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Failed to create a JVM with the requested environment. #291

Open JeBiUKD opened 10 months ago

JeBiUKD commented 10 months ago

Dear all,

I have been working successfully with the package before but face problems when setting up PyImageJ on a different computer.

The problem already occurs in the initialization.

Here is a minimal script:

import imagej
ij = imagej.init(mode='interactive')

Error message:

JVMNotFoundException Traceback (most recent call last) Cell In[1], line 4 2 import imagej 3 # os.environ["JAVA_HOME"] ="C:/ProgramData/Miniconda3/envs/kymo/Library/jre/bin/server" ----> 4 ij = imagej.init(mode='interactive')

File C:\ProgramData\Miniconda3\envs\kymo\lib\site-packages\imagej__init__.py:1200, in init(ij_dir_or_version_or_endpoint, mode, add_legacy, headless) 1197 raise EnvironmentError("Sorry, the interactive mode is not available on macOS.") 1199 if not sj.jvm_started(): -> 1200 success = _create_jvm(ij_dir_or_version_or_endpoint, mode, add_legacy) 1201 if not success: 1202 raise RuntimeError("Failed to create a JVM with the requested environment.")

File C:\ProgramData\Miniconda3\envs\kymo\lib\site-packages\imagej__init__.py:1318, in _create_jvm(ij_dir_or_version_or_endpoint, mode, add_legacy) 1316 sj.config.add_option("-Djava.awt.headless=true") 1317 try: -> 1318 if hasattr(sj, "jvm_version") and sj.jvm_version()[0] >= 9: 1319 # Disable illegal reflection access warnings. 1320 sj.config.add_option("--add-opens=java.base/java.lang=ALL-UNNAMED") 1321 sj.config.add_option("--add-opens=java.base/java.util=ALL-UNNAMED")

File C:\ProgramData\Miniconda3\envs\kymo\lib\site-packages\scyjava_java.py:121, in jvm_version() 116 return jvm_version 118 # JPype was clueless, which means the JVM has probably not started yet. 119 # Let's look for a java executable, and ask via 'java -version'. --> 121 default_jvm_path = jpype.getDefaultJVMPath() 122 if not default_jvm_path: 123 raise RuntimeError("Cannot glean the default JVM path")

File C:\ProgramData\Miniconda3\envs\kymo\lib\site-packages\jpype_jvmfinder.py:74, in getDefaultJVMPath() 72 else: 73 finder = LinuxJVMFinder() ---> 74 return finder.get_jvm_path()

File C:\ProgramData\Miniconda3\envs\kymo\lib\site-packages\jpype_jvmfinder.py:212, in JVMFinder.get_jvm_path(self) 210 if jvm_notsupport_ext is not None: 211 raise jvm_notsupport_ext --> 212 raise JVMNotFoundException("No JVM shared library file ({0}) " 213 "found. Try setting up the JAVA_HOME " 214 "environment variable properly." 215 .format(self._libfile))

JVMNotFoundException: No JVM shared library file (jvm.dll) found. Try setting up the JAVA_HOME environment variable properly.

I then tried to set the JAVA_HOME environment: 

import imagej
import os
import imagej.doctor
imagej.doctor.debug_to_stderr()

os.environ["JAVA_HOME"] ="C:\Program Files\AdoptOpenJDK\jre-8.0.242.08-hotspot"
# ij = imagej.init('2.9.0')
ij = imagej.init(mode='interactive')

Then I get the following error message:

Using newest ImageJ2 release Using newest ImageJ2 release Adding jars from endpoints ['net.imagej:imagej', 'net.imagej:imagej-legacy:MANAGED', 'org.scijava:scijava-config:MANAGED', 'io.scif:scifio-labeling:0.3.1', 'net.imglib2:imglib2-imglyb:1.1.0'] Adding jars from endpoints ['net.imagej:imagej', 'net.imagej:imagej-legacy:MANAGED', 'org.scijava:scijava-config:MANAGED', 'io.scif:scifio-labeling:0.3.1', 'net.imglib2:imglib2-imglyb:1.1.0'] Using endpoints ['net.imagej:imagej', 'io.scif:scifio-labeling:0.3.1', 'net.imagej:imagej-legacy:MANAGED', 'net.imglib2:imglib2-imglyb:1.1.0', 'org.scijava:scijava-config:MANAGED'] Using endpoints ['net.imagej:imagej', 'io.scif:scifio-labeling:0.3.1', 'net.imagej:imagej-legacy:MANAGED', 'net.imglib2:imglib2-imglyb:1.1.0', 'org.scijava:scijava-config:MANAGED'] Getting verbose level: 0 Getting verbose level: 0 Getting verbose level: 0 Getting verbose level: 0 Returning expanded coordinate net.imagej:imagej. Returning expanded coordinate net.imagej:imagej. Returning expanded coordinate io.scif:scifio-labeling:0.3.1. Returning expanded coordinate io.scif:scifio-labeling:0.3.1. Returning expanded coordinate net.imagej:imagej-legacy:MANAGED. Returning expanded coordinate net.imagej:imagej-legacy:MANAGED. Returning expanded coordinate net.imglib2:imglib2-imglyb:1.1.0. Returning expanded coordinate net.imglib2:imglib2-imglyb:1.1.0. Returning expanded coordinate org.scijava:scijava-config:MANAGED. Returning expanded coordinate org.scijava:scijava-config:MANAGED. First time start-up may be slow. Downloaded dependencies will be cached for shorter start-up times in subsequent executions. First time start-up may be slow. Downloaded dependencies will be cached for shorter start-up times in subsequent executions. Executing: ('C:\ProgramData\Miniconda3\envs\kymo\Library\bin\mvn.CMD', '-B', '-f', 'C:\Users\BellmanJe\.jgo\net.imagej\imagej\RELEASE\5dacb2d74cc139236f7db62ac3391755ef26a277311eab7c4c9f89d2892a0367\pom.xml', 'dependency:resolve') Executing: ('C:\ProgramData\Miniconda3\envs\kymo\Library\bin\mvn.CMD', '-B', '-f', 'C:\Users\BellmanJe\.jgo\net.imagej\imagej\RELEASE\5dacb2d74cc139236f7db62ac3391755ef26a277311eab7c4c9f89d2892a0367\pom.xml', 'dependency:resolve') Failed to bootstrap the artifact. Failed to bootstrap the artifact.

Possible solutions: Possible solutions:

  • Double check the endpoint for correctness (https://search.maven.org/).
  • Double check the endpoint for correctness (https://search.maven.org/).
  • Add needed repositories to ~/.jgorc [repositories] block (see README).
  • Add needed repositories to ~/.jgorc [repositories] block (see README).
  • Try with an explicit version number (release metadata might be wrong).
  • Try with an explicit version number (release metadata might be wrong).

Full Maven error output: Full Maven error output: [INFO] Scanning for projects... [INFO] Scanning for projects... [INFO] Downloading from central: https://repo.maven.apache.org/maven2/net/imagej/imagej/maven-metadata.xml [INFO] Downloading from central: https://repo.maven.apache.org/maven2/net/imagej/imagej/maven-metadata.xml [WARNING] Could not transfer metadata net.imagej:imagej/maven-metadata.xml from/to central (https://repo.maven.apache.org/maven2): Connect to repo.maven.apache.org:443 [repo.maven.apache.org/151.101.64.215, repo.maven.apache.org/151.101.128.215, repo.maven.apache.org/151.101.192.215, repo.maven.apache.org/151.101.0.215] failed: connect timed out [WARNING] Could not transfer metadata net.imagej:imagej/maven-metadata.xml from/to central (https://repo.maven.apache.org/maven2): Connect to repo.maven.apache.org:443 [repo.maven.apache.org/151.101.64.215, repo.maven.apache.org/151.101.128.215, repo.maven.apache.org/151.101.192.215, repo.maven.apache.org/151.101.0.215] failed: connect timed out [WARNING] [WARNING] [WARNING] Some problems were encountered while building the effective model for net.imagej-BOOTSTRAPPER:imagej-BOOTSTRAPPER:jar:0 [WARNING] Some problems were encountered while building the effective model for net.imagej-BOOTSTRAPPER:imagej-BOOTSTRAPPER:jar:0 [WARNING] 'dependencies.dependency.version' for net.imagej:imagej:jar is either LATEST or RELEASE (both of them are being deprecated) @ line 10, column 97 [WARNING] 'dependencies.dependency.version' for net.imagej:imagej:jar is either LATEST or RELEASE (both of them are being deprecated) @ line 10, column 97 [WARNING] 'dependencyManagement.dependencies.dependency.version' for net.imagej:imagej:pom is either LATEST or RELEASE (both of them are being deprecated) @ line 8, column 98 [WARNING] 'dependencyManagement.dependencies.dependency.version' for net.imagej:imagej:pom is either LATEST or RELEASE (both of them are being deprecated) @ line 8, column 98 [WARNING] [WARNING] [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build. [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build. [WARNING] [WARNING] [WARNING] For this reason, future Maven versions might no longer support building such malformed projects. [WARNING] For this reason, future Maven versions might no longer support building such malformed projects. [WARNING] [WARNING] [INFO] Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-clean-plugin/3.2.0/maven-clean-plugin-3.2.0.pom [INFO] Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-clean-plugin/3.2.0/maven-clean-plugin-3.2.0.pom [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-clean-plugin:3.2.0: Plugin org.apache.maven.plugins:maven-clean-plugin:3.2.0 or one of its dependencies could not be resolved: Failed to read artifact descriptor for org.apache.maven.plugins:maven-clean-plugin:jar:3.2.0 [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-clean-plugin:3.2.0: Plugin org.apache.maven.plugins:maven-clean-plugin:3.2.0 or one of its dependencies could not be resolved: Failed to read artifact descriptor for org.apache.maven.plugins:maven-clean-plugin:jar:3.2.0 [INFO] Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-resources-plugin/3.3.1/maven-resources-plugin-3.3.1.pom [INFO] Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-resources-plugin/3.3.1/maven-resources-plugin-3.3.1.pom [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-resources-plugin:3.3.1: Plugin org.apache.maven.plugins:maven-resources-plugin:3.3.1 or one of its dependencies could not be resolved: Failed to read artifact descriptor for org.apache.maven.plugins:maven-resources-plugin:jar:3.3.1 [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-resources-plugin:3.3.1: Plugin org.apache.maven.plugins:maven-resources-plugin:3.3.1 or one of its dependencies could not be resolved: Failed to read artifact descriptor for org.apache.maven.plugins:maven-resources-plugin:jar:3.3.1 [INFO] Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-jar-plugin/3.3.0/maven-jar-plugin-3.3.0.pom [INFO] Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-jar-plugin/3.3.0/maven-jar-plugin-3.3.0.pom [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-jar-plugin:3.3.0: Plugin org.apache.maven.plugins:maven-jar-plugin:3.3.0 or one of its dependencies could not be resolved: Failed to read artifact descriptor for org.apache.maven.plugins:maven-jar-plugin:jar:3.3.0 [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-jar-plugin:3.3.0: Plugin org.apache.maven.plugins:maven-jar-plugin:3.3.0 or one of its dependencies could not be resolved: Failed to read artifact descriptor for org.apache.maven.plugins:maven-jar-plugin:jar:3.3.0 [INFO] Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-compiler-plugin/3.11.0/maven-compiler-plugin-3.11.0.pom [INFO] Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-compiler-plugin/3.11.0/maven-compiler-plugin-3.11.0.pom [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-compiler-plugin:3.11.0: Plugin org.apache.maven.plugins:maven-compiler-plugin:3.11.0 or one of its dependencies could not be resolved: Failed to read artifact descriptor for org.apache.maven.plugins:maven-compiler-plugin:jar:3.11.0 [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-compiler-plugin:3.11.0: Plugin org.apache.maven.plugins:maven-compiler-plugin:3.11.0 or one of its dependencies could not be resolved: Failed to read artifact descriptor for org.apache.maven.plugins:maven-compiler-plugin:jar:3.11.0 [INFO] Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-surefire-plugin/3.1.2/maven-surefire-plugin-3.1.2.pom [INFO] Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-surefire-plugin/3.1.2/maven-surefire-plugin-3.1.2.pom [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-surefire-plugin:3.1.2: Plugin org.apache.maven.plugins:maven-surefire-plugin:3.1.2 or one of its dependencies could not be resolved: Failed to read artifact descriptor for org.apache.maven.plugins:maven-surefire-plugin:jar:3.1.2 [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-surefire-plugin:3.1.2: Plugin org.apache.maven.plugins:maven-surefire-plugin:3.1.2 or one of its dependencies could not be resolved: Failed to read artifact descriptor for org.apache.maven.plugins:maven-surefire-plugin:jar:3.1.2 [INFO] Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-install-plugin/3.1.1/maven-install-plugin-3.1.1.pom [INFO] Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-install-plugin/3.1.1/maven-install-plugin-3.1.1.pom [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-install-plugin:3.1.1: Plugin org.apache.maven.plugins:maven-install-plugin:3.1.1 or one of its dependencies could not be resolved: Failed to read artifact descriptor for org.apache.maven.plugins:maven-install-plugin:jar:3.1.1 [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-install-plugin:3.1.1: Plugin org.apache.maven.plugins:maven-install-plugin:3.1.1 or one of its dependencies could not be resolved: Failed to read artifact descriptor for org.apache.maven.plugins:maven-install-plugin:jar:3.1.1 [INFO] Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-deploy-plugin/3.1.1/maven-deploy-plugin-3.1.1.pom [INFO] Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-deploy-plugin/3.1.1/maven-deploy-plugin-3.1.1.pom [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-deploy-plugin:3.1.1: Plugin org.apache.maven.plugins:maven-deploy-plugin:3.1.1 or one of its dependencies could not be resolved: Failed to read artifact descriptor for org.apache.maven.plugins:maven-deploy-plugin:jar:3.1.1 [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-deploy-plugin:3.1.1: Plugin org.apache.maven.plugins:maven-deploy-plugin:3.1.1 or one of its dependencies could not be resolved: Failed to read artifact descriptor for org.apache.maven.plugins:maven-deploy-plugin:jar:3.1.1 [INFO] Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-site-plugin/3.12.1/maven-site-plugin-3.12.1.pom [INFO] Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-site-plugin/3.12.1/maven-site-plugin-3.12.1.pom [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-site-plugin:3.12.1: Plugin org.apache.maven.plugins:maven-site-plugin:3.12.1 or one of its dependencies could not be resolved: Failed to read artifact descriptor for org.apache.maven.plugins:maven-site-plugin:jar:3.12.1 [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-site-plugin:3.12.1: Plugin org.apache.maven.plugins:maven-site-plugin:3.12.1 or one of its dependencies could not be resolved: Failed to read artifact descriptor for org.apache.maven.plugins:maven-site-plugin:jar:3.12.1 [INFO] Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-antrun-plugin/3.1.0/maven-antrun-plugin-3.1.0.pom [INFO] Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-antrun-plugin/3.1.0/maven-antrun-plugin-3.1.0.pom [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-antrun-plugin:3.1.0: Plugin org.apache.maven.plugins:maven-antrun-plugin:3.1.0 or one of its dependencies could not be resolved: Failed to read artifact descriptor for org.apache.maven.plugins:maven-antrun-plugin:jar:3.1.0 [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-antrun-plugin:3.1.0: Plugin org.apache.maven.plugins:maven-antrun-plugin:3.1.0 or one of its dependencies could not be resolved: Failed to read artifact descriptor for org.apache.maven.plugins:maven-antrun-plugin:jar:3.1.0 [INFO] Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-assembly-plugin/3.6.0/maven-assembly-plugin-3.6.0.pom [INFO] Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-assembly-plugin/3.6.0/maven-assembly-plugin-3.6.0.pom [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:3.6.0: Plugin org.apache.maven.plugins:maven-assembly-plugin:3.6.0 or one of its dependencies could not be resolved: Failed to read artifact descriptor for org.apache.maven.plugins:maven-assembly-plugin:jar:3.6.0 [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-assembly-plugin:3.6.0: Plugin org.apache.maven.plugins:maven-assembly-plugin:3.6.0 or one of its dependencies could not be resolved: Failed to read artifact descriptor for org.apache.maven.plugins:maven-assembly-plugin:jar:3.6.0 [INFO] Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-dependency-plugin/3.6.0/maven-dependency-plugin-3.6.0.pom [INFO] Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-dependency-plugin/3.6.0/maven-dependency-plugin-3.6.0.pom [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-dependency-plugin:3.6.0: Plugin org.apache.maven.plugins:maven-dependency-plugin:3.6.0 or one of its dependencies could not be resolved: Failed to read artifact descriptor for org.apache.maven.plugins:maven-dependency-plugin:jar:3.6.0 [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-dependency-plugin:3.6.0: Plugin org.apache.maven.plugins:maven-dependency-plugin:3.6.0 or one of its dependencies could not be resolved: Failed to read artifact descriptor for org.apache.maven.plugins:maven-dependency-plugin:jar:3.6.0 [INFO] Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-release-plugin/3.0.1/maven-release-plugin-3.0.1.pom [INFO] Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-release-plugin/3.0.1/maven-release-plugin-3.0.1.pom [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:3.0.1: Plugin org.apache.maven.plugins:maven-release-plugin:3.0.1 or one of its dependencies could not be resolved: Failed to read artifact descriptor for org.apache.maven.plugins:maven-release-plugin:jar:3.0.1 [WARNING] Failed to retrieve plugin descriptor for org.apache.maven.plugins:maven-release-plugin:3.0.1: Plugin org.apache.maven.plugins:maven-release-plugin:3.0.1 or one of its dependencies could not be resolved: Failed to read artifact descriptor for org.apache.maven.plugins:maven-release-plugin:jar:3.0.1 [INFO] Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-metadata.xml [INFO] Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-metadata.xml [INFO] Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/mojo/maven-metadata.xml [INFO] Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/mojo/maven-metadata.xml [WARNING] Could not transfer metadata org.apache.maven.plugins/maven-metadata.xml from/to central (https://repo.maven.apache.org/maven2): Connect to repo.maven.apache.org:443 [repo.maven.apache.org/151.101.64.215, repo.maven.apache.org/151.101.128.215, repo.maven.apache.org/151.101.192.215, repo.maven.apache.org/151.101.0.215] failed: connect timed out [WARNING] Could not transfer metadata org.apache.maven.plugins/maven-metadata.xml from/to central (https://repo.maven.apache.org/maven2): Connect to repo.maven.apache.org:443 [repo.maven.apache.org/151.101.64.215, repo.maven.apache.org/151.101.128.215, repo.maven.apache.org/151.101.192.215, repo.maven.apache.org/151.101.0.215] failed: connect timed out [WARNING] Could not transfer metadata org.codehaus.mojo/maven-metadata.xml from/to central (https://repo.maven.apache.org/maven2): Connect to repo.maven.apache.org:443 [repo.maven.apache.org/151.101.64.215, repo.maven.apache.org/151.101.128.215, repo.maven.apache.org/151.101.192.215, repo.maven.apache.org/151.101.0.215] failed: connect timed out [WARNING] Could not transfer metadata org.codehaus.mojo/maven-metadata.xml from/to central (https://repo.maven.apache.org/maven2): Connect to repo.maven.apache.org:443 [repo.maven.apache.org/151.101.64.215, repo.maven.apache.org/151.101.128.215, repo.maven.apache.org/151.101.192.215, repo.maven.apache.org/151.101.0.215] failed: connect timed out [WARNING] org.apache.maven.plugins/maven-metadata.xml failed to transfer from https://repo.maven.apache.org/maven2 during a previous attempt. This failure was cached in the local repository and resolution will not be reattempted until the update interval of central has elapsed or updates are forced. Original error: Could not transfer metadata org.apache.maven.plugins/maven-metadata.xml from/to central (https://repo.maven.apache.org/maven2): Connect to repo.maven.apache.org:443 [repo.maven.apache.org/151.101.64.215, repo.maven.apache.org/151.101.128.215, repo.maven.apache.org/151.101.192.215, repo.maven.apache.org/151.101.0.215] failed: connect timed out [WARNING] org.apache.maven.plugins/maven-metadata.xml failed to transfer from https://repo.maven.apache.org/maven2 during a previous attempt. This failure was cached in the local repository and resolution will not be reattempted until the update interval of central has elapsed or updates are forced. Original error: Could not transfer metadata org.apache.maven.plugins/maven-metadata.xml from/to central (https://repo.maven.apache.org/maven2): Connect to repo.maven.apache.org:443 [repo.maven.apache.org/151.101.64.215, repo.maven.apache.org/151.101.128.215, repo.maven.apache.org/151.101.192.215, repo.maven.apache.org/151.101.0.215] failed: connect timed out [WARNING] org.codehaus.mojo/maven-metadata.xml failed to transfer from https://repo.maven.apache.org/maven2 during a previous attempt. This failure was cached in the local repository and resolution will not be reattempted until the update interval of central has elapsed or updates are forced. Original error: Could not transfer metadata org.codehaus.mojo/maven-metadata.xml from/to central (https://repo.maven.apache.org/maven2): Connect to repo.maven.apache.org:443 [repo.maven.apache.org/151.101.64.215, repo.maven.apache.org/151.101.128.215, repo.maven.apache.org/151.101.192.215, repo.maven.apache.org/151.101.0.215] failed: connect timed out [WARNING] org.codehaus.mojo/maven-metadata.xml failed to transfer from https://repo.maven.apache.org/maven2 during a previous attempt. This failure was cached in the local repository and resolution will not be reattempted until the update interval of central has elapsed or updates are forced. Original error: Could not transfer metadata org.codehaus.mojo/maven-metadata.xml from/to central (https://repo.maven.apache.org/maven2): Connect to repo.maven.apache.org:443 [repo.maven.apache.org/151.101.64.215, repo.maven.apache.org/151.101.128.215, repo.maven.apache.org/151.101.192.215, repo.maven.apache.org/151.101.0.215] failed: connect timed out [INFO] ------------------------------------------------------------------------ [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] ------------------------------------------------------------------------ [INFO] Total time: 09:21 min [INFO] Total time: 09:21 min [INFO] Finished at: 2023-11-03T10:23:17+01:00 [INFO] Finished at: 2023-11-03T10:23:17+01:00 [INFO] ------------------------------------------------------------------------ [INFO] ------------------------------------------------------------------------ [ERROR] No plugin found for prefix 'dependency' in the current project and in the plugin groups [org.apache.maven.plugins, org.codehaus.mojo] available from the repositories [local (C:\Users\BellmanJe.m2\repository), central (https://repo.maven.apache.org/maven2)] -> [Help 1] [ERROR] No plugin found for prefix 'dependency' in the current project and in the plugin groups [org.apache.maven.plugins, org.codehaus.mojo] available from the repositories [local (C:\Users\BellmanJe.m2\repository), central (https://repo.maven.apache.org/maven2)] -> [Help 1] [ERROR] [ERROR] [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch. [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] Re-run Maven using the -X switch to enable full debug logging. [ERROR] [ERROR] [ERROR] For more information about the errors and possible solutions, please read the following articles: [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/NoPluginFoundForPrefixException [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/NoPluginFoundForPrefixException

RuntimeError Traceback (most recent call last) Cell In[2], line 8 6 os.environ["JAVA_HOME"] ="C:\Program Files\AdoptOpenJDK\jre-8.0.242.08-hotspot" 7 # ij = imagej.init('2.9.0') ----> 8 ij = imagej.init(mode='interactive') 9 ij.ui().showUI()

File C:\ProgramData\Miniconda3\envs\kymo\lib\site-packages\imagej__init__.py:1202, in init(ij_dir_or_version_or_endpoint, mode, add_legacy, headless) 1200 success = _create_jvm(ij_dir_or_version_or_endpoint, mode, add_legacy) 1201 if not success: -> 1202 raise RuntimeError("Failed to create a JVM with the requested environment.") 1204 if mode == Mode.GUI: 1205 # Show the GUI and block. 1206 if macos: 1207 # NB: This will block the calling (main) thread forever!

RuntimeError: Failed to create a JVM with the requested environment.

Here is my conda environment list:

packages in environment at C:\ProgramData\Miniconda3\envs\kymo:

#

Name Version Build Channel

aiofiles 22.1.0 pyhd8ed1ab_0 conda-forge aiosqlite 0.19.0 pyhd8ed1ab_0 conda-forge anyio 4.0.0 pyhd8ed1ab_0 conda-forge aom 3.5.0 h63175ca_0 conda-forge argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge argon2-cffi-bindings 21.2.0 py38h91455d4_4 conda-forge arrow 1.3.0 pyhd8ed1ab_0 conda-forge asttokens 2.4.1 pyhd8ed1ab_0 conda-forge async-lru 2.0.4 pyhd8ed1ab_0 conda-forge attrs 23.1.0 pyh71513ae_1 conda-forge babel 2.13.1 pyhd8ed1ab_0 conda-forge backcall 0.2.0 pyh9f0ad1d_0 conda-forge backports 1.0 pyhd8ed1ab_3 conda-forge backports.functools_lru_cache 1.6.5 pyhd8ed1ab_0 conda-forge beautifulsoup4 4.12.2 pyha770c72_0 conda-forge bleach 6.1.0 pyhd8ed1ab_0 conda-forge blosc 1.21.5 hdccc3a2_0 conda-forge brotli 1.0.9 h0e60522_4 conda-forge brotli-python 1.0.9 py38hd3f51b4_9 conda-forge bzip2 1.0.8 h8ffe710_4 conda-forge c-blosc2 2.10.5 h183a6f4_0 conda-forge ca-certificates 2023.7.22 h56e8100_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge certifi 2023.7.22 pyhd8ed1ab_0 conda-forge cffi 1.16.0 py38h91455d4_0 conda-forge cfitsio 4.2.0 h9ebe7e4_0 conda-forge charls 2.4.2 h1537add_0 conda-forge charset-normalizer 3.3.1 pyhd8ed1ab_0 conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge comm 0.1.4 pyhd8ed1ab_0 conda-forge contourpy 1.1.1 py38hb1fd069_1 conda-forge cryptography 41.0.5 py38h95f5157_0 conda-forge cycler 0.12.1 pyhd8ed1ab_0 conda-forge dav1d 1.2.1 hcfcfb64_0 conda-forge debugpy 1.8.0 py38hd3f51b4_1 conda-forge decorator 5.1.1 pyhd8ed1ab_0 conda-forge defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge entrypoints 0.4 pyhd8ed1ab_0 conda-forge exceptiongroup 1.1.3 pyhd8ed1ab_0 conda-forge executing 2.0.1 pyhd8ed1ab_0 conda-forge fonttools 4.43.1 py38h91455d4_0 conda-forge fqdn 1.5.1 pyhd8ed1ab_0 conda-forge freetype 2.12.1 hdaf720e_2 conda-forge gettext 0.21.1 h5728263_0 conda-forge giflib 5.2.1 h64bf75a_3 conda-forge glib 2.78.0 h12be248_0 conda-forge glib-tools 2.78.0 h12be248_0 conda-forge gst-plugins-base 1.22.6 h001b923_2 conda-forge gstreamer 1.22.6 hb4038d2_2 conda-forge icu 70.1 h0e60522_0 conda-forge idna 3.4 pyhd8ed1ab_0 conda-forge imagecodecs 2023.1.23 py38h38923f3_0 conda-forge imglyb 2.1.0 pyha21a80b_0 conda-forge importlib-metadata 6.8.0 pyha770c72_0 conda-forge importlib-resources 6.1.0 pyhd8ed1ab_0 conda-forge importlib_metadata 6.8.0 hd8ed1ab_0 conda-forge importlib_resources 6.1.0 pyhd8ed1ab_0 conda-forge intel-openmp 2023.2.0 h57928b3_50497 conda-forge ipykernel 6.26.0 pyha63f2e9_0 conda-forge ipython 8.12.2 pyh08f2357_0 conda-forge ipython_genutils 0.2.0 py_1 conda-forge ipywidgets 8.1.1 pyhd8ed1ab_0 conda-forge isoduration 20.11.0 pyhd8ed1ab_0 conda-forge jedi 0.19.1 pyhd8ed1ab_0 conda-forge jgo 1.0.5 pyhd8ed1ab_0 conda-forge jinja2 3.1.2 pyhd8ed1ab_1 conda-forge jpeg 9e hcfcfb64_3 conda-forge jpype1 1.4.1 py38hb1fd069_1 conda-forge json5 0.9.14 pyhd8ed1ab_0 conda-forge jsonpointer 2.4 py38haa244fe_3 conda-forge jsonschema 4.19.2 pyhd8ed1ab_0 conda-forge jsonschema-specifications 2023.7.1 pyhd8ed1ab_0 conda-forge jsonschema-with-format-nongpl 4.19.2 pyhd8ed1ab_0 conda-forge jupyter 1.0.0 pyhd8ed1ab_10 conda-forge jupyter-lsp 2.2.0 pyhd8ed1ab_0 conda-forge jupyter_client 8.5.0 pyhd8ed1ab_0 conda-forge jupyter_console 6.6.3 pyhd8ed1ab_0 conda-forge jupyter_core 5.5.0 py38haa244fe_0 conda-forge jupyter_events 0.8.0 pyhd8ed1ab_0 conda-forge jupyter_server 2.9.1 pyhd8ed1ab_0 conda-forge jupyter_server_fileid 0.9.0 pyhd8ed1ab_0 conda-forge jupyter_server_terminals 0.4.4 pyhd8ed1ab_1 conda-forge jupyter_server_ydoc 0.8.0 pyhd8ed1ab_0 conda-forge jupyter_ydoc 0.3.4 pyhd8ed1ab_0 conda-forge jupyterlab 4.0.7 pyhd8ed1ab_0 conda-forge jupyterlab_pygments 0.2.2 pyhd8ed1ab_0 conda-forge jupyterlab_server 2.25.0 pyhd8ed1ab_0 conda-forge jupyterlab_widgets 3.0.9 pyhd8ed1ab_0 conda-forge jxrlib 1.1 h8ffe710_2 conda-forge kiwisolver 1.4.5 py38hb1fd069_1 conda-forge krb5 1.20.1 heb0366b_0 conda-forge labeling 0.1.12 pyhd8ed1ab_1 conda-forge lcms2 2.15 ha5c8aab_0 conda-forge lerc 4.0.0 h63175ca_0 conda-forge libaec 1.1.2 h63175ca_1 conda-forge libavif 0.11.1 ha7b97ba_2 conda-forge libblas 3.9.0 19_win64_mkl conda-forge libbrotlicommon 1.0.9 hcfcfb64_9 conda-forge libbrotlidec 1.0.9 hcfcfb64_9 conda-forge libbrotlienc 1.0.9 hcfcfb64_9 conda-forge libcblas 3.9.0 19_win64_mkl conda-forge libclang 15.0.7 default_h77d9078_3 conda-forge libclang13 15.0.7 default_h77d9078_3 conda-forge libcurl 8.1.2 h68f0423_0 conda-forge libdeflate 1.17 hcfcfb64_0 conda-forge libffi 3.4.2 h8ffe710_5 conda-forge libglib 2.78.0 he8f3873_0 conda-forge libhwloc 2.9.3 default_haede6df_1009 conda-forge libiconv 1.17 h8ffe710_0 conda-forge liblapack 3.9.0 19_win64_mkl conda-forge libogg 1.3.4 h8ffe710_1 conda-forge libpng 1.6.39 h19919ed_0 conda-forge libpq 15.3 ha9684e8_1 conda-forge libsodium 1.0.18 h8d14728_1 conda-forge libsqlite 3.43.2 hcfcfb64_0 conda-forge libssh2 1.11.0 h7dfc565_0 conda-forge libtiff 4.5.0 hf8721a0_2 conda-forge libvorbis 1.3.7 h0e60522_0 conda-forge libwebp-base 1.3.2 hcfcfb64_0 conda-forge libxcb 1.13 hcd874cb_1004 conda-forge libxml2 2.11.5 hc3477c8_1 conda-forge libxslt 1.1.37 h6070c61_1 conda-forge libzlib 1.2.13 hcfcfb64_5 conda-forge libzopfli 1.0.3 h0e60522_0 conda-forge lxml 4.9.3 py38h5a3a0f9_1 conda-forge lz4-c 1.9.4 hcfcfb64_0 conda-forge m2w64-gcc-libgfortran 5.3.0 6 conda-forge m2w64-gcc-libs 5.3.0 7 conda-forge m2w64-gcc-libs-core 5.3.0 7 conda-forge m2w64-gmp 6.1.0 2 conda-forge m2w64-libwinpthread-git 5.0.0.4634.697f757 2 conda-forge markupsafe 2.1.3 py38h91455d4_1 conda-forge matplotlib-base 3.7.3 py38h2724991_0 conda-forge matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge maven 3.9.5 h57928b3_0 conda-forge mistune 3.0.1 pyhd8ed1ab_0 conda-forge mkl 2023.2.0 h6a75c08_50496 conda-forge msys2-conda-epoch 20160418 1 conda-forge munkres 1.1.4 pyh9f0ad1d_0 conda-forge nbclassic 1.0.0 pyhb4ecaf3_1 conda-forge nbclient 0.8.0 pyhd8ed1ab_0 conda-forge nbconvert 7.10.0 pyhd8ed1ab_0 conda-forge nbconvert-core 7.10.0 pyhd8ed1ab_0 conda-forge nbconvert-pandoc 7.10.0 pyhd8ed1ab_0 conda-forge nbformat 5.9.2 pyhd8ed1ab_0 conda-forge nest-asyncio 1.5.8 pyhd8ed1ab_0 conda-forge notebook 7.0.6 pyhd8ed1ab_0 conda-forge notebook-shim 0.2.3 pyhd8ed1ab_0 conda-forge numpy 1.24.4 py38h1d91fd2_0 conda-forge openjdk 8.0.382 h57928b3_0 conda-forge openjpeg 2.5.0 ha2aaf27_2 conda-forge openssl 3.1.4 hcfcfb64_0 conda-forge overrides 7.4.0 pyhd8ed1ab_0 conda-forge packaging 23.2 pyhd8ed1ab_0 conda-forge pandas 1.5.3 py38h5846ac1_1 conda-forge pandoc 3.1.3 h57928b3_0 conda-forge pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge parso 0.8.3 pyhd8ed1ab_0 conda-forge pcre2 10.40 h17e33f8_0 conda-forge pickleshare 0.7.5 py_1003 conda-forge pillow 9.4.0 py38h087119c_1 conda-forge pip 23.3.1 pyhd8ed1ab_0 conda-forge pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge platformdirs 3.11.0 pyhd8ed1ab_0 conda-forge ply 3.11 py_1 conda-forge pooch 1.8.0 pyhd8ed1ab_0 conda-forge prometheus_client 0.18.0 pyhd8ed1ab_0 conda-forge prompt-toolkit 3.0.39 pyha770c72_0 conda-forge prompt_toolkit 3.0.39 hd8ed1ab_0 conda-forge psutil 5.9.5 py38h91455d4_1 conda-forge pthread-stubs 0.4 hcd874cb_1001 conda-forge pthreads-win32 2.9.1 hfa6e2cd_3 conda-forge pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge pycparser 2.21 pyhd8ed1ab_0 conda-forge pygments 2.16.1 pyhd8ed1ab_0 conda-forge pyimagej 1.4.1 py38haa244fe_0 conda-forge pyopenssl 23.3.0 pyhd8ed1ab_0 conda-forge pyparsing 3.1.1 pyhd8ed1ab_0 conda-forge pyqt 5.15.9 py38hd6c051e_5 conda-forge pyqt5-sip 12.12.2 py38hd3f51b4_5 conda-forge pyrsistent 0.20.0 py38h91455d4_0 conda-forge pysocks 1.7.1 pyh0701188_6 conda-forge python 3.8.18 h4de0772_0_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-fastjsonschema 2.18.1 pyhd8ed1ab_0 conda-forge python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge python_abi 3.8 4_cp38 conda-forge pytz 2023.3.post1 pyhd8ed1ab_0 conda-forge pywin32 306 py38hd3f51b4_2 conda-forge pywinpty 2.0.12 py38hd3f51b4_0 conda-forge pyyaml 6.0.1 py38h91455d4_1 conda-forge pyzmq 25.1.1 py38hdecc13b_2 conda-forge qt-main 5.15.8 h720456b_6 conda-forge qtconsole 5.4.4 pyhd8ed1ab_0 conda-forge qtconsole-base 5.4.4 pyha770c72_0 conda-forge qtpy 2.4.1 pyhd8ed1ab_0 conda-forge referencing 0.30.2 pyhd8ed1ab_0 conda-forge requests 2.31.0 pyhd8ed1ab_0 conda-forge rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge rpds-py 0.10.6 py38h4900a04_0 conda-forge scipy 1.10.1 py38h1aea9ed_3 conda-forge scyjava 1.9.1 pyhd8ed1ab_0 conda-forge send2trash 1.8.2 pyh08f2357_0 conda-forge setuptools 68.2.2 pyhd8ed1ab_0 conda-forge sip 6.7.12 py38hd3f51b4_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge snappy 1.1.10 hfb803bf_0 conda-forge sniffio 1.3.0 pyhd8ed1ab_0 conda-forge soupsieve 2.5 pyhd8ed1ab_1 conda-forge sqlite 3.43.2 hcfcfb64_0 conda-forge stack_data 0.6.2 pyhd8ed1ab_0 conda-forge symlink-exe-runtime 1.0 hcfcfb64_0 conda-forge tbb 2021.10.0 h91493d7_2 conda-forge terminado 0.17.0 pyh08f2357_0 conda-forge tifffile 2023.7.10 pyhd8ed1ab_0 conda-forge tinycss2 1.2.1 pyhd8ed1ab_0 conda-forge tk 8.6.13 hcfcfb64_0 conda-forge toml 0.10.2 pyhd8ed1ab_0 conda-forge tomli 2.0.1 pyhd8ed1ab_0 conda-forge tornado 6.3.3 py38h91455d4_1 conda-forge traitlets 5.13.0 pyhd8ed1ab_0 conda-forge types-python-dateutil 2.8.19.14 pyhd8ed1ab_0 conda-forge typing-extensions 4.8.0 hd8ed1ab_0 conda-forge typing_extensions 4.8.0 pyha770c72_0 conda-forge typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge ucrt 10.0.22621.0 h57928b3_0 conda-forge unicodedata2 15.1.0 py38h91455d4_0 conda-forge uri-template 1.3.0 pyhd8ed1ab_0 conda-forge urllib3 2.0.7 pyhd8ed1ab_0 conda-forge vc 14.3 h64f974e_17 conda-forge vc14_runtime 14.36.32532 hdcecf7f_17 conda-forge vs2015_runtime 14.36.32532 h05e6639_17 conda-forge wcwidth 0.2.9 pyhd8ed1ab_0 conda-forge webcolors 1.13 pyhd8ed1ab_0 conda-forge webencodings 0.5.1 pyhd8ed1ab_2 conda-forge websocket-client 1.6.4 pyhd8ed1ab_0 conda-forge wheel 0.41.3 pyhd8ed1ab_0 conda-forge widgetsnbextension 4.0.9 pyhd8ed1ab_0 conda-forge win_inet_pton 1.1.0 pyhd8ed1ab_6 conda-forge winpty 0.4.3 4 conda-forge xarray 2023.1.0 pyhd8ed1ab_0 conda-forge xorg-libxau 1.0.11 hcd874cb_0 conda-forge xorg-libxdmcp 1.1.3 hcd874cb_0 conda-forge xz 5.2.6 h8d14728_0 conda-forge y-py 0.6.2 py38h4900a04_0 conda-forge yaml 0.2.5 h8ffe710_2 conda-forge ypy-websocket 0.8.4 pyhd8ed1ab_0 conda-forge zeromq 4.3.5 h63175ca_0 conda-forge zfp 1.0.0 h63175ca_4 conda-forge zipp 3.17.0 pyhd8ed1ab_0 conda-forge zlib 1.2.13 hcfcfb64_5 conda-forge zlib-ng 2.0.7 hcfcfb64_0 conda-forge zstd 1.5.5 h12be248_0 conda-forge

Please let me know what I am doing wrong.

Best, Jessica

NicoKiaru commented 10 months ago

Is it still failing today? Maybe you tried unluckily during a maven.scijava.org server downtime?

JeBiUKD commented 10 months ago

No unfortunately it still does not work.

ctrueden commented 10 months ago

@JeBiUKD I think the JAVA_HOME needs to be set further up the directory chain. Try:

os.environ["JAVA_HOME"] ="C:/ProgramData/Miniconda3/envs/kymo/Library"

and

os.environ["JAVA_HOME"] ="C:/ProgramData/Miniconda3/envs/kymo/Library/jre"

If neither of those works, try also with backslashes \ instead of forward slashes /?

@hinerm Do you have experience with setting the JAVA_HOME variable on Windows from Python? Does it work? How should it be?

JeBiUKD commented 10 months ago

Thank you for the suggestions. I have tried this already and I think the JAVA_HOME set up actually worked.

I have the feeling that the download from maven seems to fail. I checked the folder structure between the two computer and noticed that my .jgo folder looks different. I transferred all the files from the computer where imagJ init did not cause a problem and now it seems to work. :)

NicoKiaru commented 10 months ago

I have the feeling that the download from maven seems to fail. I checked the folder structure between the two computer and noticed that my .jgo folder looks different. I transferred all the files from the computer where imagJ init did not cause a problem and now it seems to work. :)

Do you have an idea of what was the difference ?

JeBiUKD commented 10 months ago

I am not sure how the .jgo folders looked before initializing ImageJ the first time on the other computer, but for the folders on my PC which had trouble initializing imagej in python was missing almost all .jar files. I transferred the missing .jar files and then it worked. Now when running the initialization I get the note that JVM is already running (similar to the other computer).