java.lang.NullPointerException at com.gzoltar.core.GZoltar.run(GZoltar.java:51) #94
Comments
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Hi @brucekuiliu |
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Hi @martinezmatias Could you help me? |
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Hi @brucekuiliu |
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Hi @martinezmatias , |
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Could you execute a test case to see if it works? for instance this one:
https://github.com/SpoonLabs/astor/blob/HEAD/src/test/java/fr/inria/astor/test/repair/approaches/JGenProgTest.java#L393
2018-05-24 15:10 GMT+02:00 Kui LIU <[email protected]>:
… Hi @martinezmatias <https://github.com/martinezmatias> ,
It still does not work.
Here is my command:
java -cp $(cat /tmp/astor-classpath.txt):/Users/kui.liu/eclipse-
workspace/astor/target/classes
fr.inria.main.evolution.AstorMain
-mode jGenProg
-srcjavafolder /src/java/
-srctestfolder /src/test/
-binjavafolder /target/classes/
-bintestfolder /target/test-classes/
-location /Users/kui.liu/eclipse-workspace/astor/examples/Math-issue-280/
-dependencies /Users/kui.liu/eclipse-workspace/astor/examples/Math-
issue-280/lib
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.
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Test cases are failed because of the same problem: java.lang.NullPointerException I test GZoltar with JDK 1.7, the problem is gone. |
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I use java 8 due the code of Astor needs java 8. |
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Hello, I also met this Exception.
when I input the follow command: |
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Hello @nju-grx Could you check if inside the project under repair (in your example /home/grx/project/defects4j/Closure_1) there is the bin folder (that one specified -binjavafolder build/classes/ ) and there are classes there? In other words, please check if you have compiled the project under repair (using maven or the Defects4J infrastructure) Regards |
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@martinezmatias Thanks for your reply. I have compiled the project under repair and checked the folder. Furthermore, I take input as closure_1 in astor(./examples/closure_1) as follows and meet the same exception.
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Hi, @martinezmatias java -cp astor-0.0.2-SNAPSHOT-jar-with-dependencies.jar fr.inria.main.evolution.AstorMain -mode jkali -location /data/math/math_70_buggy -package org.apache.commons -jvm4testexecution /home/kaka/tool/jdk1.7.0_80/bin/ -failing org.apache.commons.math.analysis.solvers.BisectionSolverTest -srcjavafolder /src/java/ -srctestfolder /src/test/ -binjavafolder /target/classes -bintestfolder /target/test-classes -flthreshold 0.5 -stopfirst true -dependencies /home/kaka/Desktop/astor/examples/libs/junit-4.4.jar Then I change the parameter "dependencies" to /home/kaka/Desktop/astor/examples/libs |
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Hi @martinezmatias I switched to Option 2 using the classpath and the repair ran successfully. Not sure if this helps. |
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I met this error today and I solved it by do the following things: What I did is to run the install command under /astor/lib/gzoltar. The install command is provided in the directory and it is "mvn install:install-file -Dfile=lib/gzoltar/com.gzoltar-0.0.3.jar -DgroupId=com.gzoltar -DartifactId=gzoltar -Dversion=0.0.3 -Dpackaging=jar" Next, I moved this directory /astor/lib/gzoltar into the /astor/examples/Math-issue-280/lib and run the install command. Then I recompile the Astor and the Math-issue-280. Then I run the command and it works successfully. This my command : Hope this could help. |
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Hi @WuYff Thanks a lot for the info. It would be amazing if you can do a PR that updates the docs explaining "if you have a NP with GZoltar [...]" Thanks |
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Dear @WuYff and @martinezmatias, I failed to see how the instructions proposed in PR #209 could address the null pointer exception, which by the way I'm also getting (a lot). Why would anyone need to (manually) install Please find below a step-by-step on how to reproduce the null pointer exception in a real bug. $ mkdir /tmp/debug_pr_209_and_issue_94
# Get Astor
$ cd /tmp/debug_pr_209_and_issue_94/astor
$ git clone https://github.com/SpoonLabs/astor.git
$ cd astor
$ git checkout 8581b1c686103352e7f6189f54437ea1e46f0c36 # latest commit as of 27/Fev/2020
$ mvn -Dmaven.repo.local=.m2 -DskipTests -DskipUTs=true -DskipITs=true package
# Get Bears benchmark
$ cd /tmp/debug_pr_209_and_issue_94
$ git clone https://github.com/bears-bugs/bears-benchmark.git
# Get 2018swecapstone-h2ms::363210218-363627522 bug
$ cd /tmp/debug_pr_209_and_issue_94/bears-benchmark
$ git checkout 6616eba1b77647d6ac1740e79931b71e580b4780 # buggy version of 2018swecapstone-h2ms::363210218-363627522
$ mvn -Dmaven.repo.local=.m2 install -DskipTests -DskipUTs=true -DskipITs=true \
-V -B -U -Dhttps.protocols=TLSv1.2 \
-Denforcer.skip=true \
-Dcheckstyle.skip=true \
-Dcobertura.skip=true \
-Djacoco.skip=true \
-Drat.skip=true \
-Drat.ignoreErrors=true \
-Drat.numUnapprovedLicenses=1000000 \
-Dlicense.skip=true \
-Dfindbugs.skip=true \
-Dgpg.skip=true \
-Dskip.npm=true \
-Dskip.gulp=true \
-Dskip.bower=true \
-Dbaseline.skip=true \
--fail-never
$ mvn -Dmaven.repo.local=.m2 dependency:build-classpath -B | egrep -v "(^\[INFO\]|^\[WARNING\])" > bug-classpath.txt
# Are there any failing test cases?
$ cd /tmp/debug_pr_209_and_issue_94/bears-benchmark
$ mvn -Dmaven.repo.local=.m2 clean test
...
Results :
Failed tests:
UserTest.testEmailIsLowerCase:54
Expected: is "[email protected]"
but: was "[email protected]"
Tests in error:
UserDetailsServiceTest.testLoadUserByUsernameIsCaseInsensitive:60 » UsernameNotFound
Tests run: 104, Failures: 1, Errors: 1, Skipped: 0
# Repair it
$ cd /tmp/debug_pr_209_and_issue_94/bears-benchmark
$ java -cp /tmp/debug_pr_209_and_issue_94/astor/target/astor-1.0.0-SNAPSHOT-jar-with-dependencies.jar fr.inria.main.evolution.AstorMain \
-seed 0 \
-mode jGenProg \
-srcjavafolder src/main/java/ \
-srctestfolder src/test/java/ \
-binjavafolder target/classes/ \
-bintestfolder target/test-classes/ \
-location /tmp/debug_pr_209_and_issue_94/bears-benchmark \
-dependencies $(cat /tmp/debug_pr_209_and_issue_94/bears-benchmark/bug-classpath.txt)
[INFO] 15:33:22,644 fr.inria.astor.core.setup.ProjectConfiguration:282 - Version of the JVM used: 1.8.0_212
[INFO] 15:33:22,646 main:381 - Java version of the JDK used to run tests: 1.8.0_212
[INFO] 15:33:22,646 main:382 - The compliance of the JVM is: 8
[INFO] 15:33:22,647 main:664 - command line arguments: [-seed 0 -mode jGenProg -srcjavafolder src/main/java/ -srctestfolder src/test/java/ -binjavafolder target/classes/ -bintestfolder target/test-classes/ -location /tmp/debug_pr_209_and_issue_94/bears-benchmark -dependencies /private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/springframework/boot/spring-boot-starter-data-rest/1.5.10.RELEASE/spring-boot-starter-data-rest-1.5.10.RELEASE.jar:/private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/springframework/boot/spring-boot-starter/1.5.10.RELEASE/spring-boot-starter-1.5.10.RELEASE.jar:/private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/springframework/boot/spring-boot/1.5.10.RELEASE/spring-boot-1.5.10.RELEASE.jar:/private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/springframework/boot/spring-boot-autoconfigure/1.5.10.RELEASE/spring-boot-autoconfigure-1.5.10.RELEASE.jar:/private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/springframework/boot/spring-boot-starter-logging/1.5.10.RELEASE/spring-boot-starter-logging-1.5.10.RELEASE.jar:/private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/ch/qos/logback/logback-classic/1.1.11/logback-classic-1.1.11.jar:/private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/ch/qos/logback/logback-core/1.1.11/logback-core-1.1.11.jar:/private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/slf4j/jul-to-slf4j/1.7.25/jul-to-slf4j-1.7.25.jar:/private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/slf4j/log4j-over-slf4j/1.7.25/log4j-over-slf4j-1.7.25.jar:/private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/yaml/snakeyaml/1.17/snakeyaml-1.17.jar:/private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/com/fasterxml/jackson/core/jackson-annotations/2.8.0/jackson-annotations-2.8.0.jar:/private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/springframework/data/spring-data-rest-webmvc/2.6.10.RELEASE/spring-data-rest-webmvc-2.6.10.RELEASE.jar:/private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/springframework/data/spring-data-rest-core/2.6.10.RELEASE/spring-data-rest-core-2.6.10.RELEASE.jar:/private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/atteo/evo-inflector/1.2.2/evo-inflector-1.2.2.jar:/private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/slf4j/jcl-over-slf4j/1.7.25/jcl-over-slf4j-1.7.25.jar:/private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/springframework/boot/spring-boot-starter-web/1.5.10.RELEASE/spring-boot-starter-web-1.5.10.RELEASE.jar:/private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/springframework/boot/spring-boot-starter-tomcat/1.5.10.RELEASE/spring-boot-starter-tomcat-1.5.10.RELEASE.jar:/private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/apache/tomcat/embed/tomcat-embed-core/8.5.27/tomcat-embed-core-8.5.27.jar:/private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/apache/tomcat/tomcat-annotations-api/8.5.27/tomcat-annotations-api-8.5.27.jar:/private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/apache/tomcat/embed/tomcat-embed-el/8.5.27/tomcat-embed-el-8.5.27.jar:/private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/apache/tomcat/embed/tomcat-embed-websocket/8.5.27/tomcat-embed-websocket-8.5.27.jar:/private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/hibernate/hibernate-validator/5.3.6.Final/hibernate-validator-5.3.6.Final.jar:/private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/javax/validation/validation-api/1.1.0.Final/validation-api-1.1.0.Final.jar:/private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/jboss/logging/jboss-logging/3.3.1.Final/jboss-logging-3.3.1.Final.jar:/private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/springframework/spring-web/4.3.14.RELEASE/spring-web-4.3.14.RELEASE.jar]
[INFO] 15:33:22,650 fr.inria.main.evolution.AstorMain:206 - Running Astor on a JDK at /Library/Java/JavaVirtualMachines/jdk1.8.0_212.jdk/Contents/Home/jre
[INFO ] fr.inria.main.AbstractMain.determineSourceFolders(AbstractMain.java:982) - Source folders: [/tmp/debug_pr_209_and_issue_94/bears-benchmark/src/main/java]
[INFO ] fr.inria.main.AbstractMain.determineSourceFolders(AbstractMain.java:1001) - Source Test folders: [/tmp/debug_pr_209_and_issue_94/bears-benchmark/src/test/java]
[INFO ] fr.inria.astor.core.solutionsearch.AstorCoreEngine.calculateSuspicious(AstorCoreEngine.java:901) - Test retrieved from classes: 9
[INFO ] fr.inria.astor.core.faultlocalization.gzoltar.GZoltarFaultLocalization.calculateSuspicious(GZoltarFaultLocalization.java:68) - -Executing Gzoltar classpath: /private/tmp/debug_pr_209_and_issue_94/./output_astor/AstorMain-bears-benchmark//bin//default from 9 classes with test cases
[INFO ] fr.inria.astor.core.faultlocalization.gzoltar.GZoltarFaultLocalization.searchSuspicious(GZoltarFaultLocalization.java:148) - Gzoltar fault localization: min susp value parameter: 0.1
[INFO ] fr.inria.astor.core.faultlocalization.gzoltar.GZoltarFaultLocalization.searchSuspicious(GZoltarFaultLocalization.java:168) - -gz-Adding classpath: [/private/tmp/debug_pr_209_and_issue_94/./output_astor/AstorMain-bears-benchmark//bin//default, /private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/springframework/boot/spring-boot-starter-data-rest/1.5.10.RELEASE/spring-boot-starter-data-rest-1.5.10.RELEASE.jar, /private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/springframework/boot/spring-boot-starter/1.5.10.RELEASE/spring-boot-starter-1.5.10.RELEASE.jar, /private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/springframework/boot/spring-boot/1.5.10.RELEASE/spring-boot-1.5.10.RELEASE.jar, /private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/springframework/boot/spring-boot-autoconfigure/1.5.10.RELEASE/spring-boot-autoconfigure-1.5.10.RELEASE.jar, /private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/springframework/boot/spring-boot-starter-logging/1.5.10.RELEASE/spring-boot-starter-logging-1.5.10.RELEASE.jar, /private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/ch/qos/logback/logback-classic/1.1.11/logback-classic-1.1.11.jar, /private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/ch/qos/logback/logback-core/1.1.11/logback-core-1.1.11.jar, /private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/slf4j/jul-to-slf4j/1.7.25/jul-to-slf4j-1.7.25.jar, /private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/slf4j/log4j-over-slf4j/1.7.25/log4j-over-slf4j-1.7.25.jar, /private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/yaml/snakeyaml/1.17/snakeyaml-1.17.jar, /private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/com/fasterxml/jackson/core/jackson-annotations/2.8.0/jackson-annotations-2.8.0.jar, /private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/springframework/data/spring-data-rest-webmvc/2.6.10.RELEASE/spring-data-rest-webmvc-2.6.10.RELEASE.jar, /private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/springframework/data/spring-data-rest-core/2.6.10.RELEASE/spring-data-rest-core-2.6.10.RELEASE.jar, /private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/atteo/evo-inflector/1.2.2/evo-inflector-1.2.2.jar, /private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/slf4j/jcl-over-slf4j/1.7.25/jcl-over-slf4j-1.7.25.jar, /private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/springframework/boot/spring-boot-starter-web/1.5.10.RELEASE/spring-boot-starter-web-1.5.10.RELEASE.jar, /private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/springframework/boot/spring-boot-starter-tomcat/1.5.10.RELEASE/spring-boot-starter-tomcat-1.5.10.RELEASE.jar, /private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/apache/tomcat/embed/tomcat-embed-core/8.5.27/tomcat-embed-core-8.5.27.jar, /private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/apache/tomcat/tomcat-annotations-api/8.5.27/tomcat-annotations-api-8.5.27.jar, /private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/apache/tomcat/embed/tomcat-embed-el/8.5.27/tomcat-embed-el-8.5.27.jar, /private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/apache/tomcat/embed/tomcat-embed-websocket/8.5.27/tomcat-embed-websocket-8.5.27.jar, /private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/hibernate/hibernate-validator/5.3.6.Final/hibernate-validator-5.3.6.Final.jar, /private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/javax/validation/validation-api/1.1.0.Final/validation-api-1.1.0.Final.jar, /private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/jboss/logging/jboss-logging/3.3.1.Final/jboss-logging-3.3.1.Final.jar, /private/tmp/debug_pr_209_and_issue_94/bears-benchmark/.m2/org/springframework/spring-web/4.3.14.RELEASE/spring-web-4.3.14.RELEASE.jar]
Exception in thread "main" java.lang.NullPointerException
at com.gzoltar.core.GZoltar.run(GZoltar.java:51)
at fr.inria.astor.core.faultlocalization.gzoltar.GZoltarFaultLocalization.searchSuspicious(GZoltarFaultLocalization.java:197)
at fr.inria.astor.core.faultlocalization.gzoltar.GZoltarFaultLocalization.calculateSuspicious(GZoltarFaultLocalization.java:87)
at fr.inria.astor.core.faultlocalization.gzoltar.GZoltarFaultLocalization.searchSuspicious(GZoltarFaultLocalization.java:42)
at fr.inria.astor.core.solutionsearch.AstorCoreEngine.calculateSuspicious(AstorCoreEngine.java:905)
at fr.inria.main.evolution.AstorMain.createEngine(AstorMain.java:115)
at fr.inria.main.evolution.AstorMain.run(AstorMain.java:169)
at fr.inria.main.evolution.AstorMain.execute(AstorMain.java:229)
at fr.inria.main.evolution.AstorMain.main(AstorMain.java:200) |
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Hi @jose |
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Hi @martinezmatias, I'm sorry, completely forgot to mention that. I'm currently using Oracle JDK 8u181-b13. -- |
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Hi @jose
Thanks for the info. I will check. I have recently found lot of NPE of Gzoltar and it's really hard to know what is happening. We would like to use another version. As we dont have the code of Gzoltar 0.1.1, Do you think it could be possible to integrate a later version of Gzoltar (i.e., that one from Gitthub)? WDYT? |
Yes, please, and I will be happy to help you with that. But first, I will have to know more details on how Astor does use GZoltar. -- |
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Hi Jose, Perfect. Astor propose an interface (here) that represents a fault localization approach. Thus, we can extend Astor with implementations of that interfaces. |
I follow the command in https://github.com/SpoonLabs/astor/blob/master/docs/getting-starting.md .
Here is my command:
java -cp $(cat /tmp/astor-classpath.txt):target/classes fr.inria.main.evolution.AstorMain -mode jGenProg -srcjavafolder /src/java/ -srctestfolder /src/test/ -binjavafolder /target/classes/ -bintestfolder /target/test-classes/ -location /Users/kui.liu/eclipse-workspace/astor/examples/Math-issue-280/ -dependencies examples/Math-issue-280/lib
2018-05-24 12:00:01,996 INFO main - command line arguments: [-mode jGenProg -srcjavafolder /src/java/ -srctestfolder /src/test/ -binjavafolder /target/classes/ -bintestfolder /target/test-classes/ -location /Users/kui.liu/eclipse-workspace/astor/examples/Math-issue-280/ -dependencies examples/Math-issue-280/lib]
[INFO ] fr.inria.main.AbstractMain.determineSourceFolders(AbstractMain.java:806) - Source folders: [/Users/kui.liu/eclipse-workspace/astor/examples/Math-issue-280/src/java]
[INFO ] fr.inria.main.AbstractMain.determineSourceFolders(AbstractMain.java:825) - Source Test folders: [/Users/kui.liu/eclipse-workspace/astor/examples/Math-issue-280/src/test]
[INFO ] fr.inria.astor.core.setup.ProjectConfiguration.addLocationToClasspath(ProjectConfiguration.java:140) - Adding to classpath junit-4.4.jar
[INFO ] fr.inria.astor.core.faultlocalization.gzoltar.GZoltarFaultLocalization.calculateSuspicious(GZoltarFaultLocalization.java:75) - -Executing Gzoltar classpath: /Users/kui.liu/eclipse-workspace/astor/./output_astor/AstorMain-Math-issue-280//bin//default from 214 classes with test cases
[INFO ] fr.inria.astor.core.faultlocalization.gzoltar.GZoltarFaultLocalization.searchSuspicious(GZoltarFaultLocalization.java:149) - Gzoltar fault localization: min susp value parameter: 0.1
[INFO ] fr.inria.astor.core.faultlocalization.gzoltar.GZoltarFaultLocalization.searchSuspicious(GZoltarFaultLocalization.java:169) - -gz-Adding classpath: [/Users/kui.liu/eclipse-workspace/astor/examples/Math-issue-280/lib/, /Users/kui.liu/eclipse-workspace/astor/examples/Math-issue-280/lib/junit-4.4.jar, /Users/kui.liu/eclipse-workspace/astor/./output_astor/AstorMain-Math-issue-280//bin//default]
Exception in thread "main" java.lang.NullPointerException
at com.gzoltar.core.GZoltar.run(GZoltar.java:51)
at fr.inria.astor.core.faultlocalization.gzoltar.GZoltarFaultLocalization.searchSuspicious(GZoltarFaultLocalization.java:196)
at fr.inria.astor.core.faultlocalization.gzoltar.GZoltarFaultLocalization.calculateSuspicious(GZoltarFaultLocalization.java:87)
at fr.inria.astor.core.faultlocalization.gzoltar.GZoltarFaultLocalization.searchSuspicious(GZoltarFaultLocalization.java:49)
at fr.inria.astor.core.solutionsearch.AstorCoreEngine.calculateSuspicious(AstorCoreEngine.java:1270)
at fr.inria.main.evolution.AstorMain.createEngine(AstorMain.java:121)
at fr.inria.main.evolution.AstorMain.run(AstorMain.java:176)
at fr.inria.main.evolution.AstorMain.execute(AstorMain.java:230)
at fr.inria.main.evolution.AstorMain.main(AstorMain.java:207)
The text was updated successfully, but these errors were encountered: