pip install javabridge fails Debian bookworm

[danielcanals2017]

Hi,

I am running Python 3.9.12. When I try to install javabridge, I get:

This is the complete message:

~$ pip install javabridge
Collecting javabridge
  Using cached javabridge-1.0.19.tar.gz (1.3 MB)
Requirement already satisfied: numpy in ./anaconda3/lib/python3.9/site-packages (from javabridge) (1.21.5)
Building wheels for collected packages: javabridge
  Building wheel for javabridge (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /home/daniel/anaconda3/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-s0lz53l9/javabridge_b94975d5c7214110afb660100a3389ac/setup.py'"'"'; __file__='"'"'/tmp/pip-install-s0lz53l9/javabridge_b94975d5c7214110afb660100a3389ac/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-j5rddnbt
       cwd: /tmp/pip-install-s0lz53l9/javabridge_b94975d5c7214110afb660100a3389ac/
  Complete output (27 lines):
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-3.9
  creating build/lib.linux-x86_64-3.9/javabridge
  copying javabridge/locate.py -> build/lib.linux-x86_64-3.9/javabridge
  copying javabridge/jutil.py -> build/lib.linux-x86_64-3.9/javabridge
  copying javabridge/__init__.py -> build/lib.linux-x86_64-3.9/javabridge
  copying javabridge/_version.py -> build/lib.linux-x86_64-3.9/javabridge
  copying javabridge/wrappers.py -> build/lib.linux-x86_64-3.9/javabridge
  copying javabridge/noseplugin.py -> build/lib.linux-x86_64-3.9/javabridge
  creating build/lib.linux-x86_64-3.9/javabridge/tests
  copying javabridge/tests/test_cpython.py -> build/lib.linux-x86_64-3.9/javabridge/tests
  copying javabridge/tests/test_wrappers.py -> build/lib.linux-x86_64-3.9/javabridge/tests
  copying javabridge/tests/__init__.py -> build/lib.linux-x86_64-3.9/javabridge/tests
  copying javabridge/tests/test_javabridge.py -> build/lib.linux-x86_64-3.9/javabridge/tests
  copying javabridge/tests/test_jutil.py -> build/lib.linux-x86_64-3.9/javabridge/tests
  creating build/lib.linux-x86_64-3.9/javabridge/jars
  copying javabridge/jars/runnablequeue.jar -> build/lib.linux-x86_64-3.9/javabridge/jars
  copying javabridge/jars/rhino-1.7R4.jar -> build/lib.linux-x86_64-3.9/javabridge/jars
  copying javabridge/jars/test.jar -> build/lib.linux-x86_64-3.9/javabridge/jars
  copying javabridge/jars/cpython.jar -> build/lib.linux-x86_64-3.9/javabridge/jars
  copying javabridge/jars/libjava2cpython.so -> build/lib.linux-x86_64-3.9/javabridge/jars
  running build_ext
  javac /tmp/pip-install-s0lz53l9/javabridge_b94975d5c7214110afb660100a3389ac/java/org/cellprofiler/runnablequeue/RunnableQueue.java
  error: command 'javac' failed: No such file or directory
  ----------------------------------------
  ERROR: Failed building wheel for javabridge
  Running setup.py clean for javabridge
Failed to build javabridge
Installing collected packages: javabridge
    Running setup.py install for javabridge ... error
    ERROR: Command errored out with exit status 1:
     command: /home/daniel/anaconda3/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-s0lz53l9/javabridge_b94975d5c7214110afb660100a3389ac/setup.py'"'"'; __file__='"'"'/tmp/pip-install-s0lz53l9/javabridge_b94975d5c7214110afb660100a3389ac/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-p0d0e4jr/install-record.txt --single-version-externally-managed --compile --install-headers /home/daniel/anaconda3/include/python3.9/javabridge
         cwd: /tmp/pip-install-s0lz53l9/javabridge_b94975d5c7214110afb660100a3389ac/
    Complete output (29 lines):
    running install
    /home/daniel/anaconda3/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
      warnings.warn(
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-3.9
    creating build/lib.linux-x86_64-3.9/javabridge
    copying javabridge/locate.py -> build/lib.linux-x86_64-3.9/javabridge
    copying javabridge/jutil.py -> build/lib.linux-x86_64-3.9/javabridge
    copying javabridge/__init__.py -> build/lib.linux-x86_64-3.9/javabridge
    copying javabridge/_version.py -> build/lib.linux-x86_64-3.9/javabridge
    copying javabridge/wrappers.py -> build/lib.linux-x86_64-3.9/javabridge
    copying javabridge/noseplugin.py -> build/lib.linux-x86_64-3.9/javabridge
    creating build/lib.linux-x86_64-3.9/javabridge/tests
    copying javabridge/tests/test_cpython.py -> build/lib.linux-x86_64-3.9/javabridge/tests
    copying javabridge/tests/test_wrappers.py -> build/lib.linux-x86_64-3.9/javabridge/tests
    copying javabridge/tests/__init__.py -> build/lib.linux-x86_64-3.9/javabridge/tests
    copying javabridge/tests/test_javabridge.py -> build/lib.linux-x86_64-3.9/javabridge/tests
    copying javabridge/tests/test_jutil.py -> build/lib.linux-x86_64-3.9/javabridge/tests
    creating build/lib.linux-x86_64-3.9/javabridge/jars
    copying javabridge/jars/runnablequeue.jar -> build/lib.linux-x86_64-3.9/javabridge/jars
    copying javabridge/jars/rhino-1.7R4.jar -> build/lib.linux-x86_64-3.9/javabridge/jars
    copying javabridge/jars/test.jar -> build/lib.linux-x86_64-3.9/javabridge/jars
    copying javabridge/jars/cpython.jar -> build/lib.linux-x86_64-3.9/javabridge/jars
    copying javabridge/jars/libjava2cpython.so -> build/lib.linux-x86_64-3.9/javabridge/jars
    running build_ext
    javac /tmp/pip-install-s0lz53l9/javabridge_b94975d5c7214110afb660100a3389ac/java/org/cellprofiler/runnablequeue/RunnableQueue.java
    error: command 'javac' failed: No such file or directory
    ----------------------------------------
ERROR: Command errored out with exit status 1: /home/daniel/anaconda3/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-s0lz53l9/javabridge_b94975d5c7214110afb660100a3389ac/setup.py'"'"'; __file__='"'"'/tmp/pip-install-s0lz53l9/javabridge_b94975d5c7214110afb660100a3389ac/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-p0d0e4jr/install-record.txt --single-version-externally-managed --compile --install-headers /home/daniel/anaconda3/include/python3.9/javabridge Check the logs for full command output.

From other issues, I tried many of the proposed solutions, but all failed. I have defined JAVA_HOME in .bashrc

$ echo $JAVA_HOME
/usr/lib/jvm/java-11-openjdk-amd64

I have included JAVA_HOME/bin in PATH

echo $PATH
/home/daniel/Dropbox/Biotools/FastQC:/home/daniel/Dropbox/Biotools/bin:/home/daniel/Dropbox/Biotools/STAR:/home/daniel/anaconda3/bin:/home/daniel/anaconda3/condabin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/usr/lib/jvm/java-11-openjdk-amd64/bin

JAva is running:

$ java --version
openjdk 11.0.14.1 2022-02-08
OpenJDK Runtime Environment (build 11.0.14.1+1-post-Debian-1)
OpenJDK 64-Bit Server VM (build 11.0.14.1+1-post-Debian-1, mixed mode, sharing)

Thank you

[LeeKamentsky]

That is bizarre - obviously the problem is that setup can't run javac, but you do have the JDK installed. Can you do javac -version?

[danielcanals2017]

Thank you for your reply. The output of this command is: $ javac -version javac 11.0.15