Closed GenevieveBuckley closed 5 years ago
Have asked our tester to upgrade her OS to Mac High Sierra 10.13.6 (to match Gen's development environment). She's doing that now.
It's weird that the Podo executable file runs fine on my machine (but not our tester's laptop).
I can launch it from the terminal and have it run successfully, doesn't matter whether my active conda environment in the terminal shell is podo-dev, my root/default conda env, or a completely bare environment with just python3.6.6 installed.
Tester has upgraded OS to Mac High Sierra, v10.13.6 (now matches the development environment OS).
Have you tried building the whole thing on the tester's machine? ie I want to see whether it's a build error or a "not bundling everything correctly" error.
No - we tried recreating the development conda environment this afternoon, but did not succeed before it got too late to continue. We'll try again later on.
More verbose output:
[58459] PyInstaller Bootloader 3.x
[58459] LOADER: executable is /Users/genevieb/Documents/GitHub/Code_repositories/podocytes/dist/Podo.app/Contents/MacOS/Podo
[58459] LOADER: homepath is /Users/genevieb/Documents/GitHub/Code_repositories/podocytes/dist/Podo.app/Contents/MacOS
[58459] LOADER: _MEIPASS2 is NULL
[58459] LOADER: archivename is /Users/genevieb/Documents/GitHub/Code_repositories/podocytes/dist/Podo.app/Contents/MacOS/Podo
[58459] LOADER: Extracting binaries
[58459] LOADER: Executing self as child
[58459] LOADER: set _MEIPASS2 to /var/folders/gz/6f0v_zhs09x38mb4td_h6py80000gn/T/_MEIIfFEDJ
[58460] PyInstaller Bootloader 3.x
[58460] LOADER: executable is /Users/genevieb/Documents/GitHub/Code_repositories/podocytes/dist/Podo.app/Contents/MacOS/Podo
[58460] LOADER: homepath is /Users/genevieb/Documents/GitHub/Code_repositories/podocytes/dist/Podo.app/Contents/MacOS
[58460] LOADER: _MEIPASS2 is /var/folders/gz/6f0v_zhs09x38mb4td_h6py80000gn/T/_MEIIfFEDJ
[58460] LOADER: archivename is /Users/genevieb/Documents/GitHub/Code_repositories/podocytes/dist/Podo.app/Contents/MacOS/Podo
[58460] LOADER: Already in the child - running user's code.
[58460] LOADER: Python library: /var/folders/gz/6f0v_zhs09x38mb4td_h6py80000gn/T/_MEIIfFEDJ/libpython3.6m.dylib
[58460] LOADER: Loaded functions from Python library.
[58460] LOADER: Manipulating environment (sys.path, sys.prefix)
[58460] LOADER: Pre-init sys.path is /var/folders/gz/6f0v_zhs09x38mb4td_h6py80000gn/T/_MEIIfFEDJ/base_library.zip:/var/folders/gz/6f0v_zhs09x38mb4td_h6py80000gn/T/_MEIIfFEDJ
[58460] LOADER: sys.prefix is /var/folders/gz/6f0v_zhs09x38mb4td_h6py80000gn/T/_MEIIfFEDJ
[58460] LOADER: Setting runtime options
[58460] LOADER: Runtime option: u
[58460] LOADER: Initializing python
[58460] LOADER: Overriding Python's sys.path
[58460] LOADER: Post-init sys.path is /var/folders/gz/6f0v_zhs09x38mb4td_h6py80000gn/T/_MEIIfFEDJ/base_library.zip:/var/folders/gz/6f0v_zhs09x38mb4td_h6py80000gn/T/_MEIIfFEDJ
[58460] LOADER: Setting sys.argv
[58460] LOADER: setting sys._MEIPASS
[58460] LOADER: importing modules from CArchive
[58460] LOADER: extracted struct
[58460] LOADER: callfunction returned...
[58460] LOADER: extracted pyimod01_os_path
[58460] LOADER: callfunction returned...
[58460] LOADER: extracted pyimod02_archive
[58460] LOADER: callfunction returned...
[58460] LOADER: extracted pyimod03_importers
[58460] LOADER: callfunction returned...
[58460] LOADER: Installing PYZ archive with Python modules.
[58460] LOADER: PYZ archive: out00-PYZ.pyz
[58460] LOADER: Running pyiboot01_bootstrap.py
[58460] LOADER: Running pyi_rth_traitlets.py
[58460] LOADER: Running pyi_rth_mplconfig.py
[58460] LOADER: Running pyi_rth_mpldata.py
[58460] LOADER: Running pyi_rth_multiprocessing.py
[58460] LOADER: Running pyi_rth_pkgres.py
[58460] LOADER: Running launch-gui.py
2018-09-12 16:56:16,728 Podocyte automated analysis program
2018-09-12 16:56:16,729 12-Sep-2018_16-56PM
2018-09-12 16:56:16,729 ========== USER INPUT ARGUMENTS ==========
2018-09-12 16:56:16,729 input_directory: /Users/genevieb/Desktop/podo_tests/input/lif
2018-09-12 16:56:16,729 output_directory: /Users/genevieb/Desktop/podo_tests/output_12Sept2018
2018-09-12 16:56:16,729 file_extension[0]: .lif
2018-09-12 16:56:16,729 glomeruli_channel_number: 1
2018-09-12 16:56:16,729 podocyte_channel_number: 2
2018-09-12 16:56:16,729 minimum_glomerular_diameter: 30.0
2018-09-12 16:56:16,729 maximum_glomerular_diameter: 300.0
2018-09-12 16:56:16,730 ======= END OF USER INPUT ARGUMENTS =======
2018-09-12 16:56:16,730 1 .lif files found.
2018-09-12 16:56:16,730 Processing file: /Users/genevieb/Desktop/podo_tests/input/lif/51559.lif
2018-09-12 16:56:17,236 Exception raised when trying to open /Users/genevieb/Desktop/podo_tests/input/lif/51559.lif:
[58460] Failed to execute script launch-gui
[58460] LOADER: OK.
[58460] LOADER: Cleaning up Python interpreter.
Traceback (most recent call last):
File "podocytes/main.py", line 44, in main
File "site-packages/pims/bioformats.py", line 361, in __init__
File "site-packages/jpype/_jpackage.py", line 62, in __call__
TypeError: Package loci.formats.ChannelFiller is not Callable
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "bin/launch-gui.py", line 3, in <module>
File "podocytes/main.py", line 47, in main
TypeError: 'type' object is not subscriptable
[58459] LOADER: Back to parent (RC: 255)
[58459] LOADER: Doing cleanup
[58459] LOADER: Freeing archive status for /Users/genevieb/Documents/GitHub/Code_repositories/podocytes/dist/Podo.app/Contents/MacOS/Podo
Status: we are bundling java, but jpype goes looking for the system java not the version we bundled. Podo.app built with pyinstaller from jni/podocuytes packaging-loci-tools branch (see PR https://github.com/monashmicroimaging/podocytes/pull/31)
I get the same error as previously:
TypeError: Package loci.formats.ChannelFiller is not Callable
Java path: /System/Library/Frameworks/JavaVM.framework/JavaVM
... although the same build runs fine on my personal laptop & on Juan's machine.
Fulll log:
2018-10-09 13:44:34,934 Podocyte automated analysis program
2018-10-09 13:44:34,934 09-Oct-2018_13-44PM
2018-10-09 13:44:34,935 ========== USER INPUT ARGUMENTS ==========
2018-10-09 13:44:34,935 input_directory: /Users/genevieb/Desktop/podo_tests/input/lif
2018-10-09 13:44:34,935 output_directory: /Users/genevieb/Desktop/podo_tests/output_9thOct_2
2018-10-09 13:44:34,935 file_extension[0]: .lif
2018-10-09 13:44:34,935 glomeruli_channel_number: 1
2018-10-09 13:44:34,935 podocyte_channel_number: 2
2018-10-09 13:44:34,935 minimum_glomerular_diameter: 30.0
2018-10-09 13:44:34,935 maximum_glomerular_diameter: 300.0
2018-10-09 13:44:34,936 ======= END OF USER INPUT ARGUMENTS =======
2018-10-09 13:44:34,975 Java path: /System/Library/Frameworks/JavaVM.framework/JavaVM
2018-10-09 13:44:34,975 1 .lif files found.
2018-10-09 13:44:34,975 Processing file: /Users/genevieb/Desktop/podo_tests/input/lif/51559.lif
2018-10-09 13:44:35,322 Exception raised when trying to open /Users/genevieb/Desktop/podo_tests/input/lif/51559.lif
2018-10-09 13:44:35,322 TypeError: Package loci.formats.ChannelFiller is not Callable
2018-10-09 13:44:35,322 No glomeruli identified in this image.
2018-10-09 13:44:35,323 ValueError: No objects to concatenate
I think this is old now, closing.
Our tester observes this when running both the Podo executable file, and the Podo bundled app v0.1.1-alpha (Mac High Sierra 10.13.5).
I observe this error only when running the Podo.app bundle (and not when running the Podo executable file, or running podocytes/main.py directly).