Opened 2 years ago

Closed 2 years ago

#10153 closed defect (fixed)

Segger: library not loaded: libsz.2.dylib

Reported by: rposert@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-14.1-arm64-arm-64bit
ChimeraX Version: 1.7rc202311140124 (2023-11-14 01:24:52 UTC)
Description
Attempting to save a `.seg` file results in the error (in log).

To reproduce:
1) Open a `.mrc` map
2) Segment the map using default settings
3) From Segger pane, File > Save segmentation

Log:
> ui mousemode right zoom

> volume defaultvalues initialColors
> #00a4c2,#fbbd00,#a00000,#ea7100,#007d31,#1d1f5e

UCSF ChimeraX version: 1.7rc202311140124 (2023-11-14)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show "Segment Map"

> open /Users/rposert/Desktop/cryosparc_P312_J95_map.mrc

Summary of feedback from opening
/Users/rposert/Desktop/cryosparc_P312_J95_map.mrc  
---  
notes | open kw {}  
  
Opened cryosparc_P312_J95_map.mrc as #1, grid size 128,128,128, pixel 3.4,
shown at level 0.103, step 1, values float32  

> select #1

2 models selected  
No segmentation chosen  
[Repeated 1 time(s)]

> open /Users/rposert/Desktop/cryosparc_P312_J95_map.mrc

Summary of feedback from opening
/Users/rposert/Desktop/cryosparc_P312_J95_map.mrc  
---  
notes | open kw {}  
  
Opened cryosparc_P312_J95_map.mrc as #2, grid size 128,128,128, pixel 3.4,
shown at level 0.103, step 1, values float32  

> close #2

No segmentation chosen  

> open /Users/rposert/Desktop/cryosparc_P312_J95_map.mrc

Summary of feedback from opening
/Users/rposert/Desktop/cryosparc_P312_J95_map.mrc  
---  
notes | open kw {}  
  
Opened cryosparc_P312_J95_map.mrc as #2, grid size 128,128,128, pixel 3.4,
shown at level 0.103, step 1, values float32  

> close #2

No segmentation chosen  
Segmenting cryosparc_P312_J95_map.mrc, density threshold 0.102567  
Showing 4 region surfaces  
289 watershed regions, grouped to 4 regions  
Showing cryosparc_P312_J95_map.seg - 4 regions, 4 surfaces  

> open /Users/rposert/Downloads/cryosparc_P312_J95_map.mrc

Summary of feedback from opening
/Users/rposert/Downloads/cryosparc_P312_J95_map.mrc  
---  
notes | open kw {}  
  
Opened cryosparc_P312_J95_map.mrc as #3, grid size 128,128,128, pixel 3.4,
shown at level 0.103, step 1, values float32  

> close #3

> save /Users/rposert/Desktop/cryosparc_P312_J95_map.seg models #2

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 1152, in SaveSegmentation  
self.SaveSegmentationAs()  
File
"/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 1163, in SaveSegmentationAs  
segfile.show_save_dialog(smod, self.path_changed_cb)  
File
"/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 160, in show_save_dialog  
show_save_file_dialog(seg.session, format = 'Segmentation',  
File
"/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/__init__.py", line 52, in save  
save_segmentation(session, path, models = models)  
File
"/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 138, in save_segmentation  
write_segmentation(seg, path)  
File
"/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 48, in write_segmentation  
import tables  
File
"/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/__init__.py", line 32, in <module>  
from .utilsextension import get_hdf5_version as _get_hdf5_version  
ImportError:
dlopen(/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/utilsextension.cpython-311-darwin.so, 0x0002): Library not
loaded: /opt/homebrew/opt/libaec/lib/libsz.2.dylib  
Referenced from: <D0BAB090-D94C-3868-92F2-276B7B989571>
/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/libhdf5.200.dylib  
Reason: tried: '/opt/homebrew/opt/libaec/lib/libsz.2.dylib' (no such file),
'/System/Volumes/Preboot/Cryptexes/OS/opt/homebrew/opt/libaec/lib/libsz.2.dylib'
(no such file), '/opt/homebrew/opt/libaec/lib/libsz.2.dylib' (no such file),
'/usr/lib/libsz.2.dylib' (no such file, not in dyld cache)  
  
ImportError:
dlopen(/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/utilsextension.cpython-311-darwin.so, 0x0002): Library not
loaded: /opt/homebrew/opt/libaec/lib/libsz.2.dylib  
Referenced from:
/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/libhdf5.200.dylib  
Reason: tried: '/opt/homebrew/opt/libaec/lib/libsz.2.dylib' (no such file),
'/System/Volumes/Preboot/Cryptexes/OS/opt/homebrew/opt/libaec/lib/libsz.2.dylib'
(no such file), '/opt/homebrew/opt/libaec/lib/libsz.2.dylib' (no such file),
'/usr/lib/libsz.2.dylib' (no such file, not in dyld cache)  
  
File
"/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/__init__.py", line 32, in  
from .utilsextension import get_hdf5_version as _get_hdf5_version  
  
See log for complete Python traceback.  
  

> save /Users/rposert/Desktop/cryosparc_P312_J95_map.seg models #2

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 1163, in SaveSegmentationAs  
segfile.show_save_dialog(smod, self.path_changed_cb)  
File
"/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 160, in show_save_dialog  
show_save_file_dialog(seg.session, format = 'Segmentation',  
File
"/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/__init__.py", line 52, in save  
save_segmentation(session, path, models = models)  
File
"/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 138, in save_segmentation  
write_segmentation(seg, path)  
File
"/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 48, in write_segmentation  
import tables  
File
"/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/__init__.py", line 32, in <module>  
from .utilsextension import get_hdf5_version as _get_hdf5_version  
ImportError:
dlopen(/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/utilsextension.cpython-311-darwin.so, 0x0002): Library not
loaded: /opt/homebrew/opt/libaec/lib/libsz.2.dylib  
Referenced from: <D0BAB090-D94C-3868-92F2-276B7B989571>
/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/libhdf5.200.dylib  
Reason: tried: '/opt/homebrew/opt/libaec/lib/libsz.2.dylib' (no such file),
'/System/Volumes/Preboot/Cryptexes/OS/opt/homebrew/opt/libaec/lib/libsz.2.dylib'
(no such file), '/opt/homebrew/opt/libaec/lib/libsz.2.dylib' (no such file),
'/usr/lib/libsz.2.dylib' (no such file, not in dyld cache)  
  
ImportError:
dlopen(/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/utilsextension.cpython-311-darwin.so, 0x0002): Library not
loaded: /opt/homebrew/opt/libaec/lib/libsz.2.dylib  
Referenced from:
/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/libhdf5.200.dylib  
Reason: tried: '/opt/homebrew/opt/libaec/lib/libsz.2.dylib' (no such file),
'/System/Volumes/Preboot/Cryptexes/OS/opt/homebrew/opt/libaec/lib/libsz.2.dylib'
(no such file), '/opt/homebrew/opt/libaec/lib/libsz.2.dylib' (no such file),
'/usr/lib/libsz.2.dylib' (no such file, not in dyld cache)  
  
File
"/Applications/ChimeraX-1.7-rc2023.11.14.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/tables/__init__.py", line 32, in  
from .utilsextension import get_hdf5_version as _get_hdf5_version  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,6
      Model Number: Z17500103LL/A
      Chip: Apple M2 Max
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 64 GB
      System Firmware Version: 10151.41.12
      OS Loader Version: 10151.41.12

Software:

    System Software Overview:

      System Version: macOS 14.1 (23B74)
      Kernel Version: Darwin 23.1.0
      Time since boot: 7 days, 21 hours, 10 minutes

Graphics/Displays:

    Apple M2 Max:

      Chipset Model: Apple M2 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 30
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        DELL U2723QE:
          Resolution: 6720 x 3780
          UI Looks like: 3360 x 1890 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.13.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.12
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7rc202311140124
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.2
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.1
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.12
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.2
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.0
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.44.0
    funcparserlib: 1.0.1
    glfw: 2.6.2
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.5.0
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.7
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.0.0
    prompt-toolkit: 3.0.41
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.1
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.3
    traitlets: 5.9.0
    typing-extensions: 4.8.0
    tzdata: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.10
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (4)

comment:1 by Eric Pettersen, 2 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Segger: library not loaded: libsz.2.dylib

comment:2 by Eric Pettersen, 2 years ago

Reported by Rich Posert

comment:3 by Tom Goddard, 2 years ago

Fails saving an HDF5 file on Mac ARM because our PyTables on Mac ARM does not work due to a missing library.

Unfortunately PyTables still does distribute a Mac ARM distribution despite 3 years of requests:

​https://github.com/PyTables/PyTables/issues/832

I think Zach made the current Mac ARM PyTables, but I guess it was never tested. Possibly it came from Homebrew. The above ticket claims homebrew can't build PyTables on Python 3.11 due to errors.

I'll look for prebuilt Mac ARM PyTables and if none are available I'll try to make a build.

comment:4 by Tom Goddard, 2 years ago

Resolution: → fixed
Status: assigned → closed

Fixed in daily build and 1.7 release candidate.

I added the missing libsz.2.dylib from homebrew to our pytables wheel on plato and changed libhdf5.200.dylib with install_name_tool to use this one instead of looking in /opt/homebrew/... and resigned the libhdf5.200.dylib.

Before coming up with that solution I tried getting pytables from anaconda. The tar file was missing libhdf5 and other dependent non-python libraries. So I installed it properly with miniconda3. It installed tables 3.9.1 which had a massive set of library dependencies including libcurl.

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