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Problem isntalling classifier #16

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OrsonMM opened this issue Sep 7, 2016 · 4 comments
Open

Problem isntalling classifier #16

OrsonMM opened this issue Sep 7, 2016 · 4 comments

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@OrsonMM
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OrsonMM commented Sep 7, 2016

Hi - Hola .
I hope your help, please.

I download classifier with command:
$git clone https://github.com/rdpstaff/classifier.git
$cd classifier #for enter.
$ls #for list:
build build.xml ivy.xml lib LICENSE manifest.mf nbproject README samplefiles src test
and finally for install classifier:
$ant -f build.xml

and have a error in one test:

-do-test-run:
[junit] Testsuite: edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierTest
[junit] testClassify
[junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0,072 sec
[junit]
[junit] ------------- Standard Output ---------------
[junit] testClassify
[junit] ------------- ---------------- ---------------
[junit] testGetName
[junit] Testsuite: edu.msu.cme.rdp.classifier.rrnaclassifier.HierarchyTreeTest
[junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0,069 sec
[junit]
[junit] ------------- Standard Error -----------------
[junit] testGetName
[junit] ------------- ---------------- ---------------
[junit] Testsuite: edu.msu.cme.rdp.classifier.rrnaclassifier.ParsedSequenceTest
[junit] testGetReversedWord
[junit] testGetWordIndex
[junit] testCreateWordIndexArr
[junit] testGetReversedSeq
[junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0,077 sec
[junit]
[junit] ------------- Standard Output ---------------
[junit] testGetReversedWord
[junit] testGetWordIndex
[junit] testCreateWordIndexArr
[junit] testGetReversedSeq
[junit] ------------- ---------------- ---------------
[junit] Testsuite: edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfoTest
[junit] testCreateTree
[junit] testCreateLogWordPriorArr
[junit] testCreateProbIndexArr
[junit] testCreateClassifier
[junit] testCreateGenusWordConditionalProbList
[junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0,565 sec
[junit]
[junit] ------------- Standard Output ---------------
[junit] testCreateTree
[junit] testCreateLogWordPriorArr
[junit] testCreateProbIndexArr
[junit] testCreateClassifier
[junit] testCreateGenusWordConditionalProbList
[junit] ------------- ---------------- ---------------
[junit] Testsuite: edu.msu.cme.rdp.classifier.rrnaclassifier.TreeFileParserTest
[junit] testParseTreeFile
[junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0,143 sec
[junit]
[junit] ------------- Standard Output ---------------
[junit] testParseTreeFile
[junit] ------------- ---------------- ---------------
[junit] Testsuite: edu.msu.cme.rdp.classifier.train.GoodWordIteratorTest
[junit] testNext
[junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0,061 sec
[junit]
[junit] ------------- Standard Output ---------------
[junit] testNext
[junit] ------------- ---------------- ---------------
[junit] Testsuite: edu.msu.cme.rdp.classifier.train.RawHierarchyTreeTest
[junit] testInitWordOccurrence()
[junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0,083 sec
[junit]
[junit] ------------- Standard Output ---------------
[junit] testInitWordOccurrence()
[junit] ------------- ---------------- ---------------
[junit] Testsuite: edu.msu.cme.rdp.classifier.train.RawSequenceParserTest
[junit] testNext()
[junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0,083 sec
[junit]
[junit] ------------- Standard Output ---------------
[junit] testNext()
[junit] ------------- ---------------- ---------------
[junit] Testsuite: edu.msu.cme.rdp.classifier.train.TreeFactoryTest
[junit] testAddSequence
[junit] Tests run: 1, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 0,139 sec
[junit]
[junit] ------------- Standard Output ---------------
[junit] testAddSequence
[junit] ------------- ---------------- ---------------
[junit] Testcase: testAddSequence(edu.msu.cme.rdp.classifier.train.TreeFactoryTest): FAILED
[junit] null expected:<G[1]> but was:<G[2]>
[junit] junit.framework.ComparisonFailure: null expected:<G[1]> but was:<G[2]>
[junit] at edu.msu.cme.rdp.classifier.train.TreeFactoryTest.testAddSequence(TreeFactoryTest.java:55)
[junit]
[junit]
[junit] Test edu.msu.cme.rdp.classifier.train.TreeFactoryTest FAILED
[junit] Testsuite: edu.msu.cme.rdp.classifier.train.validation.AddLogsTest
[junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0,07 sec
[junit]
[junit] Testsuite: edu.msu.cme.rdp.classifier.train.validation.DecisionMakerTest
[junit] testGetBestClasspath
[junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0,54 sec
[junit]
[junit] ------------- Standard Output ---------------
[junit] testGetBestClasspath
[junit] ------------- ---------------- ---------------
[junit] Testsuite: edu.msu.cme.rdp.classifier.train.validation.GoodWordIteratorTest
[junit] testNext
[junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0,072 sec
[junit]
[junit] ------------- Standard Output ---------------
[junit] testNext
[junit] ------------- ---------------- ---------------
[junit] Testsuite: edu.msu.cme.rdp.classifier.train.validation.HierarchyTreeTest
[junit] testHideSeq
[junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0,133 sec
[junit]
[junit] ------------- Standard Output ---------------
[junit] testHideSeq
[junit] ------------- ---------------- ---------------
[junit] Testsuite: edu.msu.cme.rdp.classifier.train.validation.NBClassifierTest
[junit] testassignClass
[junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0,107 sec
[junit]
[junit] ------------- Standard Output ---------------
[junit] testassignClass
[junit] ------------- ---------------- ---------------
[junit] Testsuite: edu.msu.cme.rdp.classifier.train.validation.SequenceParserTest
[junit] testNext()
[junit] testHasNext
[junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0,088 sec
[junit]
[junit] ------------- Standard Output ---------------
[junit] testHasNext
[junit] ------------- ---------------- ---------------
[junit] ------------- Standard Error -----------------
[junit] testNext()
[junit] ------------- ---------------- ---------------
[junit] Testsuite: edu.msu.cme.rdp.classifier.train.validation.TreeFactoryTest
[junit] testAddSequence
[junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0,092 sec
[junit]
[junit] ------------- Standard Output ---------------
[junit] testAddSequence
[junit] ------------- ---------------- ---------------

test-report:

-post-test-run:

BUILD FAILED
/home/orson/RDPTools/classifier/nbproject/build-impl.xml:1304: Some tests failed; see details above.

Total time: 10 seconds

Please. Help me. Thanks
@rdpstaffmsu
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There are dependancies that require the git clone of the RDPTools package (
https://github.com/rdpstaff/RDPTools). Or, you just need to download
Classifier from Sourceforge (
https://sourceforge.net/projects/rdp-classifier/). Let me know if neither
one works for you. Thank you.

Benli Chai
RDP Staff

On Wed, Sep 7, 2016 at 12:54 PM, Orson notifications@github.com wrote:

Hi - Hola .
I hope your help, please.

I download classifier with command:
$git clone https://github.com/rdpstaff/classifier.git
$cd classifier #for enter.
$ls #for list:
build build.xml ivy.xml lib LICENSE manifest.mf nbproject README
samplefiles src test
and finally for install classifier:
$ant -f build.xml

and have a error in one test:

###################################################################
-do-test-run:
[junit] Testsuite: edu.msu.cme.rdp.classifier.
rrnaclassifier.ClassifierTest
[junit] testClassify
[junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed:
0,072 sec
[junit]
[junit] ------------- Standard Output ---------------
[junit] testClassify
[junit] ------------- ---------------- ---------------
[junit] testGetName
[junit] Testsuite: edu.msu.cme.rdp.classifier.rrnaclassifier.
HierarchyTreeTest
[junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed:
0,069 sec
[junit]
[junit] ------------- Standard Error -----------------
[junit] testGetName
[junit] ------------- ---------------- ---------------
[junit] Testsuite: edu.msu.cme.rdp.classifier.rrnaclassifier.
ParsedSequenceTest
[junit] testGetReversedWord
[junit] testGetWordIndex
[junit] testCreateWordIndexArr
[junit] testGetReversedSeq
[junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed:
0,077 sec
[junit]
[junit] ------------- Standard Output ---------------
[junit] testGetReversedWord
[junit] testGetWordIndex
[junit] testCreateWordIndexArr
[junit] testGetReversedSeq
[junit] ------------- ---------------- ---------------
[junit] Testsuite: edu.msu.cme.rdp.classifier.rrnaclassifier.
TrainingInfoTest
[junit] testCreateTree
[junit] testCreateLogWordPriorArr
[junit] testCreateProbIndexArr
[junit] testCreateClassifier
[junit] testCreateGenusWordConditionalProbList
[junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed:
0,565 sec
[junit]
[junit] ------------- Standard Output ---------------
[junit] testCreateTree
[junit] testCreateLogWordPriorArr
[junit] testCreateProbIndexArr
[junit] testCreateClassifier
[junit] testCreateGenusWordConditionalProbList
[junit] ------------- ---------------- ---------------
[junit] Testsuite: edu.msu.cme.rdp.classifier.rrnaclassifier.
TreeFileParserTest
[junit] testParseTreeFile
[junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed:
0,143 sec
[junit]
[junit] ------------- Standard Output ---------------
[junit] testParseTreeFile
[junit] ------------- ---------------- ---------------
[junit] Testsuite: edu.msu.cme.rdp.classifier.train.GoodWordIteratorTest
[junit] testNext
[junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed:
0,061 sec
[junit]
[junit] ------------- Standard Output ---------------
[junit] testNext
[junit] ------------- ---------------- ---------------
[junit] Testsuite: edu.msu.cme.rdp.classifier.train.RawHierarchyTreeTest
[junit] testInitWordOccurrence()
[junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed:
0,083 sec
[junit]
[junit] ------------- Standard Output ---------------
[junit] testInitWordOccurrence()
[junit] ------------- ---------------- ---------------
[junit] Testsuite: edu.msu.cme.rdp.classifier.train.RawSequenceParserTest
[junit] testNext()
[junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed:
0,083 sec
[junit]
[junit] ------------- Standard Output ---------------
[junit] testNext()
[junit] ------------- ---------------- ---------------
[junit] Testsuite: edu.msu.cme.rdp.classifier.train.TreeFactoryTest
[junit] testAddSequence
[junit] Tests run: 1, Failures: 1, Errors: 0, Skipped: 0, Time elapsed:
0,139 sec
[junit]
[junit] ------------- Standard Output ---------------
[junit] testAddSequence
[junit] ------------- ---------------- ---------------
[junit] Testcase: testAddSequence(edu.msu.cme.rdp.classifier.train.TreeFactoryTest):
FAILED
[junit] null expected: but was:
[junit] junit.framework.ComparisonFailure: null expected: but was:
[junit] at edu.msu.cme.rdp.classifier.train.TreeFactoryTest.
testAddSequence(TreeFactoryTest.java:55)
[junit]
[junit]
[junit] Test edu.msu.cme.rdp.classifier.train.TreeFactoryTest FAILED
[junit] Testsuite: edu.msu.cme.rdp.classifier.train.validation.AddLogsTest
[junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed:
0,07 sec
[junit]
[junit] Testsuite: edu.msu.cme.rdp.classifier.train.validation.
DecisionMakerTest
[junit] testGetBestClasspath
[junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed:
0,54 sec
[junit]
[junit] ------------- Standard Output ---------------
[junit] testGetBestClasspath
[junit] ------------- ---------------- ---------------
[junit] Testsuite: edu.msu.cme.rdp.classifier.train.validation.
GoodWordIteratorTest
[junit] testNext
[junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed:
0,072 sec
[junit]
[junit] ------------- Standard Output ---------------
[junit] testNext
[junit] ------------- ---------------- ---------------
[junit] Testsuite: edu.msu.cme.rdp.classifier.train.validation.
HierarchyTreeTest
[junit] testHideSeq
[junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed:
0,133 sec
[junit]
[junit] ------------- Standard Output ---------------
[junit] testHideSeq
[junit] ------------- ---------------- ---------------
[junit] Testsuite: edu.msu.cme.rdp.classifier.train.validation.
NBClassifierTest
[junit] testassignClass
[junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed:
0,107 sec
[junit]
[junit] ------------- Standard Output ---------------
[junit] testassignClass
[junit] ------------- ---------------- ---------------
[junit] Testsuite: edu.msu.cme.rdp.classifier.train.validation.
SequenceParserTest
[junit] testNext()
[junit] testHasNext
[junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed:
0,088 sec
[junit]
[junit] ------------- Standard Output ---------------
[junit] testHasNext
[junit] ------------- ---------------- ---------------
[junit] ------------- Standard Error -----------------
[junit] testNext()
[junit] ------------- ---------------- ---------------
[junit] Testsuite: edu.msu.cme.rdp.classifier.train.validation.
TreeFactoryTest
[junit] testAddSequence
[junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed:
0,092 sec
[junit]
[junit] ------------- Standard Output ---------------
[junit] testAddSequence
[junit] ------------- ---------------- ---------------

test-report:

-post-test-run:

BUILD FAILED
/home/orson/RDPTools/classifier/nbproject/build-impl.xml:1304: Some tests
failed; see details above.

Total time: 10 seconds

Please. Help me. Thanks

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@OrsonMM
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Author

OrsonMM commented Sep 7, 2016

Yes actually I download rdp-classifier of https://sourceforge.net/projects/rdp-classifier/rdp_classifier_2.11
and in folder dist appear classifier.jar. apparently, all works okey.
But if I tried with command $ ant -f build.xml and again obtain the same error. I Think that
It's works but I can't understand why dont pass the test.

I see the file in rdp_classifier_2.11/test/edu/msu/cme/rdp/classifier/train/TreeFactoryTest.java

line 55
assertEquals(((RawHierarchyTree) genusNodeList.get(1)).getName(), "G2");

I print the value of these line. It returns G1 and compare these with G2 and obiously the not are equal.
System.out.println(((RawHierarchyTree) genusNodeList.get(1)).getName());

[junit] testAddSequence
[junit] G1
[junit] ------------- ---------------- ---------------
[junit] Testcase: testAddSequence(edu.msu.cme.rdp.classifier.train.TreeFactoryTest):    FAILED
[junit] null expected:G[1] but was:G[2]
[junit] junit.framework.ComparisonFailure: null expected:<G[1]> but was:<G[2]>
[junit]     at edu.msu.cme.rdp.classifier.train.TreeFactoryTest.testAddSequence(TreeFactoryTest.java:55)
[junit] 
[junit] 
[junit] Test edu.msu.cme.rdp.classifier.train.TreeFactoryTest FAILED
[junit] Testsuite: edu.msu.cme.rdp.classifier.train.validation.AddLogsTest
[junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0,07 sec
[junit] 
[junit] Testsuite: edu.msu.cme.rdp.classifier.train.validation.DecisionMakerTest
[junit] testGetBestClasspath
[junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0,524 sec
[junit] 
[junit] ------------- Standard Output ---------------

Maybe I wrong.

@ghost
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ghost commented Sep 12, 2017 •
edited by ghost
Loading

@OrsonMM Hi! I've encountered the same problem as you some time ago (see below) and was wondering if you found a way to overcome it? Appreciate any help! Thank you!

Yes actually I download rdp-classifier of https://sourceforge.net/projects/rdp-classifier/rdp_classifier_2.11
and in folder dist appear classifier.jar. apparently, all works okey.
But if I tried with command $ ant -f build.xml and again obtain the same error. I Think that
It's works but I can't understand why dont pass the test.

I see the file in rdp_classifier_2.11/test/edu/msu/cme/rdp/classifier/train/TreeFactoryTest.java

line 55
assertEquals(((RawHierarchyTree) genusNodeList.get(1)).getName(), "G2");

I print the value of these line. It returns G1 and compare these with G2 and obiously the not are equal.
System.out.println(((RawHierarchyTree) genusNodeList.get(1)).getName());

[junit] testAddSequence
[junit] G1
[junit] ------------- ---------------- ---------------
[junit] Testcase: testAddSequence(edu.msu.cme.rdp.classifier.train.TreeFactoryTest): FAILED
[junit] null expected:G[1] but was:G[2]
[junit] junit.framework.ComparisonFailure: null expected:<G[1]> but was:<G[2]>
[junit] at edu.msu.cme.rdp.classifier.train.TreeFactoryTest.testAddSequence(TreeFactoryTest.java:55)
[junit]
[junit]
[junit] Test edu.msu.cme.rdp.classifier.train.TreeFactoryTest FAILED
[junit] Testsuite: edu.msu.cme.rdp.classifier.train.validation.AddLogsTest
[junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0,07 sec
[junit]
[junit] Testsuite: edu.msu.cme.rdp.classifier.train.validation.DecisionMakerTest
[junit] testGetBestClasspath
[junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0,524 sec
[junit]
[junit] ------------- Standard Output ---------------

@mortonjt
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Would there be any interest in getting this installation progress update in bioconda? It would be great if these dependencies could be bundled ahead of time ...

@mortonjt mortonjt mentioned this issue Jun 28, 2018
Open
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@mortonjt @rdpstaffmsu @OrsonMM