m2/repository/org/eclipse/jetty/jetty-websocket/8.1.15.v20140411/jetty-websocket-8.1.15.v20140411.jar, /home/ross/.m2/repository/org/eclipse/jetty/jetty-util/8.1.15.v20140411/jetty-util-8.1.15.v20140411.jar, /home/ross/.m2/repository/org/eclipse/jetty/jetty-io/8.1.15.v20140411/jetty-io-8.1.15.v20140411.jar, /home/ross/.m2/repository/org/eclipse/jetty/jetty-http/8.1.15.v20140411/jetty-http-8.1.15.v20140411.jar, /home/ross/.m2/repository/com/google/code/gson/gson/2.3.1/gson-2.3.1.jar, /home/ross/.m2/repository/net/sf/saxon/Saxon-HE/9.6.0-3/Saxon-HE-9.6.0-3.jar, /home/ross/.m2/repository/org/xml-cml/svg2xml/0.1-SNAPSHOT/svg2xml-0.1-SNAPSHOT.jar, /home/ross/.m2/repository/org/xml-cml/pdf2svg/1.1-SNAPSHOT/pdf2svg-1.1-SNAPSHOT.jar, /home/ross/.m2/repository/org/apache/pdfbox/pdfbox/1.8.8/pdfbox-1.8.8.jar, /home/ross/.m2/repository/org/apache/pdfbox/fontbox/1.8.8/fontbox-1.8.8.jar, /home/ross/.m2/repository/org/apache/pdfbox/jempbox/1.8.8/jempbox-1.8.8.jar, /home/ross/.m2/repository/org/bouncycastle/bcprov-jdk16/1.46/bcprov-jdk16-1.46.jar, /home/ross/.m2/repository/org/jsoup/jsoup/1.8.2/jsoup-1.8.2.jar, /home/ross/.m2/repository/xmlunit/xmlunit/1.4/xmlunit-1.4.jar, /home/ross/.m2/repository/org/xml-cml/diagramanalyzer/0.1-SNAPSHOT/diagramanalyzer-0.1-SNAPSHOT.jar, /home/ross/.m2/repository/org/xml-cml/javaocrnew/0.1-SNAPSHOT/javaocrnew-0.1-SNAPSHOT.jar, /home/ross/.m2/repository/org/xml-cml/imageanalysis/0.1-SNAPSHOT/imageanalysis-0.1-SNAPSHOT.jar, /home/ross/.m2/repository/org/boofcv/io/0.17/io-0.17.jar, /home/ross/.m2/repository/org/ddogleg/ddogleg/0.5/ddogleg-0.5.jar, /home/ross/.m2/repository/org/boofcv/ip/0.17/ip-0.17.jar, /home/ross/.m2/repository/com/thoughtworks/xstream/xstream/1.4.7/xstream-1.4.7.jar, /home/ross/.m2/repository/xmlpull/xmlpull/1.1.3.1/xmlpull-1.1.3.1.jar, /home/ross/.m2/repository/xpp3/xpp3_min/1.1.4c/xpp3_min-1.1.4c.jar, /home/ross/.m2/repository/org/georegression/georegression/0.6/georegression-0.6.jar, /home/ross/.m2/repository/com/googlecode/efficient-java-matrix-library/ejml/0.25/ejml-0.25.jar, /home/ross/.m2/repository/org/boofcv/feature/0.17/feature-0.17.jar, /home/ross/.m2/repository/org/boofcv/visualize/0.17/visualize-0.17.jar, /home/ross/.m2/repository/org/boofcv/recognition/0.17/recognition-0.17.jar, /home/ross/.m2/repository/org/boofcv/sfm/0.17/sfm-0.17.jar, /home/ross/.m2/repository/org/boofcv/calibration/0.17/calibration-0.17.jar, /home/ross/.m2/repository/org/boofcv/geo/0.17/geo-0.17.jar, /home/ross/.m2/repository/org/imgscalr/imgscalr-lib/4.2/imgscalr-lib-4.2.jar, /home/ross/.m2/repository/org/xml-cml/svgbuilder/0.1-SNAPSHOT/svgbuilder-0.1-SNAPSHOT.jar, /home/ross/.m2/repository/com/google/code/findbugs/jsr305/2.0.2/jsr305-2.0.2.jar, /home/ross/.m2/repository/org/apache/lucene/lucene-core/4.10.3/lucene-core-4.10.3.jar, /home/ross/.m2/repository/org/apache/lucene/lucene-analyzers-common/4.10.3/lucene-analyzers-common-4.10.3.jar, /home/ross/.m2/repository/com/google/guava/guava/18.0/guava-18.0.jar, /home/ross/.m2/repository/blogspot/software-and-algorithms/stern-library/0.1/stern-library-0.1.jar, /home/ross/.m2/repository/org/vafer/jdeb/1.3/jdeb-1.3.jar, /home/ross/.m2/repository/commons-io/commons-io/2.4/commons-io-2.4.jar, /home/ross/.m2/repository/org/apache/commons/commons-compress/1.7/commons-compress-1.7.jar, /home/ross/.m2/repository/org/tukaani/xz/1.4/xz-1.4.jar, /home/ross/.m2/repository/org/apache/maven/maven-core/3.2.2/maven-core-3.2.2.jar, /home/ross/.m2/repository/org/apache/maven/maven-model/3.2.2/maven-model-3.2.2.jar, /home/ross/.m2/repository/org/apache/maven/maven-settings/3.2.2/maven-settings-3.2.2.jar, /home/ross/.m2/repository/org/apache/maven/maven-settings-builder/3.2.2/maven-settings-builder-3.2.2.jar, /home/ross/.m2/repository/org/apache/maven/maven-repository-metadata/3.2.2/maven-repository-metadata-3.2.2.jar, /home/ross/.m2/repository/org/apache/maven/maven-artifact/3.2.2/maven-artifact-3.2.2.jar, /home/ross/.m2/repository/org/apache/maven/maven-model-builder/3.2.2/maven-model-builder-3.2.2.jar, /home/ross/.m2/repository/org/apache/maven/maven-aether-provider/3.2.2/maven-aether-provider-3.2.2.jar, /home/ross/.m2/repository/org/eclipse/aether/aether-spi/0.9.0.M2/aether-spi-0.9.0.M2.jar, /home/ross/.m2/repository/org/eclipse/aether/aether-impl/0.9.0.M2/aether-impl-0.9.0.M2.jar, /home/ross/.m2/repository/org/eclipse/aether/aether-api/0.9.0.M2/aether-api-0.9.0.M2.jar, /home/ross/.m2/repository/org/eclipse/aether/aether-util/0.9.0.M2/aether-util-0.9.0.M2.jar, /home/ross/.m2/repository/org/eclipse/sisu/org.eclipse.sisu.plexus/0.0.0.M5/org.eclipse.sisu.plexus-0.0.0.M5.jar, /home/ross/.m2/repository/javax/enterprise/cdi-api/1.0/cdi-api-1.0.jar, /home/ross/.m2/repository/javax/annotation/jsr250-api/1.0/jsr250-api-1.0.jar, /home/ross/.m2/repository/javax/inject/javax.inject/1/javax.inject-1.jar, /home/ross/.m2/repository/org/sonatype/sisu/sisu-guice/3.1.0/sisu-guice-3.1.0-no_aop.jar, /home/ross/.m2/repository/aopalliance/aopalliance/1.0/aopalliance-1.0.jar, /home/ross/.m2/repository/org/eclipse/sisu/org.eclipse.sisu.inject/0.0.0.M5/org.eclipse.sisu.inject-0.0.0.M5.jar, /home/ross/.m2/repository/org/codehaus/plexus/plexus-interpolation/1.19/plexus-interpolation-1.19.jar, /home/ross/.m2/repository/org/codehaus/plexus/plexus-utils/3.0.17/plexus-utils-3.0.17.jar, /home/ross/.m2/repository/org/codehaus/plexus/plexus-classworlds/2.5.1/plexus-classworlds-2.5.1.jar, /home/ross/.m2/repository/org/codehaus/plexus/plexus-component-annotations/1.5.5/plexus-component-annotations-1.5.5.jar, /home/ross/.m2/repository/org/sonatype/plexus/plexus-sec-dispatcher/1.3/plexus-sec-dispatcher-1.3.jar, /home/ross/.m2/repository/org/sonatype/plexus/plexus-cipher/1.4/plexus-cipher-1.4.jar, /home/ross/.m2/repository/org/apache/maven/maven-plugin-api/3.2.2/maven-plugin-api-3.2.2.jar, /home/ross/.m2/repository/org/apache/ant/ant/1.9.3/ant-1.9.3.jar, /home/ross/.m2/repository/org/apache/ant/ant-launcher/1.9.3/ant-launcher-1.9.3.jar, /home/ross/.m2/repository/org/bouncycastle/bcpg-jdk15on/1.51/bcpg-jdk15on-1.51.jar, /home/ross/.m2/repository/org/bouncycastle/bcprov-jdk15on/1.51/bcprov-jdk15on-1.51.jar, /home/ross/.m2/repository/com/jayway/jsonpath/json-path/2.0.0/json-path-2.0.0.jar, /home/ross/.m2/repository/org/slf4j/slf4j-api/1.7.10/slf4j-api-1.7.10.jar, /home/ross/.m2/repository/net/minidev/json-smart/2.1.1/json-smart-2.1.1.jar, /home/ross/.m2/repository/net/minidev/asm/1.0.2/asm-1.0.2.jar, /home/ross/.m2/repository/asm/asm/3.3.1/asm-3.3.1.jar]
[DEBUG]   (f) compileSourceRoots = [/home/ross/workspace/pluto-20150818/ami-plugin/src/main/java]
[DEBUG]   (f) compilerId = javac
[DEBUG]   (f) debug = true
[DEBUG]   (f) failOnError = true
[DEBUG]   (f) fork = false
[DEBUG]   (f) optimize = false
[DEBUG]   (f) outputDirectory = /home/ross/workspace/pluto-20150818/ami-plugin/target/classes
[DEBUG]   (f) outputFileName = ami2-0.1-SNAPSHOT
[DEBUG]   (f) projectArtifact = org.xml-cml:ami2:jar:0.1-SNAPSHOT
[DEBUG]   (f) showDeprecation = false
[DEBUG]   (f) showWarnings = false
[DEBUG]   (f) staleMillis = 0
[DEBUG]   (f) verbose = false
[DEBUG] -- end configuration --
[DEBUG] Using compiler 'javac'.
[DEBUG] Source directories: [/home/ross/workspace/pluto-20150818/ami-plugin/src/main/java]
[DEBUG] Classpath: [/home/ross/workspace/pluto-20150818/ami-plugin/target/classes
 /home/ross/.m2/repository/org/xml-cml/norma/0.1-SNAPSHOT/norma-0.1-SNAPSHOT.jar
 /home/ross/.m2/repository/org/xml-cml/cmine/0.1-SNAPSHOT/cmine-0.1-SNAPSHOT.jar
 /home/ross/.m2/repository/org/xml-cml/html/0.2-SNAPSHOT/html-0.2-SNAPSHOT.jar
 /home/ross/.m2/repository/org/xml-cml/svg/0.2-SNAPSHOT/svg-0.2-SNAPSHOT.jar
 /home/ross/.m2/repository/org/xml-cml/euclid/1.1-SNAPSHOT/euclid-1.1-SNAPSHOT.jar
 /home/ross/.m2/repository/log4j/log4j/1.2.16/log4j-1.2.16.jar
 /home/ross/.m2/repository/org/apache/commons/commons-math/2.2/commons-math-2.2.jar
 /home/ross/.m2/repository/joda-time/joda-time/1.6.2/joda-time-1.6.2.jar
 /home/ross/.m2/repository/xom/xom/1.2.5/xom-1.2.5.jar
 /home/ross/.m2/repository/xml-apis/xml-apis/1.4.01/xml-apis-1.4.01.jar
 /home/ross/.m2/repository/jtidy/jtidy/4aug2000r7-dev/jtidy-4aug2000r7-dev.jar
 /home/ross/.m2/repository/org/ccil/cowan/tagsoup/tagsoup/1.2/tagsoup-1.2.jar
 /home/ross/.m2/repository/net/sourceforge/htmlunit/htmlunit/2.15/htmlunit-2.15.jar
 /home/ross/.m2/repository/xalan/xalan/2.7.1/xalan-2.7.1.jar
 /home/ross/.m2/repository/xalan/serializer/2.7.1/serializer-2.7.1.jar
 /home/ross/.m2/repository/commons-collections/commons-collections/3.2.1/commons-collections-3.2.1.jar
 /home/ross/.m2/repository/org/apache/commons/commons-lang3/3.3.2/commons-lang3-3.3.2.jar
 /home/ross/.m2/repository/org/apache/httpcomponents/httpclient/4.3.3/httpclient-4.3.3.jar
 /home/ross/.m2/repository/org/apache/httpcomponents/httpcore/4.3.2/httpcore-4.3.2.jar
 /home/ross/.m2/repository/org/apache/httpcomponents/httpmime/4.3.3/httpmime-4.3.3.jar
 /home/ross/.m2/repository/commons-codec/commons-codec/1.9/commons-codec-1.9.jar
 /home/ross/.m2/repository/net/sourceforge/htmlunit/htmlunit-core-js/2.15/htmlunit-core-js-2.15.jar
 /home/ross/.m2/repository/xerces/xercesImpl/2.11.0/xercesImpl-2.11.0.jar
 /home/ross/.m2/repository/net/sourceforge/nekohtml/nekohtml/1.9.21/nekohtml-1.9.21.jar
 /home/ross/.m2/repository/net/sourceforge/cssparser/cssparser/0.9.14/cssparser-0.9.14.jar
 /home/ross/.m2/repository/org/w3c/css/sac/1.3/sac-1.3.jar
 /home/ross/.m2/repository/commons-logging/commons-logging/1.1.3/commons-logging-1.1.3.jar
 /home/ross/.m2/repository/org/eclipse/jetty/jetty-websocket/8.1.15.v20140411/jetty-websocket-8.1.15.v20140411.jar
 /home/ross/.m2/repository/org/eclipse/jetty/jetty-util/8.1.15.v20140411/jetty-util-8.1.15.v20140411.jar
 /home/ross/.m2/repository/org/eclipse/jetty/jetty-io/8.1.15.v20140411/jetty-io-8.1.15.v20140411.jar
 /home/ross/.m2/repository/org/eclipse/jetty/jetty-http/8.1.15.v20140411/jetty-http-8.1.15.v20140411.jar
 /home/ross/.m2/repository/com/google/code/gson/gson/2.3.1/gson-2.3.1.jar
 /home/ross/.m2/repository/net/sf/saxon/Saxon-HE/9.6.0-3/Saxon-HE-9.6.0-3.jar
 /home/ross/.m2/repository/org/xml-cml/svg2xml/0.1-SNAPSHOT/svg2xml-0.1-SNAPSHOT.jar
 /home/ross/.m2/repository/org/xml-cml/pdf2svg/1.1-SNAPSHOT/pdf2svg-1.1-SNAPSHOT.jar
 /home/ross/.m2/repository/org/apache/pdfbox/pdfbox/1.8.8/pdfbox-1.8.8.jar
 /home/ross/.m2/repository/org/apache/pdfbox/fontbox/1.8.8/fontbox-1.8.8.jar
 /home/ross/.m2/repository/org/apache/pdfbox/jempbox/1.8.8/jempbox-1.8.8.jar
 /home/ross/.m2/repository/org/bouncycastle/bcprov-jdk16/1.46/bcprov-jdk16-1.46.jar
 /home/ross/.m2/repository/org/jsoup/jsoup/1.8.2/jsoup-1.8.2.jar
 /home/ross/.m2/repository/xmlunit/xmlunit/1.4/xmlunit-1.4.jar
 /home/ross/.m2/repository/org/xml-cml/diagramanalyzer/0.1-SNAPSHOT/diagramanalyzer-0.1-SNAPSHOT.jar
 /home/ross/.m2/repository/org/xml-cml/javaocrnew/0.1-SNAPSHOT/javaocrnew-0.1-SNAPSHOT.jar
 /home/ross/.m2/repository/org/xml-cml/imageanalysis/0.1-SNAPSHOT/imageanalysis-0.1-SNAPSHOT.jar
 /home/ross/.m2/repository/org/boofcv/io/0.17/io-0.17.jar
 /home/ross/.m2/repository/org/ddogleg/ddogleg/0.5/ddogleg-0.5.jar
 /home/ross/.m2/repository/org/boofcv/ip/0.17/ip-0.17.jar
 /home/ross/.m2/repository/com/thoughtworks/xstream/xstream/1.4.7/xstream-1.4.7.jar
 /home/ross/.m2/repository/xmlpull/xmlpull/1.1.3.1/xmlpull-1.1.3.1.jar
 /home/ross/.m2/repository/xpp3/xpp3_min/1.1.4c/xpp3_min-1.1.4c.jar
 /home/ross/.m2/repository/org/georegression/georegression/0.6/georegression-0.6.jar
 /home/ross/.m2/repository/com/googlecode/efficient-java-matrix-library/ejml/0.25/ejml-0.25.jar
 /home/ross/.m2/repository/org/boofcv/feature/0.17/feature-0.17.jar
 /home/ross/.m2/repository/org/boofcv/visualize/0.17/visualize-0.17.jar
 /home/ross/.m2/repository/org/boofcv/recognition/0.17/recognition-0.17.jar
 /home/ross/.m2/repository/org/boofcv/sfm/0.17/sfm-0.17.jar
 /home/ross/.m2/repository/org/boofcv/calibration/0.17/calibration-0.17.jar
 /home/ross/.m2/repository/org/boofcv/geo/0.17/geo-0.17.jar
 /home/ross/.m2/repository/org/imgscalr/imgscalr-lib/4.2/imgscalr-lib-4.2.jar
 /home/ross/.m2/repository/org/xml-cml/svgbuilder/0.1-SNAPSHOT/svgbuilder-0.1-SNAPSHOT.jar
 /home/ross/.m2/repository/com/google/code/findbugs/jsr305/2.0.2/jsr305-2.0.2.jar
 /home/ross/.m2/repository/org/apache/lucene/lucene-core/4.10.3/lucene-core-4.10.3.jar
 /home/ross/.m2/repository/org/apache/lucene/lucene-analyzers-common/4.10.3/lucene-analyzers-common-4.10.3.jar
 /home/ross/.m2/repository/com/google/guava/guava/18.0/guava-18.0.jar
 /home/ross/.m2/repository/blogspot/software-and-algorithms/stern-library/0.1/stern-library-0.1.jar
 /home/ross/.m2/repository/org/vafer/jdeb/1.3/jdeb-1.3.jar
 /home/ross/.m2/repository/commons-io/commons-io/2.4/commons-io-2.4.jar
 /home/ross/.m2/repository/org/apache/commons/commons-compress/1.7/commons-compress-1.7.jar
 /home/ross/.m2/repository/org/tukaani/xz/1.4/xz-1.4.jar
 /home/ross/.m2/repository/org/apache/maven/maven-core/3.2.2/maven-core-3.2.2.jar
 /home/ross/.m2/repository/org/apache/maven/maven-model/3.2.2/maven-model-3.2.2.jar
 /home/ross/.m2/repository/org/apache/maven/maven-settings/3.2.2/maven-settings-3.2.2.jar
 /home/ross/.m2/repository/org/apache/maven/maven-settings-builder/3.2.2/maven-settings-builder-3.2.2.jar
 /home/ross/.m2/repository/org/apache/maven/maven-repository-metadata/3.2.2/maven-repository-metadata-3.2.2.jar
 /home/ross/.m2/repository/org/apache/maven/maven-artifact/3.2.2/maven-artifact-3.2.2.jar
 /home/ross/.m2/repository/org/apache/maven/maven-model-builder/3.2.2/maven-model-builder-3.2.2.jar
 /home/ross/.m2/repository/org/apache/maven/maven-aether-provider/3.2.2/maven-aether-provider-3.2.2.jar
 /home/ross/.m2/repository/org/eclipse/aether/aether-spi/0.9.0.M2/aether-spi-0.9.0.M2.jar
 /home/ross/.m2/repository/org/eclipse/aether/aether-impl/0.9.0.M2/aether-impl-0.9.0.M2.jar
 /home/ross/.m2/repository/org/eclipse/aether/aether-api/0.9.0.M2/aether-api-0.9.0.M2.jar
 /home/ross/.m2/repository/org/eclipse/aether/aether-util/0.9.0.M2/aether-util-0.9.0.M2.jar
 /home/ross/.m2/repository/org/eclipse/sisu/org.eclipse.sisu.plexus/0.0.0.M5/org.eclipse.sisu.plexus-0.0.0.M5.jar
 /home/ross/.m2/repository/javax/enterprise/cdi-api/1.0/cdi-api-1.0.jar
 /home/ross/.m2/repository/javax/annotation/jsr250-api/1.0/jsr250-api-1.0.jar
 /home/ross/.m2/repository/javax/inject/javax.inject/1/javax.inject-1.jar
 /home/ross/.m2/repository/org/sonatype/sisu/sisu-guice/3.1.0/sisu-guice-3.1.0-no_aop.jar
 /home/ross/.m2/repository/aopalliance/aopalliance/1.0/aopalliance-1.0.jar
 /home/ross/.m2/repository/org/eclipse/sisu/org.eclipse.sisu.inject/0.0.0.M5/org.eclipse.sisu.inject-0.0.0.M5.jar
 /home/ross/.m2/repository/org/codehaus/plexus/plexus-interpolation/1.19/plexus-interpolation-1.19.jar
 /home/ross/.m2/repository/org/codehaus/plexus/plexus-utils/3.0.17/plexus-utils-3.0.17.jar
 /home/ross/.m2/repository/org/codehaus/plexus/plexus-classworlds/2.5.1/plexus-classworlds-2.5.1.jar
 /home/ross/.m2/repository/org/codehaus/plexus/plexus-component-annotations/1.5.5/plexus-component-annotations-1.5.5.jar
 /home/ross/.m2/repository/org/sonatype/plexus/plexus-sec-dispatcher/1.3/plexus-sec-dispatcher-1.3.jar
 /home/ross/.m2/repository/org/sonatype/plexus/plexus-cipher/1.4/plexus-cipher-1.4.jar
 /home/ross/.m2/repository/org/apache/maven/maven-plugin-api/3.2.2/maven-plugin-api-3.2.2.jar
 /home/ross/.m2/repository/org/apache/ant/ant/1.9.3/ant-1.9.3.jar
 /home/ross/.m2/repository/org/apache/ant/ant-launcher/1.9.3/ant-launcher-1.9.3.jar
 /home/ross/.m2/repository/org/bouncycastle/bcpg-jdk15on/1.51/bcpg-jdk15on-1.51.jar
 /home/ross/.m2/repository/org/bouncycastle/bcprov-jdk15on/1.51/bcprov-jdk15on-1.51.jar
 /home/ross/.m2/repository/com/jayway/jsonpath/json-path/2.0.0/json-path-2.0.0.jar
 /home/ross/.m2/repository/org/slf4j/slf4j-api/1.7.10/slf4j-api-1.7.10.jar
 /home/ross/.m2/repository/net/minidev/json-smart/2.1.1/json-smart-2.1.1.jar
 /home/ross/.m2/repository/net/minidev/asm/1.0.2/asm-1.0.2.jar
 /home/ross/.m2/repository/asm/asm/3.3.1/asm-3.3.1.jar]
[DEBUG] Output directory: /home/ross/workspace/pluto-20150818/ami-plugin/target/classes
[DEBUG] Classpath:
[DEBUG]  /home/ross/workspace/pluto-20150818/ami-plugin/target/classes
[DEBUG]  /home/ross/.m2/repository/org/xml-cml/norma/0.1-SNAPSHOT/norma-0.1-SNAPSHOT.jar
[DEBUG]  /home/ross/.m2/repository/org/xml-cml/cmine/0.1-SNAPSHOT/cmine-0.1-SNAPSHOT.jar
[DEBUG]  /home/ross/.m2/repository/org/xml-cml/html/0.2-SNAPSHOT/html-0.2-SNAPSHOT.jar
[DEBUG]  /home/ross/.m2/repository/org/xml-cml/svg/0.2-SNAPSHOT/svg-0.2-SNAPSHOT.jar
[DEBUG]  /home/ross/.m2/repository/org/xml-cml/euclid/1.1-SNAPSHOT/euclid-1.1-SNAPSHOT.jar
[DEBUG]  /home/ross/.m2/repository/log4j/log4j/1.2.16/log4j-1.2.16.jar
[DEBUG]  /home/ross/.m2/repository/org/apache/commons/commons-math/2.2/commons-math-2.2.jar
[DEBUG]  /home/ross/.m2/repository/joda-time/joda-time/1.6.2/joda-time-1.6.2.jar
[DEBUG]  /home/ross/.m2/repository/xom/xom/1.2.5/xom-1.2.5.jar
[DEBUG]  /home/ross/.m2/repository/xml-apis/xml-apis/1.4.01/xml-apis-1.4.01.jar
[DEBUG]  /home/ross/.m2/repository/jtidy/jtidy/4aug2000r7-dev/jtidy-4aug2000r7-dev.jar
[DEBUG]  /home/ross/.m2/repository/org/ccil/cowan/tagsoup/tagsoup/1.2/tagsoup-1.2.jar
[DEBUG]  /home/ross/.m2/repository/net/sourceforge/htmlunit/htmlunit/2.15/htmlunit-2.15.jar
[DEBUG]  /home/ross/.m2/repository/xalan/xalan/2.7.1/xalan-2.7.1.jar
[DEBUG]  /home/ross/.m2/repository/xalan/serializer/2.7.1/serializer-2.7.1.jar
[DEBUG]  /home/ross/.m2/repository/commons-collections/commons-collections/3.2.1/commons-collections-3.2.1.jar
[DEBUG]  /home/ross/.m2/repository/org/apache/commons/commons-lang3/3.3.2/commons-lang3-3.3.2.jar
[DEBUG]  /home/ross/.m2/repository/org/apache/httpcomponents/httpclient/4.3.3/httpclient-4.3.3.jar
[DEBUG]  /home/ross/.m2/repository/org/apache/httpcomponents/httpcore/4.3.2/httpcore-4.3.2.jar
[DEBUG]  /home/ross/.m2/repository/org/apache/httpcomponents/httpmime/4.3.3/httpmime-4.3.3.jar
[DEBUG]  /home/ross/.m2/repository/commons-codec/commons-codec/1.9/commons-codec-1.9.jar
[DEBUG]  /home/ross/.m2/repository/net/sourceforge/htmlunit/htmlunit-core-js/2.15/htmlunit-core-js-2.15.jar
[DEBUG]  /home/ross/.m2/repository/xerces/xercesImpl/2.11.0/xercesImpl-2.11.0.jar
[DEBUG]  /home/ross/.m2/repository/net/sourceforge/nekohtml/nekohtml/1.9.21/nekohtml-1.9.21.jar
[DEBUG]  /home/ross/.m2/repository/net/sourceforge/cssparser/cssparser/0.9.14/cssparser-0.9.14.jar
[DEBUG]  /home/ross/.m2/repository/org/w3c/css/sac/1.3/sac-1.3.jar
[DEBUG]  /home/ross/.m2/repository/commons-logging/commons-logging/1.1.3/commons-logging-1.1.3.jar
[DEBUG]  /home/ross/.m2/repository/org/eclipse/jetty/jetty-websocket/8.1.15.v20140411/jetty-websocket-8.1.15.v20140411.jar
[DEBUG]  /home/ross/.m2/repository/org/eclipse/jetty/jetty-util/8.1.15.v20140411/jetty-util-8.1.15.v20140411.jar
[DEBUG]  /home/ross/.m2/repository/org/eclipse/jetty/jetty-io/8.1.15.v20140411/jetty-io-8.1.15.v20140411.jar
[DEBUG]  /home/ross/.m2/repository/org/eclipse/jetty/jetty-http/8.1.15.v20140411/jetty-http-8.1.15.v20140411.jar
[DEBUG]  /home/ross/.m2/repository/com/google/code/gson/gson/2.3.1/gson-2.3.1.jar
[DEBUG]  /home/ross/.m2/repository/net/sf/saxon/Saxon-HE/9.6.0-3/Saxon-HE-9.6.0-3.jar
[DEBUG]  /home/ross/.m2/repository/org/xml-cml/svg2xml/0.1-SNAPSHOT/svg2xml-0.1-SNAPSHOT.jar
[DEBUG]  /home/ross/.m2/repository/org/xml-cml/pdf2svg/1.1-SNAPSHOT/pdf2svg-1.1-SNAPSHOT.jar
[DEBUG]  /home/ross/.m2/repository/org/apache/pdfbox/pdfbox/1.8.8/pdfbox-1.8.8.jar
[DEBUG]  /home/ross/.m2/repository/org/apache/pdfbox/fontbox/1.8.8/fontbox-1.8.8.jar
[DEBUG]  /home/ross/.m2/repository/org/apache/pdfbox/jempbox/1.8.8/jempbox-1.8.8.jar
[DEBUG]  /home/ross/.m2/repository/org/bouncycastle/bcprov-jdk16/1.46/bcprov-jdk16-1.46.jar
[DEBUG]  /home/ross/.m2/repository/org/jsoup/jsoup/1.8.2/jsoup-1.8.2.jar
[DEBUG]  /home/ross/.m2/repository/xmlunit/xmlunit/1.4/xmlunit-1.4.jar
[DEBUG]  /home/ross/.m2/repository/org/xml-cml/diagramanalyzer/0.1-SNAPSHOT/diagramanalyzer-0.1-SNAPSHOT.jar
[DEBUG]  /home/ross/.m2/repository/org/xml-cml/javaocrnew/0.1-SNAPSHOT/javaocrnew-0.1-SNAPSHOT.jar
[DEBUG]  /home/ross/.m2/repository/org/xml-cml/imageanalysis/0.1-SNAPSHOT/imageanalysis-0.1-SNAPSHOT.jar
[DEBUG]  /home/ross/.m2/repository/org/boofcv/io/0.17/io-0.17.jar
[DEBUG]  /home/ross/.m2/repository/org/ddogleg/ddogleg/0.5/ddogleg-0.5.jar
[DEBUG]  /home/ross/.m2/repository/org/boofcv/ip/0.17/ip-0.17.jar
[DEBUG]  /home/ross/.m2/repository/com/thoughtworks/xstream/xstream/1.4.7/xstream-1.4.7.jar
[DEBUG]  /home/ross/.m2/repository/xmlpull/xmlpull/1.1.3.1/xmlpull-1.1.3.1.jar
[DEBUG]  /home/ross/.m2/repository/xpp3/xpp3_min/1.1.4c/xpp3_min-1.1.4c.jar
[DEBUG]  /home/ross/.m2/repository/org/georegression/georegression/0.6/georegression-0.6.jar
[DEBUG]  /home/ross/.m2/repository/com/googlecode/efficient-java-matrix-library/ejml/0.25/ejml-0.25.jar
[DEBUG]  /home/ross/.m2/repository/org/boofcv/feature/0.17/feature-0.17.jar
[DEBUG]  /home/ross/.m2/repository/org/boofcv/visualize/0.17/visualize-0.17.jar
[DEBUG]  /home/ross/.m2/repository/org/boofcv/recognition/0.17/recognition-0.17.jar
[DEBUG]  /home/ross/.m2/repository/org/boofcv/sfm/0.17/sfm-0.17.jar
[DEBUG]  /home/ross/.m2/repository/org/boofcv/calibration/0.17/calibration-0.17.jar
[DEBUG]  /home/ross/.m2/repository/org/boofcv/geo/0.17/geo-0.17.jar
[DEBUG]  /home/ross/.m2/repository/org/imgscalr/imgscalr-lib/4.2/imgscalr-lib-4.2.jar
[DEBUG]  /home/ross/.m2/repository/org/xml-cml/svgbuilder/0.1-SNAPSHOT/svgbuilder-0.1-SNAPSHOT.jar
[DEBUG]  /home/ross/.m2/repository/com/google/code/findbugs/jsr305/2.0.2/jsr305-2.0.2.jar
[DEBUG]  /home/ross/.m2/repository/org/apache/lucene/lucene-core/4.10.3/lucene-core-4.10.3.jar
[DEBUG]  /home/ross/.m2/repository/org/apache/lucene/lucene-analyzers-common/4.10.3/lucene-analyzers-common-4.10.3.jar
[DEBUG]  /home/ross/.m2/repository/com/google/guava/guava/18.0/guava-18.0.jar
[DEBUG]  /home/ross/.m2/repository/blogspot/software-and-algorithms/stern-library/0.1/stern-library-0.1.jar
[DEBUG]  /home/ross/.m2/repository/org/vafer/jdeb/1.3/jdeb-1.3.jar
[DEBUG]  /home/ross/.m2/repository/commons-io/commons-io/2.4/commons-io-2.4.jar
[DEBUG]  /home/ross/.m2/repository/org/apache/commons/commons-compress/1.7/commons-compress-1.7.jar
[DEBUG]  /home/ross/.m2/repository/org/tukaani/xz/1.4/xz-1.4.jar
[DEBUG]  /home/ross/.m2/repository/org/apache/maven/maven-core/3.2.2/maven-core-3.2.2.jar
[DEBUG]  /home/ross/.m2/repository/org/apache/maven/maven-model/3.2.2/maven-model-3.2.2.jar
[DEBUG]  /home/ross/.m2/repository/org/apache/maven/maven-settings/3.2.2/maven-settings-3.2.2.jar
[DEBUG]  /home/ross/.m2/repository/org/apache/maven/maven-settings-builder/3.2.2/maven-settings-builder-3.2.2.jar
[DEBUG]  /home/ross/.m2/repository/org/apache/maven/maven-repository-metadata/3.2.2/maven-repository-metadata-3.2.2.jar
[DEBUG]  /home/ross/.m2/repository/org/apache/maven/maven-artifact/3.2.2/maven-artifact-3.2.2.jar
[DEBUG]  /home/ross/.m2/repository/org/apache/maven/maven-model-builder/3.2.2/maven-model-builder-3.2.2.jar
[DEBUG]  /home/ross/.m2/repository/org/apache/maven/maven-aether-provider/3.2.2/maven-aether-provider-3.2.2.jar
[DEBUG]  /home/ross/.m2/repository/org/eclipse/aether/aether-spi/0.9.0.M2/aether-spi-0.9.0.M2.jar
[DEBUG]  /home/ross/.m2/repository/org/eclipse/aether/aether-impl/0.9.0.M2/aether-impl-0.9.0.M2.jar
[DEBUG]  /home/ross/.m2/repository/org/eclipse/aether/aether-api/0.9.0.M2/aether-api-0.9.0.M2.jar
[DEBUG]  /home/ross/.m2/repository/org/eclipse/aether/aether-util/0.9.0.M2/aether-util-0.9.0.M2.jar
[DEBUG]  /home/ross/.m2/repository/org/eclipse/sisu/org.eclipse.sisu.plexus/0.0.0.M5/org.eclipse.sisu.plexus-0.0.0.M5.jar
[DEBUG]  /home/ross/.m2/repository/javax/enterprise/cdi-api/1.0/cdi-api-1.0.jar
[DEBUG]  /home/ross/.m2/repository/javax/annotation/jsr250-api/1.0/jsr250-api-1.0.jar
[DEBUG]  /home/ross/.m2/repository/javax/inject/javax.inject/1/javax.inject-1.jar
[DEBUG]  /home/ross/.m2/repository/org/sonatype/sisu/sisu-guice/3.1.0/sisu-guice-3.1.0-no_aop.jar
[DEBUG]  /home/ross/.m2/repository/aopalliance/aopalliance/1.0/aopalliance-1.0.jar
[DEBUG]  /home/ross/.m2/repository/org/eclipse/sisu/org.eclipse.sisu.inject/0.0.0.M5/org.eclipse.sisu.inject-0.0.0.M5.jar
[DEBUG]  /home/ross/.m2/repository/org/codehaus/plexus/plexus-interpolation/1.19/plexus-interpolation-1.19.jar
[DEBUG]  /home/ross/.m2/repository/org/codehaus/plexus/plexus-utils/3.0.17/plexus-utils-3.0.17.jar
[DEBUG]  /home/ross/.m2/repository/org/codehaus/plexus/plexus-classworlds/2.5.1/plexus-classworlds-2.5.1.jar
[DEBUG]  /home/ross/.m2/repository/org/codehaus/plexus/plexus-component-annotations/1.5.5/plexus-component-annotations-1.5.5.jar
[DEBUG]  /home/ross/.m2/repository/org/sonatype/plexus/plexus-sec-dispatcher/1.3/plexus-sec-dispatcher-1.3.jar
[DEBUG]  /home/ross/.m2/repository/org/sonatype/plexus/plexus-cipher/1.4/plexus-cipher-1.4.jar
[DEBUG]  /home/ross/.m2/repository/org/apache/maven/maven-plugin-api/3.2.2/maven-plugin-api-3.2.2.jar
[DEBUG]  /home/ross/.m2/repository/org/apache/ant/ant/1.9.3/ant-1.9.3.jar
[DEBUG]  /home/ross/.m2/repository/org/apache/ant/ant-launcher/1.9.3/ant-launcher-1.9.3.jar
[DEBUG]  /home/ross/.m2/repository/org/bouncycastle/bcpg-jdk15on/1.51/bcpg-jdk15on-1.51.jar
[DEBUG]  /home/ross/.m2/repository/org/bouncycastle/bcprov-jdk15on/1.51/bcprov-jdk15on-1.51.jar
[DEBUG]  /home/ross/.m2/repository/com/jayway/jsonpath/json-path/2.0.0/json-path-2.0.0.jar
[DEBUG]  /home/ross/.m2/repository/org/slf4j/slf4j-api/1.7.10/slf4j-api-1.7.10.jar
[DEBUG]  /home/ross/.m2/repository/net/minidev/json-smart/2.1.1/json-smart-2.1.1.jar
[DEBUG]  /home/ross/.m2/repository/net/minidev/asm/1.0.2/asm-1.0.2.jar
[DEBUG]  /home/ross/.m2/repository/asm/asm/3.3.1/asm-3.3.1.jar
[DEBUG] Source roots:
[DEBUG]  /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java
[INFO] Compiling 83 source files to /home/ross/workspace/pluto-20150818/ami-plugin/target/classes
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 4.311s
[INFO] Finished at: Tue Aug 18 13:17:37 BST 2015
[INFO] Final Memory: 16M/216M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:2.0.2:compile (default-compile) on project ami2: Compilation failure: Compilation failure:
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/dummy/DummySearcher.java:[27,2] error: annotations are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable annotations)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/dummy/DummySearcher.java:[34,34] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/dummy/DummySearcher.java:[36,23] error: for-each loops are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable for-each loops)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/phylotree/SVGXTreeNode.java:[41,5] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/MatcherResult.java:[26,13] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/MatcherResult.java:[109,37] error: for-each loops are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable for-each loops)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/MatcherResult.java:[120,2] error: annotations are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable annotations)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/AMIPlugin.java:[22,11] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/sequence/SequenceSearcher.java:[17,2] error: annotations are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable annotations)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/identifier/IdentifierArgProcessor.java:[49,6] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/identifier/IdentifierArgProcessor.java:[56,28] error: for-each loops are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable for-each loops)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/phylotree/nexml/NexmlEdge.java:[76,2] error: annotations are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable annotations)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/phylotree/nexml/NexmlTrees.java:[23,13] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/phylotree/nexml/NexmlTrees.java:[40,24] error: for-each loops are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable for-each loops)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/phylotree/Names.java:[20,6] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/phylotree/Names.java:[24,19] error: for-each loops are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable for-each loops)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/AMISearcher.java:[66,5] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/AMISearcher.java:[67,25] error: for-each loops are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable for-each loops)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/AMISearcher.java:[91,2] error: annotations are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable annotations)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/phylotree/nexml/NexmlFactory.java:[37,12] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/phylotree/nexml/NexmlFactory.java:[119,27] error: for-each loops are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable for-each loops)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/lookups/GenbankResultAnalyzer.java:[222,7] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/word/WordSetWrapper.java:[36,12] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/word/WordSetWrapper.java:[94,21] error: for-each loops are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable for-each loops)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/species/SpeciesArgProcessor.java:[67,2] error: annotations are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable annotations)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/phylotree/nexml/NexmlOtus.java:[17,12] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/phylotree/nexml/NexmlOtus.java:[31,27] error: for-each loops are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable for-each loops)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/word/WordResultsElementList.java:[23,37] error: for-each loops are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable for-each loops)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/phylotree/SVGXTree.java:[65,5] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/phylotree/SVGXTree.java:[190,36] error: for-each loops are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable for-each loops)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/species/SpeciesResultsElement.java:[29,2] error: annotations are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable annotations)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/species/SpeciesResultsElement.java:[30,12] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/species/SpeciesResultsElement.java:[33,36] error: for-each loops are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable for-each loops)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/species/SpeciesSearcher.java:[28,2] error: annotations are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable annotations)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/species/SpeciesSearcher.java:[49,34] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/species/SpeciesSearcher.java:[52,24] error: for-each loops are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable for-each loops)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/phylotree/nexml/NexmlNode.java:[36,13] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/phylotree/nexml/NexmlNode.java:[164,2] error: annotations are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable annotations)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/phylotree/nexml/NexmlNode.java:[185,27] error: for-each loops are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable for-each loops)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/species/NameMultimap.java:[28,17] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/species/NameMultimap.java:[47,20] error: for-each loops are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable for-each loops)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/lookups/GenbankLookup.java:[31,36] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/phylotree/LineContainer.java:[20,13] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/regex/CompoundRegexList.java:[15,50] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/regex/CompoundRegexList.java:[35,2] error: annotations are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable annotations)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/regex/CompoundRegexList.java:[38,35] error: for-each loops are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable for-each loops)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/regex/RegexSearcher.java:[23,5] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/regex/RegexSearcher.java:[45,37] error: for-each loops are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable for-each loops)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/regex/CompoundRegex.java:[34,13] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/regex/CompoundRegex.java:[48,37] error: for-each loops are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable for-each loops)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/regex/CompoundRegex.java:[58,2] error: annotations are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable annotations)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/species/LinneanNamer.java:[27,17] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/species/LinneanNamer.java:[71,27] error: for-each loops are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable for-each loops)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/regex/RegexArgProcessor.java:[34,12] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/regex/RegexArgProcessor.java:[96,35] error: for-each loops are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable for-each loops)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/regex/RegexArgProcessor.java:[115,2] error: annotations are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable annotations)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/phylotree/nexml/NexmlNEXML.java:[22,13] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/phylotree/nexml/NexmlNEXML.java:[37,22] error: for-each loops are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable for-each loops)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/AMIArgProcessor.java:[55,13] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/AMIArgProcessor.java:[128,20] error: for-each loops are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable for-each loops)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/AMIArgProcessor.java:[163,2] error: annotations are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable annotations)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/species/LinneanName.java:[43,2] error: annotations are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable annotations)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/regex/RegexComponent.java:[65,26] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/regex/RegexComponent.java:[100,22] error: for-each loops are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable for-each loops)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/regex/RegexComponent.java:[331,2] error: annotations are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable annotations)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/NamedGroupList.java:[29,13] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/NamedGroupList.java:[47,2] error: annotations are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable annotations)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/NamedGroupList.java:[55,29] error: for-each loops are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable for-each loops)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/phylotree/PhyloTreeArgProcessor.java:[140,20] error: for-each loops are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable for-each loops)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/phylotree/PhyloTreeArgProcessor.java:[348,37] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/gene/GeneSearcher.java:[29,2] error: annotations are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable annotations)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/gene/GeneSearcher.java:[50,34] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/gene/GeneSearcher.java:[52,23] error: for-each loops are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable for-each loops)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/word/WordCollectionFactory.java:[47,13] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/word/WordCollectionFactory.java:[109,35] error: for-each loops are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable for-each loops)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/lookups/ENALookup.java:[41,36] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/lookups/ENALookup.java:[53,2] error: annotations are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable annotations)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/word/WordResultsElement.java:[40,12] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/word/WordResultsElement.java:[51,35] error: for-each loops are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable for-each loops)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/lookups/WikipediaLookup.java:[87,2] error: annotations are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable annotations)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/word/WordArgProcessor.java:[37,25] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/word/WordArgProcessor.java:[208,21] error: for-each loops are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable for-each loops)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/phylotree/PhyloResultsElement.java:[18,35] error: for-each loops are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable for-each loops)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/simple/SimpleArgProcessor.java:[26,15] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/simple/SimpleArgProcessor.java:[65,2] error: annotations are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable annotations)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/phylotree/nexml/NexmlTree.java:[28,13] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/phylotree/nexml/NexmlTree.java:[58,21] error: for-each loops are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable for-each loops)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/phylotree/PhyloTreeSVGAnalyzer.java:[38,13] error: generics are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/phylotree/PhyloTreeSVGAnalyzer.java:[82,3] error: annotations are not supported in -source 1.3
[ERROR] 
[ERROR] (use -source 5 or higher to enable annotations)
[ERROR] /home/ross/workspace/pluto-20150818/ami-plugin/src/main/java/org/xmlcml/ami2/plugins/phylotree/PhyloTreeSVGAnalyzer.java:[160,31] error: for-each loops are not supported in -source 1.3
[ERROR] -> [Help 1]
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:2.0.2:compile (default-compile) on project ami2: Compilation failure
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:213)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:84)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:59)
    at org.apache.maven.lifecycle.internal.LifecycleStarter.singleThreadedBuild(LifecycleStarter.java:183)
    at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:161)
    at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:320)
    at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:156)
    at org.apache.maven.cli.MavenCli.execute(MavenCli.java:537)
    at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:196)
    at org.apache.maven.cli.MavenCli.main(MavenCli.java:141)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229)
    at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415)
    at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356)
Caused by: org.apache.maven.plugin.CompilationFailureException: Compilation failure
    at org.apache.maven.plugin.AbstractCompilerMojo.execute(AbstractCompilerMojo.java:516)
    at org.apache.maven.plugin.CompilerMojo.execute(CompilerMojo.java:114)
    at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:101)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:209)
    ... 19 more
[ERROR] 
[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

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