Install error even though JDK is installed

[LizMcQuillan]

I'm using Python 3.7 on a Mac, for context.

Attempting to install using pip results in the following error:

Collecting javabridge==1.0.18
  Using cached https://files.pythonhosted.org/packages/a6/a0/c59bccabed99b1d4ac68166c59c679b375bfca75b78688b52c541b711578/javabridge-1.0.18.tar.gz
    Complete output from command python setup.py egg_info:
    Could not find Java JRE compatible with x86_64 architecture
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/private/var/folders/04/76dktb_j6hj2qq9tx78jrzyc0000gp/T/pip-install-salp76k4/javabridge/setup.py", line 402, in <module>
        ext_modules=ext_modules(),
      File "/private/var/folders/04/76dktb_j6hj2qq9tx78jrzyc0000gp/T/pip-install-salp76k4/javabridge/setup.py", line 95, in ext_modules
        raise Exception("JVM not found")
    Exception: JVM not found
    
    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/04/76dktb_j6hj2qq9tx78jrzyc0000gp/T/pip-install-salp76k4/javabridge/

with Conda results in the following error:

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: / 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                                                                                   
                                                                                                                                         
UnsatisfiableError: The following specifications were found                                                                              
to be incompatible with the existing python installation in your environment:

  - javabridge -> python[version='2.7.*|3.4.*|3.5.*|3.6.*']
  - javabridge -> python[version='>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0']

If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to.  Your current python version
is (python=3.7).  Note that conda will not change your python version to a different minor version
unless you explicitly specify that.

The following specifications were found to be incompatible with each other:

Package setuptools conflicts for:
javabridge -> setuptools
python=3.7 -> pip -> setuptools
Package ca-certificates conflicts for:
python=3.7 -> openssl[version='>=1.1.1a,<1.1.2a'] -> ca-certificates
javabridge -> python=3.5 -> ca-certificates
Package pip conflicts for:
javabridge -> python=3.5 -> pip
python=3.7 -> pip
Package certifi conflicts for:
python=3.7 -> pip -> setuptools -> certifi[version='>=2016.09']
Package wheel conflicts for:
javabridge -> python=3.5 -> pip -> wheel
python=3.7 -> pip -> wheel

I've uninstalled and reinstalled JDK and Java after reading other issues, so I'm not sure what else to try.

[LeeKamentsky]

I would set the JAVA_HOME environment variable to the location where the JVM is installed and try the pip install again. We've had some unresolved issues with the Mac, Anaconda and frameworks (e.g. issue #111).

…

On Thu, Sep 12, 2019 at 2:39 PM Liz ***@***.***> wrote: I'm using Python 3.7 on a Mac, for context. Attempting to install using pip results in the following error: ERROR: Command errored out with exit status 1: command: /Users/lmcquillan/anaconda3/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/04/76dktb_j6hj2qq9tx78jrzyc0000gp/T/pip-req-build-h65dxq1g/setup.py'"'"'; __file__='"'"'/private/var/folders/04/76dktb_j6hj2qq9tx78jrzyc0000gp/T/pip-req-build-h65dxq1g/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base pip-egg-info cwd: /private/var/folders/04/76dktb_j6hj2qq9tx78jrzyc0000gp/T/pip-req-build-h65dxq1g/ Complete output (8 lines): Could not find Java JRE compatible with x86_64 architecture Traceback (most recent call last): File "<string>", line 1, in <module> File "/private/var/folders/04/76dktb_j6hj2qq9tx78jrzyc0000gp/T/pip-req-build-h65dxq1g/setup.py", line 405, in <module> ext_modules=ext_modules(), File "/private/var/folders/04/76dktb_j6hj2qq9tx78jrzyc0000gp/T/pip-req-build-h65dxq1g/setup.py", line 98, in ext_modules raise Exception("JVM not found") Exception: JVM not found ---------------------------------------- ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. with Conda results in the following error: Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: / Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment: - javabridge -> python[version='2.7.*|3.4.*|3.5.*|3.6.*'] - javabridge -> python[version='>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0'] If python is on the left-most side of the chain, that's the version you've asked for. When python appears to the right, that indicates that the thing on the left is somehow not available for the python version you are constrained to. Your current python version is (python=3.7). Note that conda will not change your python version to a different minor version unless you explicitly specify that. The following specifications were found to be incompatible with each other: Package setuptools conflicts for: javabridge -> setuptools python=3.7 -> pip -> setuptools Package ca-certificates conflicts for: python=3.7 -> openssl[version='>=1.1.1a,<1.1.2a'] -> ca-certificates javabridge -> python=3.5 -> ca-certificates Package pip conflicts for: javabridge -> python=3.5 -> pip python=3.7 -> pip Package certifi conflicts for: python=3.7 -> pip -> setuptools -> certifi[version='>=2016.09'] Package wheel conflicts for: javabridge -> python=3.5 -> pip -> wheel python=3.7 -> pip -> wheel I've uninstalled and reinstalled JDK and Java after reading other issues, so I'm not sure what else to try. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#168?email_source=notifications&email_token=AAFBH5O4WSHTLYHZLG73SRDQJKEHTA5CNFSM4IWIFORKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HLCCG2A>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAFBH5OHL5FS76QAPU4CVMDQJKEHTANCNFSM4IWIFORA> .

[LizMcQuillan]

I've tried setting JAVA_HOME, also tried reinstalling JDK and Java altogether. All to no avail.

[ptth222]

I had essentially the same error and fixed it using

export JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_251.jdk/Contents/Home

I did not try by using the new JDK 14.

[LizMcQuillan]

In the end, the only thing that worked was creating a fresh virtual env and doing all the installations over again.

[ghost]

I was running into the same issue. Here's what worked for me:

1. Make sure you have JAVA SDK8 installed
   • Installation was not working for me with SDK14, and only worked when I installed SDK 8
   • To check which versions you have installed (there may be multiple): /usr/libexec/java_home -V
   • If you need to install SDK 8, download from Oracle here
2. Make sure that JAVA_HOME is pointing to the correct place!
   • Find the path corresponding to SDK 8 using: /usr/libexec/java_home -V
   • export that path to JAVA_HOME
     • Example for my machine: export JAVA_HOME="/Library/Java/JavaVirtualMachines/jdk1.8.0_261.jdk/Contents/Home"
3. pip install javabridge