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asad / ReactionDecoder

Reaction Decoder Tool (RDT) - Atom Atom Mapping Tool
GNU Lesser General Public License v3.0
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error while installing ReactionDecoder in Debian 9 "Stretch" #10

Closed diaspj closed 4 years ago

diaspj commented 5 years ago

ERROR INFORMATION:

root@bn:~/Programs_software/ReactionDecoder-master# mvn -DskipTests=true install [INFO] Scanning for projects... [WARNING] The project uk.ac.ebi.rdt:rdt:jar:2.2.0-SNAPSHOT uses prerequisites which is only intended for maven-plugin projects but not for non maven-plugin projects. For such purposes you should use the maven-enforcer-plugin. See https://maven.apache.org/enforcer/enforcer-rules/requireMavenVersion.html [INFO] [INFO] -------------------------< uk.ac.ebi.rdt:rdt >-------------------------- [INFO] Building rdt 2.2.0-SNAPSHOT [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ rdt --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /root/Programs_software/ReactionDecoder-master/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:2.3.2:compile (default-compile) @ rdt --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ rdt --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 23240 resources [INFO] [INFO] --- maven-compiler-plugin:2.3.2:testCompile (default-testCompile) @ rdt --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.12.4:test (default-test) @ rdt --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ rdt --- [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ rdt --- [INFO] Installing /root/Programs_software/ReactionDecoder-master/target/rdt-2.2.0-SNAPSHOT.jar to /root/.m2/repository/uk/ac/ebi/rdt/rdt/2.2.0-SNAPSHOT/rdt-2.2.0-SNAPSHOT.jar [INFO] Installing /root/Programs_software/ReactionDecoder-master/pom.xml to /root/.m2/repository/uk/ac/ebi/rdt/rdt/2.2.0-SNAPSHOT/rdt-2.2.0-SNAPSHOT.pom [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 1.963 s [INFO] Finished at: 2019-06-04T11:25:22+01:00 [INFO] ------------------------------------------------------------------------ root@bn:~/Programs_software/ReactionDecoder-master# mvn install [INFO] Scanning for projects... [WARNING] The project uk.ac.ebi.rdt:rdt:jar:2.2.0-SNAPSHOT uses prerequisites which is only intended for maven-plugin projects but not for non maven-plugin projects. For such purposes you should use the maven-enforcer-plugin. See https://maven.apache.org/enforcer/enforcer-rules/requireMavenVersion.html [INFO] [INFO] -------------------------< uk.ac.ebi.rdt:rdt >-------------------------- [INFO] Building rdt 2.2.0-SNAPSHOT [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ rdt --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /root/Programs_software/ReactionDecoder-master/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:2.3.2:compile (default-compile) @ rdt --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ rdt --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 23240 resources [INFO] [INFO] --- maven-compiler-plugin:2.3.2:testCompile (default-testCompile) @ rdt --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.12.4:test (default-test) @ rdt --- [INFO] Surefire report directory: /root/Programs_software/ReactionDecoder-master/target/surefire-reports

T E S T S

Running uk.ac.bioinception.SMILES2AAMTest uk.ac.ebi.reactionblast.mechanism.ReactionMechanismTool WARN: Unmapped atoms present in this reaction(MAX) algorithm. Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.412 sec Running uk.ac.ebi.aamtool.RXNMappingTest Mapping Reaction R00011 uk.ac.ebi.reactionblast.tools.MappingUtility ERROR: SEVERE Failed to generate image: Container has no bonds. Mapping Reaction R00014 Mapping Reaction R00023 uk.ac.ebi.reactionblast.tools.MappingUtility ERROR: SEVERE Failed to generate image: Container has no bonds. Mapping Reaction R00025 Mapping Reaction R00045 Mapping Reaction R00093 uk.ac.ebi.reactionblast.tools.MappingUtility ERROR: SEVERE Failed to generate image: Container has no bonds. Mapping Reaction R00097 uk.ac.ebi.reactionblast.mechanism.ReactionMechanismTool WARN: Unmapped atoms present in this reaction(MIN) algorithm. uk.ac.ebi.reactionblast.mechanism.ReactionMechanismTool WARN: Unmapped atoms present in this reaction(MAX) algorithm. uk.ac.ebi.reactionblast.mechanism.ReactionMechanismTool WARN: Unmapped atoms present in this reaction(MIXTURE) algorithm. uk.ac.ebi.reactionblast.tools.MappingUtility ERROR: SEVERE Failed to generate image: Container has no bonds. Mapping Reaction R00114 uk.ac.ebi.reactionblast.tools.MappingUtility ERROR: SEVERE Failed to generate image: Container has no bonds. formedCleavedWFingerprint ID=R00114:Bond Cleaved and Formed (5) [C-H:2.0, C-N:2.0, C-O:1.0, C=O:1.0, H-O:1.0]

Mapping Reaction R00307 Mapping Reaction R00344 Mapping Reaction R00630 Mapping Reaction R00959 Mapping Reaction R01015 Mapping Reaction R01068 Mapping Reaction R01081 Mapping Reaction R01145 Mapping Reaction R01148 Mapping Reaction R01394 Mapping Reaction R01432 Mapping Reaction R01518 Mapping Reaction R01529 Mapping Reaction R01557 Mapping Reaction R01569 Mapping Reaction R01715 Mapping Reaction R01717 Mapping Reaction R01819 Mapping Reaction R01903 uk.ac.ebi.reactionblast.tools.MappingUtility ERROR: SEVERE Failed to generate image: Container has no bonds. Mapping Reaction R02007 Mapping Reaction R02555 uk.ac.ebi.reactionblast.tools.MappingUtility ERROR: SEVERE Failed to generate image: Container has no bonds. Mapping Reaction R02707 Mapping Reaction R02718 Mapping Reaction R02918 Mapping Reaction R02996 Mapping Reaction R03020 Mapping Reaction R03063 Mapping Reaction R03187 Mapping Reaction R03332 Mapping Reaction R03364 Mapping Reaction R03627 Mapping Reaction R03673 Mapping Reaction R03959 Mapping Reaction R03979 Mapping Reaction R04165 Mapping Reaction R04333 Mapping Reaction R04538 Mapping Reaction R04558 Mapping Reaction R05069 Mapping Reaction R05071 Mapping Reaction R05137 Mapping Reaction R05217 uk.ac.ebi.reactionblast.tools.MappingUtility ERROR: SEVERE Failed to generate image: Container has no bonds. Mapping Reaction R05219 Mapping Reaction R05421 Mapping Reaction R05645 Mapping Reaction R06361 Mapping Reaction R06989 Mapping Reaction R07322 Mapping Reaction R07393 Mapping Reaction R07635 Mapping Reaction R07965 uk.ac.ebi.reactionblast.tools.MappingUtility ERROR: SEVERE Failed to generate image: Container has no bonds. Mapping Reaction R08639 Mapping Reaction R08761 uk.ac.ebi.reactionblast.tools.MappingUtility ERROR: SEVERE Failed to generate image: Container has no bonds. Mapping Reaction R09087 Mapping Reaction aromaticity_check Mapping Reaction R01561 Mapping Reaction R01194 Mapping Reaction R01188 Mapping Reaction 204 uk.ac.ebi.reactionblast.tools.MappingUtility ERROR: SEVERE Failed to generate image: Container has no bonds. Mapping Reaction 25405 Mapping Reaction R00004 Tests run: 70, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 487.307 sec <<< FAILURE! R04558(uk.ac.ebi.aamtool.RXNMappingTest) Time elapsed: 2.631 sec <<< FAILURE! java.lang.AssertionError: expected:<4> but was:<5> at org.junit.Assert.fail(Assert.java:88) at org.junit.Assert.failNotEquals(Assert.java:743) at org.junit.Assert.assertEquals(Assert.java:118) at org.junit.Assert.assertEquals(Assert.java:555) at org.junit.Assert.assertEquals(Assert.java:542) at uk.ac.ebi.aamtool.RXNMappingTest.R04558(RXNMappingTest.java:1035) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:47) at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12) at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:44) at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17) at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:271) at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:70) at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:50) at org.junit.runners.ParentRunner$3.run(ParentRunner.java:238) at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:63) at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:236) at org.junit.runners.ParentRunner.access$000(ParentRunner.java:53) at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:229) at org.junit.runners.ParentRunner.run(ParentRunner.java:309) at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:252) at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:141) at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:112) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionUtils.java:189) at org.apache.maven.surefire.booter.ProviderFactory$ProviderProxy.invoke(ProviderFactory.java:165) at org.apache.maven.surefire.booter.ProviderFactory.invokeProvider(ProviderFactory.java:85) at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:115) at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:75)

Running org.openscience.smsd.mcs.MCSTest MCS C1OC(CO)C(O)C1O Tests run: 14, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 63.373 sec

Results :

Failed tests: R04558(uk.ac.ebi.aamtool.RXNMappingTest): expected:<4> but was:<5>

Tests run: 86, Failures: 1, Errors: 0, Skipped: 0

[INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 09:20 min [INFO] Finished at: 2019-06-04T11:34:51+01:00 [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.12.4:test (default-test) on project rdt: There are test failures. [ERROR] [ERROR] Please refer to /root/Programs_software/ReactionDecoder-master/target/surefire-reports for the individual test results. [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

asad commented 4 years ago

Thanks. Please try with these two commands 5) mvn -P local clean install -DskipTests=true (fast single jar compilation, skip test) 6) mvn -P local clean install (single jar compilation with test)