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    skalarproduktraum synchronize #476
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  • Jun 15 14:56
    skalarproduktraum synchronize #476
Ulrik Günther
@skalarproduktraum
@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)
Kyle I S Harrington
@kephale
@skalarproduktraum hm ok i dont know what the deal is on windows, but i do get past that on linux
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
Ulrik Günther
@skalarproduktraum
ya just saw it actually fails on the mkdir
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.
Ulrik Günther
@skalarproduktraum
now i get a hard crash in the c runtime :-D
Kyle I S Harrington
@kephale
jgo's directory naming probably makes sense but seems a little silly
Ulrik Günther
@skalarproduktraum
same behaviour btw from git bash and cmd.exe, just checked for testing
Kyle I S Harrington
@kephale
if only it was the string's hash or smth
Ulrik Günther
@skalarproduktraum
windows 10 should not have a problem with that anymore (see link), but the behaviour is opt-in
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
Kyle I S Harrington
@kephale
i wonder if it could be the jvm version as well
Ulrik Günther
@skalarproduktraum
@kephale that issues looks spot-on
and the jvm is the 11 azul jdk it's probably getting via conda
Kyle I S Harrington
@kephale
Hmph
Ulrik Günther
@skalarproduktraum
so i guess, we'd have to fix that nasty transitive dependency issue
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
Kyle I S Harrington
@kephale
@skalarproduktraum yeah should work (just need jitpack to build and such)
but i'd love to have it working with the gradle-based PRs
Ulrik Günther
@skalarproduktraum
@kephale along similar lines, what update site should be used if you want to put sciview in a current fiji atm?
the ageratum one?
Kyle I S Harrington
@kephale
which is maven based
gradle has yet to work on update sites
due to the transitive dep stuff
which is another reason that i was trying to get this working in python since it seems to reproduce the transitive dep issue without requiring fiddling with update sites
Ulrik Günther
@skalarproduktraum
@kephale the ageratum update site is missing essentially all natives
so i guess getting it going on gradle has ultrahigh prio now :D
Kyle I S Harrington
@kephale
ageratum is the last maven
thats the idea
and when ageratum is stable we archive it to a branch and move on
gradle has so many obstacles that we needed something to actually work
glad that ageratum is finally being tested on windows
folks are already using it, but afaik linux users only
if natives are missing, then we should solve it
Ulrik Günther
@skalarproduktraum
lwjgl natives are missing, spirvcrossj natives are missing
ffmpeg, jogl, jocl are there
Kyle I S Harrington
@kephale
so i'll note that it would be much better to switch to gradle here, but it has been multiple months and it just doesnt move fast enough so we had to do something since the sciview update site has been literally just bitrotting