pyimagej image.init() FileNotFoundError: [Errno 2] No such file or directory: ~.m2/repository/io/scif/scifio-labeling/0.3.1/scifio-labeling-0.3.1.jar #278

mamba create -n pyimagej -c conda-forge python=3.8 pyimagej openjdk=11 ipykernel
wget https://downloads.imagej.net/fiji/latest/fiji-linux64.zip 
unzip fiji-linux64.zip 
rm fiji-linux64.zip

FileNotFoundError: No such file or directory: ~/.m2/repository/io/scif/scifio-labeling/0.3.1/scifio-labeling-0.3.1.jar' -> ~/.jgo/io.scif/scifio-labeling/0.3.1/64d37f756ce9b31af4b9413862ddb4fdae7bd1d10bdfadd417d693b8642fc2e3/scifio-labeling-0.3.1.jar

-------------------------------------------------

Local path to ImageJ2 installation given: /home/jovyan/code/image-analysis/imagej/Fiji.app
Added 507 JARs to the Java classpath.
Adding jars from endpoints ['io.scif:scifio-labeling:0.3.1', 'net.imglib2:imglib2-imglyb:1.1.0']
Using endpoints ['io.scif:scifio-labeling:0.3.1', 'net.imglib2:imglib2-imglyb:1.1.0']
Getting verbose level: 2
Getting verbose level: 2
Returning expanded coordinate io.scif:scifio-labeling:0.3.1.
Returning expanded coordinate net.imglib2:imglib2-imglyb:1.1.0.
First time start-up may be slow. Downloaded dependencies will be cached for shorter start-up times in subsequent executions.
Executing: ('/opt/conda/envs/pyimagej/bin/mvn', '-B', '-f', '/home/jovyan/.jgo/io.scif/scifio-labeling/0.3.1/64d37f756ce9b31af4b9413862ddb4fdae7bd1d10bdfadd417d693b8642fc2e3/pom.xml', 'dependency:resolve', '-X')
Relevant mvn output: [INFO]    io.scif:scifio-labeling:jar:0.3.1:compile -- module io.scif.labeling [auto]
Linking source /home/jovyan/.m2/repository/io/scif/scifio-labeling/0.3.1/scifio-labeling-0.3.1.jar to target /home/jovyan/.jgo/io.scif/scifio-labeling/0.3.1/64d37f756ce9b31af4b9413862ddb4fdae7bd1d10bdfadd417d693b8642fc2e3/scifio-labeling-0.3.1.jar with link_type auto
Linking source /home/jovyan/.m2/repository/io/scif/scifio-labeling/0.3.1/scifio-labeling-0.3.1.jar to target /home/jovyan/.jgo/io.scif/scifio-labeling/0.3.1/64d37f756ce9b31af4b9413862ddb4fdae7bd1d10bdfadd417d693b8642fc2e3/scifio-labeling-0.3.1.jar with link_type hard
---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
Cell In[7], line 1
----> 1 ij = imagej.init(os.path.join(base_dir, 'Fiji.app'), mode='headless')

File /opt/conda/envs/pyimagej/lib/python3.8/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 /opt/conda/envs/pyimagej/lib/python3.8/site-packages/imagej/__init__.py:1424, in _create_jvm(ij_dir_or_version_or_endpoint, mode, add_legacy)
   1421 sj.config.endpoints.extend(original_endpoints)
   1423 try:
-> 1424     sj.start_jvm()
   1425 except subprocess.CalledProcessError as e:
   1426     # Check to see if initialization failed due to "un-managed"
   1427     # imagej-legacy
   1428     err_lines = []

File /opt/conda/envs/pyimagej/lib/python3.8/site-packages/scyjava/_java.py:190, in start_jvm(options)
    188     endpoints = endpoints[:1] + sorted(endpoints[1:])
    189     _logger.debug("Using endpoints %s", endpoints)
--> 190     _, workspace = jgo.resolve_dependencies(
    191         "+".join(endpoints),
    192         m2_repo=scyjava.config.get_m2_repo(),
    193         cache_dir=scyjava.config.get_cache_dir(),
    194         manage_dependencies=scyjava.config.get_manage_deps(),
    195         repositories=repositories,
    196         verbose=scyjava.config.get_verbose(),
    197         shortcuts=scyjava.config.get_shortcuts(),
    198     )
    199     jpype.addClassPath(os.path.join(workspace, "*"))
    201 # HACK: Try to set JAVA_HOME if it isn't already.

File /opt/conda/envs/pyimagej/lib/python3.8/site-packages/jgo/jgo.py:712, in resolve_dependencies(endpoint_string, cache_dir, m2_repo, link_type, update_cache, force_update, manage_dependencies, repositories, shortcuts, verbose)
    709 relevant_jars.append(jar_file_in_workspace)
    711 try:
--> 712     link(
    713         os.path.join(m2_repo, *g.split("."), a, version, jar_file),
    714         jar_file_in_workspace,
    715         link_type=link_type,
    716     )
    717 except FileExistsError:
    718     # Do not throw exception if target file exists.
    719     pass

File /opt/conda/envs/pyimagej/lib/python3.8/site-packages/jgo/jgo.py:222, in link(source, link_name, link_type)
    220 except OSError as e:
    221     if e.errno != 18:
--> 222         raise e
    223 try:
    224     return link(source=source, link_name=link_name, link_type="soft")

File /opt/conda/envs/pyimagej/lib/python3.8/site-packages/jgo/jgo.py:219, in link(source, link_name, link_type)
    217 elif link_type.lower() == "auto":
    218     try:
--> 219         return link(source=source, link_name=link_name, link_type="hard")
    220     except OSError as e:
    221         if e.errno != 18:

File /opt/conda/envs/pyimagej/lib/python3.8/site-packages/jgo/jgo.py:214, in link(source, link_name, link_type)
    212     return os.symlink(source, link_name)
    213 elif link_type.lower() == "hard":
--> 214     return os.link(source, link_name)
    215 elif link_type.lower() == "copy":
    216     return shutil.copyfile(source, link_name)

FileNotFoundError: [Errno 2] No such file or directory: '/home/jovyan/.m2/repository/io/scif/scifio-labeling/0.3.1/scifio-labeling-0.3.1.jar' -> '/home/jovyan/.jgo/io.scif/scifio-labeling/0.3.1/64d37f756ce9b31af4b9413862ddb4fdae7bd1d10bdfadd417d693b8642fc2e3/scifio-labeling-0.3.1.jar'

Checking Python:

--> Python executable = /opt/conda/envs/pyimagej/bin/python

Checking environment:
--> CONDA_PREFIX = /opt/conda/envs/pyimagej
--> Python executable matches Conda environment.

Checking Python dependencies:
--> jgo: /opt/conda/envs/pyimagej/lib/python3.8/site-packages/jgo/__init__.py
--> scyjava: /opt/conda/envs/pyimagej/lib/python3.8/site-packages/scyjava/__init__.py
--> imglyb: /opt/conda/envs/pyimagej/lib/python3.8/site-packages/imglyb/__init__.py
--> pyimagej: /opt/conda/envs/pyimagej/lib/python3.8/site-packages/imagej/__init__.py

Checking Maven:
--> Maven executable = /opt/conda/envs/pyimagej/bin/mvn
$ mvn -v
Apache Maven 3.9.3 (246d85a6ebec21fd45a0f9abd2a99906f92a4707)
Maven home: /opt/conda/envs/pyimagej/opt/maven
Java version: 11.0.15-internal, vendor: Oracle Corporation, runtime: /opt/conda/envs/pyimagej/lib/jvm
Default locale: en_US, platform encoding: UTF-8
OS name: "linux", version: "6.1.36-unraid", arch: "amd64", family: "unix"

Checking Java:
--> JAVA_HOME = /opt/conda/envs/pyimagej/lib/jvm
--> Java executable = /opt/conda/envs/pyimagej/bin/java
$ java -version
openjdk version "11.0.15-internal" 2022-04-19
OpenJDK Runtime Environment (build 11.0.15-internal+0-adhoc..src)
OpenJDK 64-Bit Server VM (build 11.0.15-internal+0-adhoc..src, mixed mode)

Great job! All looks good.