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ytchen0323 / cloud-scale-bwamem

Apache License 2.0
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Trouble in compling #4

Open rydrydryd opened 8 years ago

rydrydryd commented 8 years ago

Hey guy! I encountered some troubles in compling. I'm wondering whether it's due to my jre version. So could you plz tell me the information about your compile environment?

rydrydryd commented 8 years ago

Error occurs when I execute mvn package -PotherOutputDir in src dir

[INFO] Scanning for projects... [WARNING] [WARNING] Some problems were encountered while building the effective model for cs.ucla.edu:jniNative:so:0.2.1 [WARNING] 'dependencies.dependency.systemPath' for cs.ucla.edu:cloud-scale-bwamem:jar should use a variable instead of a hard-coded path /home/ryd/Git/cloud-scale-bwamem/target/cloud-scale-bwamem-0.2.2-assembly.jar @ line 19, column 19 [WARNING] 'build.plugins.plugin.version' for org.codehaus.mojo:native-maven-plugin is missing. @ line 33, column 15 [WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-compiler-plugin is missing. @ line 25, column 15 [WARNING] [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build. [WARNING] [WARNING] For this reason, future Maven versions might no longer support building such malformed projects. [WARNING] [INFO]
[INFO] ------------------------------------------------------------------------ [INFO] Building JNI Pair-End Smith-Waterman AVX Library 0.2.1 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- native-maven-plugin:1.0-alpha-8:initialize (default-initialize) @ jniNative --- [INFO] [INFO] --- native-maven-plugin:1.0-alpha-8:unzipinc (default-unzipinc) @ jniNative --- [INFO] [INFO] --- native-maven-plugin:1.0-alpha-8:javah (default-javah) @ jniNative --- [INFO] [INFO] --- native-maven-plugin:1.0-alpha-8:javah (javah) @ jniNative --- [INFO] /bin/sh -c cd /home/ryd/Git/cloud-scale-bwamem/target && javah -o /home/ryd/Git/cloud-scale-bwamem/target/custom-javah/jni_mate_sw.h -classpath /home/ryd/Git/cloud-scale-bwamem/target/classes:/home/ryd/Git/cloud-scale-bwamem/target/cloud-scale-bwamem-0.2.2-assembly.jar cs.ucla.edu.bwaspark.jni.HelloWorld cs.ucla.edu.bwaspark.jni.MateSWType cs.ucla.edu.bwaspark.jni.SeqSWType cs.ucla.edu.bwaspark.jni.MateSWJNI cs.ucla.edu.bwaspark.datatype.MemAlnRegType cs.ucla.edu.bwaspark.datatype.MemOptType cs.ucla.edu.bwaspark.datatype.MemPeStat cs.ucla.edu.bwaspark.datatype.FASTQSingleNode error: error reading /home/ryd/Git/cloud-scale-bwamem/target/cloud-scale-bwamem-0.2.2-assembly.jar; too many entries in ZIP file com.sun.tools.javac.util.Abort at com.sun.tools.javac.comp.Check.completionError(Check.java:169) at com.sun.tools.javadoc.DocEnv.loadClass(DocEnv.java:149) at com.sun.tools.javadoc.RootDocImpl.(RootDocImpl.java:77) at com.sun.tools.javadoc.JavadocTool.getRootDocImpl(JavadocTool.java:156) at com.sun.tools.javadoc.Start.parseAndExecute(Start.java:330) at com.sun.tools.javadoc.Start.begin(Start.java:128) at com.sun.tools.javadoc.Main.execute(Main.java:66) at com.sun.tools.javah.Main.main(Main.java:147) javadoc: error - fatal error 2 errors [INFO] [INFO] --- native-maven-plugin:1.0-alpha-8:compile (default-compile) @ jniNative --- [INFO] /bin/sh -c cd /home/ryd/Git/cloud-scale-bwamem/src && gcc -s -fPIC -O2 -I/home/ryd/Git/cloud-scale-bwamem/src/main/native -I/home/ryd/Git/cloud-scale-bwamem/target/custom-javah -I/opt/oracle-jre-bin-1.7.0.80/../include -I/opt/oracle-jre-bin-1.7.0.80/../include/linux -o/home/ryd/Git/cloud-scale-bwamem/target/objs/jni_hello_world.o -c /home/ryd/Git/cloud-scale-bwamem/src/main/native/jni_hello_world.c /home/ryd/Git/cloud-scale-bwamem/src/main/native/jni_hello_world.c:21:71: fatal error: jni_mate_sw.h: No such file or directory

include // generated by javah via maven-native-plugin

                                                                   ^

compilation terminated. [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 1.995 s [INFO] Finished at: 2016-03-29T22:52:28+08:00 [INFO] Final Memory: 7M/109M [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.codehaus.mojo:native-maven-plugin:1.0-alpha-8:compile (default-compile) on project jniNative: Error executing command line. Exit code:1 -> [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/MojoExecutionException

ytchen0323 commented 8 years ago

Hi, To identify the error, could you provide the following information?

  1. Have you successfully pass the first command "system "mvn clean package";"?
  2. Do you use Java 8 or Java 7? We have tested that currently we cannot support Java 8 because use some packages come from the other group. If you use Java 7, in general there should be no problem. We have tested both Java 1.7.0_75 and 1.7.0_79.
  3. The second error message seems to be some problems about files not found under the given path. Maybe you can share your modified .pom file?

Thanks, Yu-Ting

rydrydryd commented 8 years ago

Thanks guy! I tried to change my jvm from jdk-1.8.0 to into jdk-1.7.0 and all things worked fine.