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Problem installing KmerFilter #1

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OrsonMM opened this issue Sep 7, 2016 · 1 comment
Open

Problem installing KmerFilter #1

OrsonMM opened this issue Sep 7, 2016 · 1 comment

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@OrsonMM
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OrsonMM commented Sep 7, 2016

Hi, Hola
Please help.

I have a problem

$git clone git clone https://github.com/rdpstaff/KmerFilter.git

$ cd KmerFilter
$ cd lib
$ ls # list these :
avalon-framework-4.1.5.jar commons-cli-1.2-javadoc.jar commons-logging-1.2.jar commons-logging-1.2-sources.jar junit-4.8.2-javadoc.jar junit-dep-4.10.jar logkit-1.0.1.jar
commons-cli-1.2.jar commons-cli-1.2-sources.jar commons-logging-1.2-javadoc.jar junit-4.8.2.jar junit-4.8.2-sources.jar log4j-1.2.17.jar servlet-api-2.3.jar

$ cd ..
$ ant -f build.xml

Give me a error

Buildfile: /home/orson/RDPTools/KmerFilter/build.xml

-pre-init:

-init-private:

-init-user:

-init-project:

-init-macrodef-property:

-do-init:

-post-init:

-init-check:

-init-ap-cmdline-properties:

-init-macrodef-javac-with-processors:

-init-macrodef-javac-without-processors:

-init-macrodef-javac:

-init-macrodef-test-impl:

-init-macrodef-junit-init:

-init-macrodef-junit-single:

-init-test-properties:

-init-macrodef-junit-batch:

-init-macrodef-junit:

-init-macrodef-junit-impl:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:test-impl

-init-macrodef-testng:

-init-macrodef-testng-impl:

-init-macrodef-test:

-init-macrodef-junit-debug:

-init-macrodef-junit-debug-batch:

-init-macrodef-junit-debug-impl:

-init-macrodef-test-debug-junit:

-init-macrodef-testng-debug:

-init-macrodef-testng-debug-impl:

-init-macrodef-test-debug-testng:

-init-macrodef-test-debug:

-init-debug-args:

-init-macrodef-nbjpda:

-init-macrodef-debug:

-init-macrodef-java:

-init-presetdef-jar:

-init-ap-cmdline-supported:

-init-ap-cmdline:

init:

-deps-jar-init:
[delete] Deleting: /home/orson/RDPTools/KmerFilter/build/built-jar.properties

deps-jar:

-warn-already-built-jar:
[propertyfile] Updating property file: /home/orson/RDPTools/KmerFilter/build/built-jar.properties

-check-call-dep:

-maybe-call-dep:

download-ivy:
[get] Getting: http://repo2.maven.org/maven2/org/apache/ivy/ivy/2.1.0-rc2/ivy-2.1.0-rc2.jar
[get] To: /home/orson/.ant/lib/ivy.jar
[get] Not modified - so not downloaded

init-ivy:

resolve:
[ivy:retrieve] :: Ivy 2.1.0-rc2 - 20090704004254 :: http://ant.apache.org/ivy/ ::
[ivy:retrieve] :: loading settings :: url = jar:file:/home/orson/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml
[ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#ReadSeq;working@orson-Satellite-C655
[ivy:retrieve] confs: [default]
[ivy:retrieve] found commons-lang#commons-lang;2.6 in public
[ivy:retrieve] found commons-cli#commons-cli;1.2 in public
[ivy:retrieve] found commons-io#commons-io;2.4 in public
[ivy:retrieve] :: resolution report :: resolve 142ms :: artifacts dl 13ms
---------------------------------------------------------------------
| | modules || artifacts |
| conf | number| search|dwnlded|evicted|| number|dwnlded|
---------------------------------------------------------------------
| default | 3 | 0 | 0 | 0 || 9 | 0 |
---------------------------------------------------------------------
[ivy:retrieve] :: retrieving :: edu.cme.rdp#ReadSeq
[ivy:retrieve] confs: [default]
[ivy:retrieve] 0 artifacts copied, 9 already retrieved (0kB/11ms)

-pre-init:

-init-private:

-init-user:

-init-project:

-init-macrodef-property:

-do-init:

-post-init:

-init-check:

-init-ap-cmdline-properties:

-init-macrodef-javac-with-processors:

-init-macrodef-javac-without-processors:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:javac

-init-macrodef-javac:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:depend

-init-macrodef-test-impl:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:test-impl

-init-macrodef-junit-init:

-init-macrodef-junit-single:

-init-test-properties:

-init-macrodef-junit-batch:

-init-macrodef-junit:

-init-macrodef-junit-impl:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:test-impl

-init-macrodef-testng:

-init-macrodef-testng-impl:

-init-macrodef-test:

-init-macrodef-junit-debug:

-init-macrodef-junit-debug-batch:

-init-macrodef-junit-debug-impl:

-init-macrodef-test-debug-junit:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:test-debug

-init-macrodef-testng-debug:

-init-macrodef-testng-debug-impl:

-init-macrodef-test-debug-testng:

-init-macrodef-test-debug:

-init-debug-args:

-init-macrodef-nbjpda:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/1:nbjpdastart

-init-macrodef-debug:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:debug

-init-macrodef-java:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/1:java

-init-presetdef-jar:

-init-ap-cmdline-supported:

-init-ap-cmdline:

init:

-deps-jar-init:

deps-jar:

-warn-already-built-jar:
[propertyfile] Updating property file: /home/orson/RDPTools/KmerFilter/build/built-jar.properties

-check-automatic-build:

-clean-after-automatic-build:

-verify-automatic-build:

-pre-pre-compile:

-pre-compile:

-copy-persistence-xml:

-compile-depend:

-do-compile:

-post-compile:

compile:

-pre-jar:

-post-jar:

jar:
[echo] To run this application from the command line without Ant, try:
[echo] java -jar "/home/orson/RDPTools/ReadSeq/dist/ReadSeq.jar"

-check-automatic-build:

-clean-after-automatic-build:

-verify-automatic-build:

-pre-pre-compile:

download-ivy:
[get] Getting: http://repo2.maven.org/maven2/org/apache/ivy/ivy/2.1.0-rc2/ivy-2.1.0-rc2.jar
[get] To: /home/orson/.ant/lib/ivy.jar
[get] Not modified - so not downloaded

init-ivy:

resolve:
[ivy:retrieve] :: loading settings :: url = jar:file:/home/orson/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml
[ivy:retrieve] :: resolving dependencies :: edu.msu.cme.rdp#kmer;working@orson-Satellite-C655
[ivy:retrieve] confs: [default]
[ivy:retrieve] found commons-cli#commons-cli;1.2 in public
[ivy:retrieve] found commons-logging#commons-logging;1.2 in public
[ivy:retrieve] found log4j#log4j;1.2.17 in public
[ivy:retrieve] found logkit#logkit;1.0.1 in public
[ivy:retrieve] found avalon-framework#avalon-framework;4.1.5 in public
[ivy:retrieve] found javax.servlet#servlet-api;2.3 in public
[ivy:retrieve] found junit#junit;4.8.2 in public
[ivy:retrieve] :: resolution report :: resolve 143ms :: artifacts dl 16ms
---------------------------------------------------------------------
| | modules || artifacts |
| conf | number| search|dwnlded|evicted|| number|dwnlded|
---------------------------------------------------------------------
| default | 7 | 0 | 0 | 0 || 13 | 0 |
---------------------------------------------------------------------
[ivy:retrieve] :: retrieving :: edu.msu.cme.rdp#kmer
[ivy:retrieve] confs: [default]
[ivy:retrieve] 0 artifacts copied, 13 already retrieved (0kB/6ms)

-pre-compile:

-copy-persistence-xml:

-compile-depend:

-do-compile:

-post-compile:

compile:

-pre-pre-compile-test:

-pre-compile-test:

-compile-test-depend:

-do-compile-test:
[javac] Compiling 10 source files to /home/orson/RDPTools/KmerFilter/build/test/classes
[javac] warning: [options] bootstrap class path not set in conjunction with -source 1.5
[javac] warning: [options] source value 1.5 is obsolete and will be removed in a future release
[javac] warning: [options] target value 1.5 is obsolete and will be removed in a future release
[javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/KmerTest.java:21: error: package org.junit does not exist
[javac] import org.junit.Test;
[javac] ^
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/KmerTest.java:22: error: package org.junit does not exist
[javac] import static org.junit.Assert.;
[javac] ^
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/ProtKmerTest.java:20: error: package org.junit does not exist
[javac] import org.junit.Test;
[javac] ^
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/ProtKmerTest.java:21: error: package org.junit does not exist
[javac] import static org.junit.Assert.;
[javac] ^
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/cli/KmerCoverageTest.java:28: error: package org.junit does not exist
[javac] import org.junit.Test;
[javac] ^
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/cli/KmerCoverageTest.java:29: error: package org.junit does not exist
[javac] import static org.junit.Assert.;
[javac] ^
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/KmerIteratorTest.java:20: error: package org.junit does not exist
[javac] import org.junit.Test;
[javac] ^
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/KmerIteratorTest.java:21: error: package org.junit does not exist
[javac] import static org.junit.Assert.;
[javac] ^
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/KmerSetTest.java:23: error: package org.junit does not exist
[javac] import org.junit.Test;
[javac] ^
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/KmerSetTest.java:24: error: package org.junit does not exist
[javac] import static org.junit.Assert.;
[javac] ^
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/ModelPositionKmerGeneratorTest.java:24: error: package org.junit does not exist
[javac] import org.junit.Test;
[javac] ^
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/ModelPositionKmerGeneratorTest.java:25: error: package org.junit does not exist
[javac] import static org.junit.Assert.;
[javac] ^
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/NuclKmerGeneratorTest.java:20: error: package org.junit does not exist
[javac] import org.junit.Test;
[javac] ^
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/NuclKmerGeneratorTest.java:21: error: package org.junit does not exist
[javac] import static org.junit.Assert.;
[javac] ^
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/ProtKmerGeneratorTest.java:20: error: package org.junit does not exist
[javac] import org.junit.Test;
[javac] ^
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/ProtKmerGeneratorTest.java:21: error: package org.junit does not exist
[javac] import static org.junit.Assert.;
[javac] ^
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/trie/KmerGeneratorTest.java:22: error: package org.junit does not exist
[javac] import org.junit.Test;
[javac] ^
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/trie/KmerGeneratorTest.java:23: error: package org.junit does not exist
[javac] import static org.junit.Assert.;
[javac] ^
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/trie/ModelPositionKmerGeneratorTest.java:22: error: package org.junit does not exist
[javac] import org.junit.Test;
[javac] ^
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/trie/ModelPositionKmerGeneratorTest.java:23: error: package org.junit does not exist
[javac] import static org.junit.Assert.;
[javac] ^
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/KmerTest.java:30: error: cannot find symbol
[javac] @test
[javac] ^
[javac] symbol: class Test
[javac] location: class KmerTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/KmerTest.java:74: error: cannot find symbol
[javac] @test
[javac] ^
[javac] symbol: class Test
[javac] location: class KmerTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/ProtKmerTest.java:36: error: cannot find symbol
[javac] @test
[javac] ^
[javac] symbol: class Test
[javac] location: class ProtKmerTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/cli/KmerCoverageTest.java:44: error: cannot find symbol
[javac] @test
[javac] ^
[javac] symbol: class Test
[javac] location: class KmerCoverageTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/KmerIteratorTest.java:29: error: cannot find symbol
[javac] @test
[javac] ^
[javac] symbol: class Test
[javac] location: class KmerIteratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/KmerSetTest.java:32: error: cannot find symbol
[javac] @test
[javac] ^
[javac] symbol: class Test
[javac] location: class KmerSetTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/ModelPositionKmerGeneratorTest.java:57: error: cannot find symbol
[javac] @test
[javac] ^
[javac] symbol: class Test
[javac] location: class ModelPositionKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/ModelPositionKmerGeneratorTest.java:84: error: cannot find symbol
[javac] @test
[javac] ^
[javac] symbol: class Test
[javac] location: class ModelPositionKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/ModelPositionKmerGeneratorTest.java:111: error: cannot find symbol
[javac] @test
[javac] ^
[javac] symbol: class Test
[javac] location: class ModelPositionKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/NuclKmerGeneratorTest.java:29: error: cannot find symbol
[javac] @test
[javac] ^
[javac] symbol: class Test
[javac] location: class NuclKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/NuclKmerGeneratorTest.java:101: error: cannot find symbol
[javac] @test
[javac] ^
[javac] symbol: class Test
[javac] location: class NuclKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/NuclKmerGeneratorTest.java:174: error: cannot find symbol
[javac] @test
[javac] ^
[javac] symbol: class Test
[javac] location: class NuclKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/ProtKmerGeneratorTest.java:29: error: cannot find symbol
[javac] @test
[javac] ^
[javac] symbol: class Test
[javac] location: class ProtKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/ProtKmerGeneratorTest.java:303: error: cannot find symbol
[javac] @test
[javac] ^
[javac] symbol: class Test
[javac] location: class ProtKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/trie/KmerGeneratorTest.java:48: error: cannot find symbol
[javac] @test
[javac] ^
[javac] symbol: class Test
[javac] location: class KmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/trie/KmerGeneratorTest.java:62: error: cannot find symbol
[javac] @test
[javac] ^
[javac] symbol: class Test
[javac] location: class KmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/trie/KmerGeneratorTest.java:77: error: cannot find symbol
[javac] @test
[javac] ^
[javac] symbol: class Test
[javac] location: class KmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/trie/ModelPositionKmerGeneratorTest.java:45: error: cannot find symbol
[javac] @test
[javac] ^
[javac] symbol: class Test
[javac] location: class ModelPositionKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/trie/ModelPositionKmerGeneratorTest.java:64: error: cannot find symbol
[javac] @test
[javac] ^
[javac] symbol: class Test
[javac] location: class ModelPositionKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/trie/ModelPositionKmerGeneratorTest.java:91: error: cannot find symbol
[javac] @test
[javac] ^
[javac] symbol: class Test
[javac] location: class ModelPositionKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/KmerTest.java:43: error: cannot find symbol
[javac] assertEquals(strKmer.toString(), kmer.toString());
[javac] ^
[javac] symbol: method assertEquals(String,String)
[javac] location: class KmerTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/KmerTest.java:52: error: cannot find symbol
[javac] assertEquals("Shift Right Original kmer: " + strKmer + ", shift=" + shift,rightShift.toString(), newKmer.toString());
[javac] ^
[javac] symbol: method assertEquals(String,String,String)
[javac] location: class KmerTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/KmerTest.java:56: error: cannot find symbol
[javac] assertEquals(rightShift.toString(), decodedStr);
[javac] ^
[javac] symbol: method assertEquals(String,String)
[javac] location: class KmerTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/KmerTest.java:65: error: cannot find symbol
[javac] assertEquals("Shift Left Original kmer: " + strKmer + ", length: " + length + ", shift=" + shift, leftShift.toString(), newKmer.toString());
[javac] ^
[javac] symbol: method assertEquals(String,String,String)
[javac] location: class KmerTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/KmerTest.java:87: error: cannot find symbol
[javac] assertEquals(expectedKmers[position - size], kmer.toString());
[javac] ^
[javac] symbol: method assertEquals(String,String)
[javac] location: class KmerTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/KmerTest.java:91: error: cannot find symbol
[javac] assertEquals(expectedKmers[position - size +1], kmer.toString());
[javac] ^
[javac] symbol: method assertEquals(String,String)
[javac] location: class KmerTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/KmerTest.java:98: error: cannot find symbol
[javac] assertEquals(expectedKmers[position - size -1], kmer.toString());
[javac] ^
[javac] symbol: method assertEquals(String,String)
[javac] location: class KmerTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/ProtKmerTest.java:53: error: cannot find symbol
[javac] assertEquals(expectedKmers[position - size], kmer.toString());
[javac] ^
[javac] symbol: method assertEquals(String,String)
[javac] location: class ProtKmerTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/ProtKmerTest.java:57: error: cannot find symbol
[javac] assertEquals(expectedKmers[position - size +1], kmer.toString());
[javac] ^
[javac] symbol: method assertEquals(String,String)
[javac] location: class ProtKmerTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/ProtKmerTest.java:64: error: cannot find symbol
[javac] assertEquals(expectedKmers[position - size -1], kmer.toString());
[javac] ^
[javac] symbol: method assertEquals(String,String)
[javac] location: class ProtKmerTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/cli/KmerCoverageTest.java:72: error: cannot find symbol
[javac] assertEquals(contig1.name, "contig1");
[javac] ^
[javac] symbol: method assertEquals(String,String)
[javac] location: class KmerCoverageTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/cli/KmerCoverageTest.java:74: error: cannot find symbol
[javac] assertEquals(contig1.coverage[0], 3, 0.005);
[javac] ^
[javac] symbol: method assertEquals(double,int,double)
[javac] location: class KmerCoverageTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/cli/KmerCoverageTest.java:75: error: cannot find symbol
[javac] assertEquals(contig1.coverage[8], 2, 0.005);
[javac] ^
[javac] symbol: method assertEquals(double,int,double)
[javac] location: class KmerCoverageTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/cli/KmerCoverageTest.java:76: error: cannot find symbol
[javac] assertEquals(contig1.coverage[9], 0.6666, 0.005);
[javac] ^
[javac] symbol: method assertEquals(double,double,double)
[javac] location: class KmerCoverageTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/cli/KmerCoverageTest.java:77: error: cannot find symbol
[javac] assertEquals(contig1.coverage[29], 0.6666, 0.005);
[javac] ^
[javac] symbol: method assertEquals(double,double,double)
[javac] location: class KmerCoverageTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/cli/KmerCoverageTest.java:82: error: cannot find symbol
[javac] assertEquals(contig2.name, "contig2");
[javac] ^
[javac] symbol: method assertEquals(String,String)
[javac] location: class KmerCoverageTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/cli/KmerCoverageTest.java:84: error: cannot find symbol
[javac] assertEquals(contig2.coverage[0], 0.6666, 0.005);
[javac] ^
[javac] symbol: method assertEquals(double,double,double)
[javac] location: class KmerCoverageTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/cli/KmerCoverageTest.java:85: error: cannot find symbol
[javac] assertEquals(contig2.coverage[20], 0.6666, 0.005);
[javac] ^
[javac] symbol: method assertEquals(double,double,double)
[javac] location: class KmerCoverageTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/cli/KmerCoverageTest.java:86: error: cannot find symbol
[javac] assertEquals(contig2.coverage[21], 1, 0.005);
[javac] ^
[javac] symbol: method assertEquals(double,int,double)
[javac] location: class KmerCoverageTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/cli/KmerCoverageTest.java:87: error: cannot find symbol
[javac] assertEquals(contig2.coverage[22], 3, 0.005);
[javac] ^
[javac] symbol: method assertEquals(double,int,double)
[javac] location: class KmerCoverageTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/cli/KmerCoverageTest.java:88: error: cannot find symbol
[javac] assertEquals(contig2.coverage[23], 2, 0.005);
[javac] ^
[javac] symbol: method assertEquals(double,int,double)
[javac] location: class KmerCoverageTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/cli/KmerCoverageTest.java:89: error: cannot find symbol
[javac] assertEquals(contig2.coverage[49], 2, 0.005);
[javac] ^
[javac] symbol: method assertEquals(double,int,double)
[javac] location: class KmerCoverageTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/cli/KmerCoverageTest.java:95: error: cannot find symbol
[javac] assertEquals(contig3.name, "contig3");
[javac] ^
[javac] symbol: method assertEquals(String,String)
[javac] location: class KmerCoverageTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/cli/KmerCoverageTest.java:97: error: cannot find symbol
[javac] assertEquals(contig3.coverage[0], 0.6666, 0.005);
[javac] ^
[javac] symbol: method assertEquals(double,double,double)
[javac] location: class KmerCoverageTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/cli/KmerCoverageTest.java:98: error: cannot find symbol
[javac] assertEquals(contig3.coverage[21], 1, 0.005);
[javac] ^
[javac] symbol: method assertEquals(double,int,double)
[javac] location: class KmerCoverageTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/cli/KmerCoverageTest.java:99: error: cannot find symbol
[javac] assertEquals(contig3.coverage[22], 0, 0.005);
[javac] ^
[javac] symbol: method assertEquals(double,int,double)
[javac] location: class KmerCoverageTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/cli/KmerCoverageTest.java:105: error: cannot find symbol
[javac] assertEquals("contig1\t1.100\t0.667\t30\t30\t1.000", summary[3]);
[javac] ^
[javac] symbol: method assertEquals(String,String)
[javac] location: class KmerCoverageTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/cli/KmerCoverageTest.java:106: error: cannot find symbol
[javac] assertEquals("contig3\t0.652\t0.667\t23\t22\t0.957", summary[4]);
[javac] ^
[javac] symbol: method assertEquals(String,String)
[javac] location: class KmerCoverageTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/cli/KmerCoverageTest.java:107: error: cannot find symbol
[javac] assertEquals("contig2\t1.440\t2.000\t50\t50\t1.000", summary[5]);
[javac] ^
[javac] symbol: method assertEquals(String,String)
[javac] location: class KmerCoverageTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/KmerIteratorTest.java:74: error: cannot find symbol
[javac] assertEquals(expectedKmers[index], val.toString());
[javac] ^
[javac] symbol: method assertEquals(String,String)
[javac] location: class KmerIteratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/KmerIteratorTest.java:90: error: cannot find symbol
[javac] assertEquals(expected60Kmers[index], val.toString());
[javac] ^
[javac] symbol: method assertEquals(String,String)
[javac] location: class KmerIteratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/KmerSetTest.java:73: error: cannot find symbol
[javac] assertEquals(values.length/2, set.size());
[javac] ^
[javac] symbol: method assertEquals(int,int)
[javac] location: class KmerSetTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/KmerSetTest.java:79: error: cannot find symbol
[javac] assertEquals(index, (int)set.get(temp));
[javac] ^
[javac] symbol: method assertEquals(int,int)
[javac] location: class KmerSetTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/ModelPositionKmerGeneratorTest.java:66: error: cannot find symbol
[javac] assertArrayEquals("Testing index " + index + " of expected " + new String(expected1.get(index)) + " compared to " + new String(result.get(index)), expected1.get(index), result.get(index));
[javac] ^
[javac] symbol: method assertArrayEquals(String,char[],char[])
[javac] location: class ModelPositionKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/ModelPositionKmerGeneratorTest.java:69: error: cannot find symbol
[javac] assertEquals(expected1.size(), result.size());
[javac] ^
[javac] symbol: method assertEquals(int,int)
[javac] location: class ModelPositionKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/ModelPositionKmerGeneratorTest.java:78: error: cannot find symbol
[javac] assertArrayEquals("Testing index " + index + " of expected " + new String(expected2.get(index)) + " compared to " + new String(result.get(index)), expected2.get(index), result.get(index));
[javac] ^
[javac] symbol: method assertArrayEquals(String,char[],char[])
[javac] location: class ModelPositionKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/ModelPositionKmerGeneratorTest.java:81: error: cannot find symbol
[javac] assertEquals(expected2.size(), result.size());
[javac] ^
[javac] symbol: method assertEquals(int,int)
[javac] location: class ModelPositionKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/ModelPositionKmerGeneratorTest.java:91: error: cannot find symbol
[javac] assertArrayEquals(new String(kmer) + " testing index " + index + " of expected " + new String(expected1.get(index)) + " compared to " + new String(kmer), expected1.get(index), kmer);
[javac] ^
[javac] symbol: method assertArrayEquals(String,char[],char[])
[javac] location: class ModelPositionKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/ModelPositionKmerGeneratorTest.java:92: error: cannot find symbol
[javac] assertEquals("Model position check", expectedModelPos1[index], kmerIt.getPosition());
[javac] ^
[javac] symbol: method assertEquals(String,int,int)
[javac] location: class ModelPositionKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/ModelPositionKmerGeneratorTest.java:96: error: cannot find symbol
[javac] assertEquals(expected1.size(), index);
[javac] ^
[javac] symbol: method assertEquals(int,int)
[javac] location: class ModelPositionKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/ModelPositionKmerGeneratorTest.java:103: error: cannot find symbol
[javac] assertArrayEquals("Testing index " + index + " of expected " + new String(expected2.get(index)) + " compared to " + new String(kmer), expected2.get(index), kmer);
[javac] ^
[javac] symbol: method assertArrayEquals(String,char[],char[])
[javac] location: class ModelPositionKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/ModelPositionKmerGeneratorTest.java:104: error: cannot find symbol
[javac] assertEquals("Model position check", expectedModelPos2[index], kmerIt.getPosition());
[javac] ^
[javac] symbol: method assertEquals(String,int,int)
[javac] location: class ModelPositionKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/ModelPositionKmerGeneratorTest.java:108: error: cannot find symbol
[javac] assertEquals(expected2.size(), index);
[javac] ^
[javac] symbol: method assertEquals(int,int)
[javac] location: class ModelPositionKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/ModelPositionKmerGeneratorTest.java:118: error: cannot find symbol
[javac] assertArrayEquals(new String(kmer) + " testing index " + index + " of expected " + new String(expected3.get(index)) + " compared to " + new String(kmer), expected3.get(index), kmer);
[javac] ^
[javac] symbol: method assertArrayEquals(String,char[],char[])
[javac] location: class ModelPositionKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/ModelPositionKmerGeneratorTest.java:119: error: cannot find symbol
[javac] assertEquals("Model position check", expectedModelPos3[index], kmerIt.getPosition());
[javac] ^
[javac] symbol: method assertEquals(String,int,int)
[javac] location: class ModelPositionKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/ModelPositionKmerGeneratorTest.java:123: error: cannot find symbol
[javac] assertEquals(expected3.size(), index);
[javac] ^
[javac] symbol: method assertEquals(int,int)
[javac] location: class ModelPositionKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/NuclKmerGeneratorTest.java:94: error: cannot find symbol
[javac] assertEquals(expected[index], val);
[javac] ^
[javac] symbol: method assertEquals(long,long)
[javac] location: class NuclKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/NuclKmerGeneratorTest.java:95: error: cannot find symbol
[javac] assertEquals(expectedKmers[index], temp.toString());
[javac] ^
[javac] symbol: method assertEquals(String,String)
[javac] location: class NuclKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/NuclKmerGeneratorTest.java:96: error: cannot find symbol
[javac] assertEquals(index + 1, kmer.getPosition());
[javac] ^
[javac] symbol: method assertEquals(int,int)
[javac] location: class NuclKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/NuclKmerGeneratorTest.java:140: error: cannot find symbol
[javac] assertEquals(expected[index], val);
[javac] ^
[javac] symbol: method assertEquals(long,long)
[javac] location: class NuclKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/NuclKmerGeneratorTest.java:141: error: cannot find symbol
[javac] assertEquals(expectedKmers[index], temp.toString());
[javac] ^
[javac] symbol: method assertEquals(String,String)
[javac] location: class NuclKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/NuclKmerGeneratorTest.java:142: error: cannot find symbol
[javac] assertEquals(index + 1, kmer.getPosition());
[javac] ^
[javac] symbol: method assertEquals(int,int)
[javac] location: class NuclKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/NuclKmerGeneratorTest.java:151: error: cannot find symbol
[javac] assertEquals(expected[index], val);
[javac] ^
[javac] symbol: method assertEquals(long,long)
[javac] location: class NuclKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/NuclKmerGeneratorTest.java:152: error: cannot find symbol
[javac] assertEquals(expectedKmers[index], temp.toString());
[javac] ^
[javac] symbol: method assertEquals(String,String)
[javac] location: class NuclKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/NuclKmerGeneratorTest.java:153: error: cannot find symbol
[javac] assertEquals(index + 31, kmer.getPosition());
[javac] ^
[javac] symbol: method assertEquals(int,int)
[javac] location: class NuclKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/NuclKmerGeneratorTest.java:165: error: cannot find symbol
[javac] assertEquals(expected[index], val);
[javac] ^
[javac] symbol: method assertEquals(long,long)
[javac] location: class NuclKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/NuclKmerGeneratorTest.java:166: error: cannot find symbol
[javac] assertEquals(expectedKmers[index], temp.toString());
[javac] ^
[javac] symbol: method assertEquals(String,String)
[javac] location: class NuclKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/NuclKmerGeneratorTest.java:167: error: cannot find symbol
[javac] assertEquals(index + 1, kmer.getPosition());
[javac] ^
[javac] symbol: method assertEquals(int,int)
[javac] location: class NuclKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/NuclKmerGeneratorTest.java:170: error: cannot find symbol
[javac] assertEquals(index, 4);
[javac] ^
[javac] symbol: method assertEquals(int,int)
[javac] location: class NuclKmerGeneratorTest
[javac] /home/orson/RDPTools/KmerFilter/test/edu/msu/cme/rdp/kmer/set/NuclKmerGeneratorTest.java:179: error: cannot find symbol
[javac] fail("Kmer size of 32 should have triggered an exception");
[javac] ^
[javac] symbol: method fail(String)
[javac] location: class NuclKmerGeneratorTest
[javac] Note: Some input files use unchecked or unsafe operations.
[javac] Note: Recompile with -Xlint:unchecked for details.
[javac] 100 errors
[javac] 4 warnings

BUILD FAILED
/home/orson/RDPTools/KmerFilter/nbproject/build-impl.xml:1251: The following error occurred while executing this line:
/home/orson/RDPTools/KmerFilter/nbproject/build-impl.xml:300: Compile failed; see the compiler error output for details.

Total time: 3 seconds

But in lib i have junit program.

Please help me.
@OrsonMM
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OrsonMM commented Sep 7, 2016

Sorry the folder lib in KmerFilter appear after run commad $ant -f build.xml

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@OrsonMM