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rdpstaff / classifier

RDP extensible sequence classifier for fungal lsu, bacterial and archaeal 16s
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Problem isntalling classifier #16

Open OrsonMM opened 7 years ago

OrsonMM commented 7 years ago

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 commented 7 years ago

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 commented 7 years ago

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 commented 6 years ago

@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 commented 6 years ago

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 ...