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imagej / imagej-launcher

The ImageJ native launcher
https://imagej.net/learn/launcher
BSD 2-Clause "Simplified" License
21 stars 23 forks source link

Build fails on Ubuntu 20.04 #70

Closed axtimwalde closed 3 years ago

axtimwalde commented 3 years ago 
mvn -e clean package
[INFO] Error stacktraces are turned on.
[INFO] Scanning for projects...
[INFO] 
[INFO] ---------------------< net.imagej:imagej-launcher >---------------------
[INFO] Building ImageJ Launcher 5.0.3
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ imagej-launcher ---
[INFO] Deleting /home/saalfeld/workspace/imagej/imagej-launcher/target
[INFO] 
[INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-rules) @ imagej-launcher ---
[INFO] Adding ignore: module-info
[INFO] Adding ignore: META-INF/versions/*/module-info
[INFO] Adding ignore: org.apache.hadoop.yarn.*.package-info
[INFO] Adding ignore: org.apache.spark.unused.UnusedStubClass
[INFO] Adding ignore: org.hibernate.stat.ConcurrentStatisticsImpl
[INFO] Adding ignore: org.junit.runner.Runner
[INFO] Adding ignore: module-info
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:regex-property (sanitize-version) @ imagej-launcher ---
[INFO] 
[INFO] --- buildnumber-maven-plugin:1.4:create (default) @ imagej-launcher ---
[INFO] Executing: /bin/sh -c cd '/home/saalfeld/workspace/imagej/imagej-launcher' && 'git' 'rev-parse' '--verify' 'HEAD'
[INFO] Working directory: /home/saalfeld/workspace/imagej/imagej-launcher
[INFO] Storing buildNumber: 3a66f7971280eb1f416efc6a9e06011afe1fd40e at timestamp: 1596489349353
[WARNING] Cannot get the branch information from the git repository: 
Detecting the current branch failed: fatal: ref HEAD is not a symbolic ref

[INFO] Executing: /bin/sh -c cd '/home/saalfeld/workspace/imagej/imagej-launcher' && 'git' 'rev-parse' '--verify' 'HEAD'
[INFO] Working directory: /home/saalfeld/workspace/imagej/imagej-launcher
[INFO] Storing buildScmBranch: UNKNOWN
[INFO] 
[INFO] --- scijava-maven-plugin:1.1.0:set-rootdir (set-rootdir) @ imagej-launcher ---
[INFO] Setting rootdir: /home/saalfeld/workspace/imagej/imagej-launcher
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ imagej-launcher ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/saalfeld/workspace/imagej/imagej-launcher/src/main/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.7.0:compile (default-compile) @ imagej-launcher ---
[INFO] Compiling 6 source files to /home/saalfeld/workspace/imagej/imagej-launcher/target/classes
[INFO] 
[INFO] --- maven-antrun-plugin:1.8:run (make) @ imagej-launcher ---
[INFO] Executing tasks

main:
     [exec] -- The C compiler identification is GNU 9.3.0
     [exec] -- Check for working C compiler: /usr/bin/cc
     [exec] -- Check for working C compiler: /usr/bin/cc -- works
     [exec] -- Detecting C compiler ABI info
     [exec] -- Detecting C compiler ABI info - done
     [exec] -- Detecting C compile features
     [exec] -- Detecting C compile features - done
     [exec] -- Configuring incomplete, errors occurred!
     [exec] See also "/home/saalfeld/workspace/imagej/imagej-launcher/target/CMakeFiles/CMakeOutput.log".
     [exec] CMake Error at /usr/share/cmake-3.16/Modules/FindPackageHandleStandardArgs.cmake:146 (message):
     [exec]   Could NOT find JNI (missing: JAVA_AWT_INCLUDE_PATH)
     [exec] Call Stack (most recent call first):
     [exec]   /usr/share/cmake-3.16/Modules/FindPackageHandleStandardArgs.cmake:393 (_FPHSA_FAILURE_MESSAGE)
     [exec]   /usr/share/cmake-3.16/Modules/FindJNI.cmake:372 (FIND_PACKAGE_HANDLE_STANDARD_ARGS)
     [exec]   CMakeLists.txt:27 (find_package)
     [exec] 
     [exec] 
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  4.567 s
[INFO] Finished at: 2020-08-03T17:15:52-04:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-antrun-plugin:1.8:run (make) on project imagej-launcher: An Ant BuildException has occured: exec returned: 1
[ERROR] around Ant part ...<exec failonerror="true" dir="/home/saalfeld/workspace/imagej/imagej-launcher/target" executable="cmake">... @ 4:108 in /home/saalfeld/workspace/imagej/imagej-launcher/target/antrun/build-main.xml
[ERROR] -> [Help 1]
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-antrun-plugin:1.8:run (make) on project imagej-launcher: An Ant BuildException has occured: exec returned: 1
around Ant part ...<exec failonerror="true" dir="/home/saalfeld/workspace/imagej/imagej-launcher/target" executable="cmake">... @ 4:108 in /home/saalfeld/workspace/imagej/imagej-launcher/target/antrun/build-main.xml
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:215)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:156)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:148)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:81)
    at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build (SingleThreadedBuilder.java:56)
    at org.apache.maven.lifecycle.internal.LifecycleStarter.execute (LifecycleStarter.java:128)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:305)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:192)
    at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:105)
    at org.apache.maven.cli.MavenCli.execute (MavenCli.java:957)
    at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:289)
    at org.apache.maven.cli.MavenCli.main (MavenCli.java:193)
    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.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced (Launcher.java:282)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launch (Launcher.java:225)
    at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode (Launcher.java:406)
    at org.codehaus.plexus.classworlds.launcher.Launcher.main (Launcher.java:347)
Caused by: org.apache.maven.plugin.MojoExecutionException: An Ant BuildException has occured: exec returned: 1
around Ant part ...<exec failonerror="true" dir="/home/saalfeld/workspace/imagej/imagej-launcher/target" executable="cmake">... @ 4:108 in /home/saalfeld/workspace/imagej/imagej-launcher/target/antrun/build-main.xml
    at org.apache.maven.plugin.antrun.AntRunMojo.execute (AntRunMojo.java:342)
    at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo (DefaultBuildPluginManager.java:137)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:210)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:156)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:148)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:81)
    at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build (SingleThreadedBuilder.java:56)
    at org.apache.maven.lifecycle.internal.LifecycleStarter.execute (LifecycleStarter.java:128)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:305)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:192)
    at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:105)
    at org.apache.maven.cli.MavenCli.execute (MavenCli.java:957)
    at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:289)
    at org.apache.maven.cli.MavenCli.main (MavenCli.java:193)
    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.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced (Launcher.java:282)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launch (Launcher.java:225)
    at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode (Launcher.java:406)
    at org.codehaus.plexus.classworlds.launcher.Launcher.main (Launcher.java:347)
Caused by: org.apache.tools.ant.BuildException: exec returned: 1
    at org.apache.tools.ant.taskdefs.ExecTask.runExecute (ExecTask.java:643)
    at org.apache.tools.ant.taskdefs.ExecTask.runExec (ExecTask.java:669)
    at org.apache.tools.ant.taskdefs.ExecTask.execute (ExecTask.java:495)
    at org.apache.tools.ant.UnknownElement.execute (UnknownElement.java:292)
    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.tools.ant.dispatch.DispatchUtils.execute (DispatchUtils.java:106)
    at org.apache.tools.ant.Task.perform (Task.java:348)
    at org.apache.tools.ant.Target.execute (Target.java:435)
    at org.apache.tools.ant.Target.performTasks (Target.java:456)
    at org.apache.tools.ant.Project.executeSortedTargets (Project.java:1393)
    at org.apache.tools.ant.Project.executeTarget (Project.java:1364)
    at org.apache.maven.plugin.antrun.AntRunMojo.execute (AntRunMojo.java:313)
    at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo (DefaultBuildPluginManager.java:137)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:210)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:156)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:148)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:81)
    at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build (SingleThreadedBuilder.java:56)
    at org.apache.maven.lifecycle.internal.LifecycleStarter.execute (LifecycleStarter.java:128)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:305)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:192)
    at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:105)
    at org.apache.maven.cli.MavenCli.execute (MavenCli.java:957)
    at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:289)
    at org.apache.maven.cli.MavenCli.main (MavenCli.java:193)
    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.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced (Launcher.java:282)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launch (Launcher.java:225)
    at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode (Launcher.java:406)
    at org.codehaus.plexus.classworlds.launcher.Launcher.main (Launcher.java:347)
[ERROR] 
[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
axtimwalde commented 3 years ago 
cat /home/saalfeld/workspace/imagej/imagej-launcher/target/CMakeFiles/CMakeOutput.log
The system is: Linux - 5.4.0-42-generic - x86_64
Compiling the C compiler identification source file "CMakeCCompilerId.c" succeeded.
Compiler: /usr/bin/cc 
Build flags: 
Id flags:  

The output was:
0

Compilation of the C compiler identification source "CMakeCCompilerId.c" produced "a.out"

The C compiler identification is GNU, found in "/home/saalfeld/workspace/imagej/imagej-launcher/target/CMakeFiles/3.16.3/CompilerIdC/a.out"

Determining if the C compiler works passed with the following output:
Change Dir: /home/saalfeld/workspace/imagej/imagej-launcher/target/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make cmTC_52af6/fast && /usr/bin/make -f CMakeFiles/cmTC_52af6.dir/build.make CMakeFiles/cmTC_52af6.dir/build
make[1]: Entering directory '/home/saalfeld/workspace/imagej/imagej-launcher/target/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_52af6.dir/testCCompiler.c.o
/usr/bin/cc    -o CMakeFiles/cmTC_52af6.dir/testCCompiler.c.o   -c /home/saalfeld/workspace/imagej/imagej-launcher/target/CMakeFiles/CMakeTmp/testCCompiler.c
Linking C executable cmTC_52af6
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_52af6.dir/link.txt --verbose=1
/usr/bin/cc      CMakeFiles/cmTC_52af6.dir/testCCompiler.c.o  -o cmTC_52af6 
make[1]: Leaving directory '/home/saalfeld/workspace/imagej/imagej-launcher/target/CMakeFiles/CMakeTmp'

Detecting C compiler ABI info compiled with the following output:
Change Dir: /home/saalfeld/workspace/imagej/imagej-launcher/target/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make cmTC_ca580/fast && /usr/bin/make -f CMakeFiles/cmTC_ca580.dir/build.make CMakeFiles/cmTC_ca580.dir/build
make[1]: Entering directory '/home/saalfeld/workspace/imagej/imagej-launcher/target/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_ca580.dir/CMakeCCompilerABI.c.o
/usr/bin/cc   -v -o CMakeFiles/cmTC_ca580.dir/CMakeCCompilerABI.c.o   -c /usr/share/cmake-3.16/Modules/CMakeCCompilerABI.c
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GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu"
ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/9/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/9/../../../../x86_64-linux-gnu/include"
#include "..." search starts here:
#include <...> search starts here:
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GNU C17 (Ubuntu 9.3.0-10ubuntu2) version 9.3.0 (x86_64-linux-gnu)
    compiled by GNU C version 9.3.0, GMP version 6.2.0, MPFR version 4.0.2, MPC version 1.1.0, isl version isl-0.22.1-GMP

GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: 18dc4c39b54390aa2b5013fb4339d43f
COLLECT_GCC_OPTIONS='-v' '-o' 'CMakeFiles/cmTC_ca580.dir/CMakeCCompilerABI.c.o' '-c' '-mtune=generic' '-march=x86-64'
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GNU assembler version 2.34 (x86_64-linux-gnu) using BFD version (GNU Binutils for Ubuntu) 2.34
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Linking C executable cmTC_ca580
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_ca580.dir/link.txt --verbose=1
/usr/bin/cc     -v CMakeFiles/cmTC_ca580.dir/CMakeCCompilerABI.c.o  -o cmTC_ca580 
Using built-in specs.
COLLECT_GCC=/usr/bin/cc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/9/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none:hsa
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Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 9.3.0-10ubuntu2' --with-bugurl=file:///usr/share/doc/gcc-9/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,gm2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-9 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
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COLLECT_GCC_OPTIONS='-v' '-o' 'cmTC_ca580' '-mtune=generic' '-march=x86-64'
make[1]: Leaving directory '/home/saalfeld/workspace/imagej/imagej-launcher/target/CMakeFiles/CMakeTmp'

Parsed C implicit include dir info from above output: rv=done
  found start of include info
  found start of implicit include info
    add: [/usr/lib/gcc/x86_64-linux-gnu/9/include]
    add: [/usr/local/include]
    add: [/usr/include/x86_64-linux-gnu]
    add: [/usr/include]
  end of search list found
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axtimwalde commented 3 years ago

Found a related bug:

https://github.com/jvm-profiling-tools/perf-map-agent/issues/53

This needs $JAVA_HOME to be set, then it builds:

JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64 mvn clean package -e