but the gradle one just doesnt work
it gives
Traceback (most recent call last):
File "ClassLoader.java", line 522, in java.lang.ClassLoader.loadClass
File "ClassLoaders.java", line 178, in jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass
File "BuiltinClassLoader.java", line 581, in jdk.internal.loader.BuiltinClassLoader.loadClass
java.lang.ClassNotFoundException: java.lang.ClassNotFoundException: com.sun.jna.Library
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "org.jpype.manager.TypeManager.java", line -1, in org.jpype.manager.TypeManager.findClassByName
File "org.jpype.manager.TypeManager.java", line -1, in org.jpype.manager.TypeManager.lookupByName
File "Class.java", line 398, in java.lang.Class.forName
File "Class.java", line -2, in java.lang.Class.forName0
File "SceneryBase.kt", line 507, in graphics.scenery.SceneryBase.<clinit>
File "LazyLogger.kt", line 26, in graphics.scenery.utils.LazyLoggerKt.LazyLogger
File "LazyLogger.kt", line 8, in graphics.scenery.utils.LazyLoggerKt.unwrapCompanionClass
File "Class.java", line 1517, in java.lang.Class.getEnclosingClass
File "Class.java", line -2, in java.lang.Class.getDeclaringClass0
File "ClassLoader.java", line 522, in java.lang.ClassLoader.loadClass
File "ClassLoaders.java", line 178, in jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass
File "BuiltinClassLoader.java", line 579, in jdk.internal.loader.BuiltinClassLoader.loadClass
File "BuiltinClassLoader.java", line 621, in jdk.internal.loader.BuiltinClassLoader.loadClassOrNull
File "BuiltinClassLoader.java", line 698, in jdk.internal.loader.BuiltinClassLoader.findClassOnClassPathOrNull
File "BuiltinClassLoader.java", line 800, in jdk.internal.loader.BuiltinClassLoader.defineClass
File "SecureClassLoader.java", line 174, in java.security.SecureClassLoader.defineClass
File "ClassLoader.java", line 1017, in java.lang.ClassLoader.defineClass
File "ClassLoader.java", line -2, in java.lang.ClassLoader.defineClass1
Exception: Java Exception
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "scripts/python_basic.py", line 42, in <module>
SciView = jimport('sc.iview.SciView')
File "/home/kharrin/anaconda3/envs/sciview/lib/python3.8/site-packages/scyjava/__init__.py", line 151, in jimport
return jpype.JClass(class_name)
File "/home/kharrin/anaconda3/envs/sciview/lib/python3.8/site-packages/jpype/_jclass.py", line 99, in __new__
return _jpype._getClass(jc)
java.lang.NoClassDefFoundError: java.lang.NoClassDefFoundError: com/sun/jna/Library
but still gradle issue
link coming in a sec
the BDV version is mismatched for sciview_ageratum, but should be right for sciview
i'm just testing out a simple layer instead of the callback stuff we had before
@kephale i am getting
$ python scripts/python_basic.py
Traceback (most recent call last):
File "scripts/python_basic.py", line 43, in <module>
HashMap = jimport('java.util.HashMap')
File "C:\Users\ulrik\Software\miniconda3\envs\sciview\lib\site-packages\scyjava\__init__.py", line 150, in jimport
start_jvm()
File "C:\Users\ulrik\Software\miniconda3\envs\sciview\lib\site-packages\scyjava\__init__.py", line 45, in start_jvm
_, workspace = jgo.resolve_dependencies(
File "C:\Users\ulrik\Software\miniconda3\envs\sciview\lib\site-packages\jgo\jgo.py", line 426, in resolve_dependencies
os.makedirs(workspace, exist_ok=True)
File "C:\Users\ulrik\Software\miniconda3\envs\sciview\lib\os.py", line 223, in makedirs
mkdir(name, mode)
FileNotFoundError: [WinError 3] The system cannot find the path specified: 'C:\\Users\\ulrik\\.jgo\\net.imagej\\imagej\\2.1.0+graphics.scenery-scenery-5de0b1e+ome-formats-bsd-6.1.1+ome-formats-gpl-6.1.1+org.jetbrains.kotlin-kotlin-stdlib-jdk8-1.4.20+org.jetbrains.kotlinx-kotlinx-coroutines-core-1.3.9+sc.fiji-bigdataviewer-core-10.1.1-SNAPSHOT+sc.iview-sciview-92add67'
(the jgo folder is empty)
(python 3.8.8, on miniconda, just fyi)
jgo is supposed to link files from m2 into the jgo directory
but i'll note that it was insanely slow to fetch the dependencies
especially given that they were already present in my m2
15 minutes or so
but your error looks like some os specific issue since it is failing on a mkdir call
i created that dir manually but it still fails
aha, found the issue
Error: Current working directory has a path longer than allowed for a
Win32 working directory.
okay, there seems to be a workaround: https://docs.microsoft.com/en-us/windows/win32/fileio/maximum-file-path-limitation?tabs=cmd
now i get a hard crash in the c runtime :-D
nevertheless, there's a cpp exception uncaught:
Stack: [0x0000001459600000,0x00000014597f0000], sp=0x00000014597e7630, free space=1949k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
C [KERNELBASE.dll+0x34b59]
C [VCRUNTIME140.dll+0x4411]
C [ntdll.dll+0xa1406]
C [_jpype.cp38-win_amd64.pyd+0x392ce]
C [_jpype.cp38-win_amd64.pyd+0x3d3d2]
C [_jpype.cp38-win_amd64.pyd+0x32585]
C 0x000001abcfb1ef97
Java frames: (J=compiled Java code, j=interpreted, Vv=VM code)
j org.jpype.manager.TypeFactoryNative.newWrapper(JJ)V+0
j org.jpype.JPypeContext.newWrapper(J)V+16
v ~StubRoutines::call_stub
j org.jpype.manager.TypeFactoryNative.newWrapper(JJ)V+0
j org.jpype.JPypeContext.newWrapper(J)V+16
v ~StubRoutines::call_stub
j org.jpype.manager.TypeFactoryNative.newWrapper(JJ)V+0
j org.jpype.JPypeContext.newWrapper(J)V+16
v ~StubRoutines::call_stub
siginfo: EXCEPTION_UNCAUGHT_CXX_EXCEPTION (0xe06d7363), ExceptionInformation=0x0000000019930520 0x00000014597ec660 0x00007ff99217e7d0 0x00007ff992100000
i wonder if it could be the jvm version as well
and the jvm is the 11 azul jdk it's probably getting via conda
7 replies
and i'd argue that probably most or even all of scenery's deps need to be transitive
@kephale it should be possible to use the versions of @elect86's PRs in the python scripts too, right?
just essentially replace the commit hashes with those from the PRs
but i'd love to have it working with the gradle-based PRs
the ageratum one?
which is maven based
gradle has yet to work on update sites