As it goes down deep in the system >>>> '/System/Volumes/Preboot/Cryptexes/OSlibglib-2.0.0.dylib'
I wonder if it could be related to the very last macOS update (15.4). Xavier > Le 13 avr. 2025 à 07:22, Xavier Brazzolotto <[email protected]> a écrit : > > Hi Bill, > > I do have a similar libglib-2-related issue. > >>>> (MacCoot:93628): GLib-GIRepository-WARNING **: 06:00:12.139: Failed to >>>> load shared library 'libgobject-2.0.0.dylib' referenced by the typelib: >>>> dlopen(libgobject-2.0.0.dylib, 0x0009): tried: 'libgobject-2.0.0.dylib' >>>> (no such file), >>>> '/System/Volumes/Preboot/Cryptexes/OSlibgobject-2.0.0.dylib' (no such >>>> file), '/usr/lib/libgobject-2.0.0.dylib' (no such file, not in dyld >>>> cache), 'libgobject-2.0.0.dylib' (no such file) >>>> >>>> (MacCoot:93628): GLib-GIRepository-WARNING **: 06:00:12.145: Failed to >>>> load shared library 'libglib-2.0.0.dylib' referenced by the typelib: >>>> dlopen(libglib-2.0.0.dylib, 0x0009): tried: 'libglib-2.0.0.dylib' (no such >>>> file), '/System/Volumes/Preboot/Cryptexes/OSlibglib-2.0.0.dylib' (no such >>>> file), '/usr/lib/libglib-2.0.0.dylib' (no such file, not in dyld cache), >>>> 'libglib-2.0.0.dylib' (no such file) > > Hope Paul or Yoshitaka will figure it out. > > Xavier > >> Le 13 avr. 2025 à 07:16, William Scott <[email protected]> a écrit : >> >> Sorry, I am getting the same thing on my laptop that doesn’t even have ccp4. >> I should have checked first. >> >> I am running into this: >> >> gi._error.GError: gi-invoke-error-quark: Could not locate >> g_option_error_quark: dlopen(libglib-2.0.0.dylib, 0x0009): tried: >> 'libglib-2.0.0.dylib' (no such file), >> '/System/Volumes/Preboot/Cryptexes/OSlibglib-2.0.0.dylib' (no such file), >> '/usr/lib/libglib-2.0.0.dylib' (no such file, not in dyld cache), >> 'libglib-2.0.0.dylib' (no such file) (1) >> debug:: safe_python_command() PyRun_SimpleString() >> coot_gui.solvent_ligands_gui() >> Traceback (most recent call last): >> File "<string>", line 1, in <module> >> NameError: name 'coot_gui' is not defined >> >> >> >>> On Apr 12, 2025, at 10:07 PM, Xavier Brazzolotto <[email protected]> >>> wrote: >>> >>> Hi Bill >>> >>> I’ve just tried to remove CCP4 from my environment and launched Coot. >>> Unfortunately, the result is the same. Coot does not open the « add Other >>> Solvent Molecules ». >>> However, the Refmac Dictionary is effectively linked to the Homebrew one. >>> >>> Xavier >>> >>>> Le 13 avr. 2025 à 06:57, William Scott <[email protected]> a écrit : >>>> >>>> Hi Xavier: >>>> >>>> It looks like the Homebrew coot is finding files associated with your ccp4 >>>> installation in /Applications. I’m not certain it is the cause of the >>>> problem, but one quick test might be to start the homebrew coot without >>>> initializing the ccp4 environment. >>>> >>>> HTH, >>>> >>>> Bill >>>> >>>> >>>>> On Apr 12, 2025, at 9:07 PM, Xavier Brazzolotto <[email protected]> >>>>> wrote: >>>>> >>>>> Dear Paul, Dear Coot users >>>>> >>>>> I’ve recently updated Coot to v 1.1.15 through Homebrew on macOS (Sequoia >>>>> 15.4, MacBookPro M2). >>>>> >>>>> I have an issue when running « add Other Solvent Molecules » in the « >>>>> Modelling » menu. >>>>> >>>>> Nothing happens. Could it be related to a recent python update or another >>>>> package ? >>>>> >>>>> debug:: safe_python_command() PyRun_SimpleString() import coot_gui >>>>> Traceback (most recent call last): >>>>> File "<string>", line 1, in <module> >>>>> File >>>>> "/opt/homebrew/Cellar/[email protected]/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/coot/coot_gui.py", >>>>> line 39, in <module> >>>>> from gi.repository import Gtk, GObject >>>>> File "<frozen importlib._bootstrap>", line 1360, in _find_and_load >>>>> File "<frozen importlib._bootstrap>", line 1331, in >>>>> _find_and_load_unlocked >>>>> File "<frozen importlib._bootstrap>", line 921, in _load_unlocked >>>>> File "<frozen importlib._bootstrap>", line 813, in module_from_spec >>>>> File >>>>> "/opt/homebrew/Cellar/[email protected]/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/gi/importer.py", >>>>> line 146, in create_module >>>>> importlib.import_module('gi.repository.' + dep.split("-")[0]) >>>>> File >>>>> "/opt/homebrew/Cellar/[email protected]/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/importlib/__init__.py", >>>>> line 90, in import_module >>>>> return _bootstrap._gcd_import(name[level:], package, level) >>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>> File "<frozen importlib._bootstrap>", line 1387, in _gcd_import >>>>> File "<frozen importlib._bootstrap>", line 1360, in _find_and_load >>>>> File "<frozen importlib._bootstrap>", line 1331, in >>>>> _find_and_load_unlocked >>>>> File "<frozen importlib._bootstrap>", line 921, in _load_unlocked >>>>> File "<frozen importlib._bootstrap>", line 813, in module_from_spec >>>>> File >>>>> "/opt/homebrew/Cellar/[email protected]/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/gi/importer.py", >>>>> line 146, in create_module >>>>> importlib.import_module('gi.repository.' + dep.split("-")[0]) >>>>> File >>>>> "/opt/homebrew/Cellar/[email protected]/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/importlib/__init__.py", >>>>> line 90, in import_module >>>>> return _bootstrap._gcd_import(name[level:], package, level) >>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>> File "<frozen importlib._bootstrap>", line 1387, in _gcd_import >>>>> File "<frozen importlib._bootstrap>", line 1360, in _find_and_load >>>>> File "<frozen importlib._bootstrap>", line 1331, in >>>>> _find_and_load_unlocked >>>>> File "<frozen importlib._bootstrap>", line 921, in _load_unlocked >>>>> File "<frozen importlib._bootstrap>", line 813, in module_from_spec >>>>> File >>>>> "/opt/homebrew/Cellar/[email protected]/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/gi/importer.py", >>>>> line 146, in create_module >>>>> importlib.import_module('gi.repository.' + dep.split("-")[0]) >>>>> File >>>>> "/opt/homebrew/Cellar/[email protected]/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/importlib/__init__.py", >>>>> line 90, in import_module >>>>> return _bootstrap._gcd_import(name[level:], package, level) >>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>> File "<frozen importlib._bootstrap>", line 1387, in _gcd_import >>>>> File "<frozen importlib._bootstrap>", line 1360, in _find_and_load >>>>> File "<frozen importlib._bootstrap>", line 1331, in >>>>> _find_and_load_unlocked >>>>> File "<frozen importlib._bootstrap>", line 921, in _load_unlocked >>>>> File "<frozen importlib._bootstrap>", line 813, in module_from_spec >>>>> File >>>>> "/opt/homebrew/Cellar/[email protected]/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/gi/importer.py", >>>>> line 146, in create_module >>>>> importlib.import_module('gi.repository.' + dep.split("-")[0]) >>>>> File >>>>> "/opt/homebrew/Cellar/[email protected]/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/importlib/__init__.py", >>>>> line 90, in import_module >>>>> return _bootstrap._gcd_import(name[level:], package, level) >>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>> File "<frozen importlib._bootstrap>", line 1387, in _gcd_import >>>>> File "<frozen importlib._bootstrap>", line 1360, in _find_and_load >>>>> File "<frozen importlib._bootstrap>", line 1331, in >>>>> _find_and_load_unlocked >>>>> File "<frozen importlib._bootstrap>", line 921, in _load_unlocked >>>>> File "<frozen importlib._bootstrap>", line 813, in module_from_spec >>>>> File >>>>> "/opt/homebrew/Cellar/[email protected]/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/gi/importer.py", >>>>> line 147, in create_module >>>>> dynamic_module = load_overrides(introspection_module) >>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>> File >>>>> "/opt/homebrew/Cellar/[email protected]/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/gi/overrides/__init__.py", >>>>> line 98, in load_overrides >>>>> override_mod = importlib.import_module(override_package_name) >>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>> File >>>>> "/opt/homebrew/Cellar/[email protected]/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/importlib/__init__.py", >>>>> line 90, in import_module >>>>> return _bootstrap._gcd_import(name[level:], package, level) >>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>> File >>>>> "/opt/homebrew/Cellar/[email protected]/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/gi/overrides/GLib.py", >>>>> line 37, in <module> >>>>> from gi import _option as option >>>>> File >>>>> "/opt/homebrew/Cellar/[email protected]/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/gi/_option.py", >>>>> line 41, in <module> >>>>> OPTION_CONTEXT_ERROR_QUARK = >>>>> GLib.quark_to_string(GLib.option_error_quark()) >>>>> >>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>> gi._error.GError: gi-invoke-error-quark: Could not locate >>>>> g_option_error_quark: dlopen(libglib-2.0.0.dylib, 0x0009): tried: >>>>> 'libglib-2.0.0.dylib' (no such file), >>>>> '/System/Volumes/Preboot/Cryptexes/OSlibglib-2.0.0.dylib' (no such file), >>>>> '/usr/lib/libglib-2.0.0.dylib' (no such file, not in dyld cache), >>>>> 'libglib-2.0.0.dylib' (no such file) (1) >>>>> debug:: safe_python_command() PyRun_SimpleString() >>>>> coot_gui.solvent_ligands_gui() >>>>> Traceback (most recent call last): >>>>> File "<string>", line 1, in <module> >>>>> NameError: name 'coot_gui' is not defined >>>>> >>>>> >>>>> I have also noticed this at Coot startup. Some warnings related to >>>>> libgobject-2.0.0.dylib >>>>> >>>>> INFO:: built with GTK 4.18.4 >>>>> pdd /opt/homebrew/Cellar/coot/1.1.15/share/coot >>>>> INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: >>>>> /Applications/ccp4-9/lib/data/monomers/ >>>>> There are 243 data in >>>>> /Applications/ccp4-9/lib/data/monomers/list/mon_lib_list.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/a/ALA.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/a/ASP.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/a/ASN.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/c/CYS.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/g/GLN.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/g/GLY.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/g/GLU.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/p/PHE.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/h/HIS.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/i/ILE.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/l/LYS.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/l/LEU.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/m/MET.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/m/MSE.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/p/PRO.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/a/ARG.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/s/SER.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/t/THR.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/v/VAL.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/t/TRP.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/t/TYR.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/p/PO4.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/s/SO4.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/g/GOL.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/c/CIT.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/e/EDO.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/a/A.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/c/C.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/g/G.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/u/U.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/d/DA.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/d/DC.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/d/DG.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/d/DT.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/h/HOH.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/n/NA.cif >>>>> DEBUG:: get_atom_selection() with file >>>>> "/opt/homebrew/Cellar/coot/1.1.15/share/coot/standard-residues.pdb" >>>>> use_gemmi: 0 >>>>> DEBUG:: in setup_python_basic() pydirectory is >>>>> /opt/homebrew/Cellar/coot/1.1.15/share/coot/../../lib/python3.12/site-packages >>>>> DEBUG:: in setup_python_basic() pkgpydirectory is >>>>> /opt/homebrew/Cellar/coot/1.1.15/share/coot/../../lib/python3.12/site-packages/coot >>>>> DEBUG:: in setup_python_basic(): d_main 0x147797640 >>>>> DEBUG:: in setup_python_basic(): sys imported >>>>> DEBUG:: in setup_python_coot_module() appending to sys path: >>>>> /opt/homebrew/Cellar/coot/1.1.15/share/coot/../../lib/python3.12/site-packages >>>>> DEBUG:: in setup_python_coot_module() appending to sys path: >>>>> /opt/homebrew/Cellar/coot/1.1.15/share/coot/../../lib/python3.12/site-packages/coot >>>>> INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: >>>>> /Applications/ccp4-9/lib/data/monomers/ >>>>> There are 243 data in >>>>> /Applications/ccp4-9/lib/data/monomers/list/mon_lib_list.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/a/ALA.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/a/ASP.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/a/ASN.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/c/CYS.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/g/GLN.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/g/GLY.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/g/GLU.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/p/PHE.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/h/HIS.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/i/ILE.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/l/LYS.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/l/LEU.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/m/MET.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/m/MSE.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/p/PRO.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/a/ARG.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/s/SER.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/t/THR.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/v/VAL.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/t/TRP.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/t/TYR.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/p/PO4.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/s/SO4.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/g/GOL.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/c/CIT.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/e/EDO.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/a/A.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/c/C.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/g/G.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/u/U.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/d/DA.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/d/DC.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/d/DG.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/d/DT.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/h/HOH.cif >>>>> There are 2 data in /Applications/ccp4-9/lib/data/monomers/n/NA.cif >>>>> DEBUG:: get_atom_selection() with file >>>>> "/opt/homebrew/Cellar/coot/1.1.15/share/coot/standard-residues.pdb" >>>>> use_gemmi: 0 >>>>> INFO:: monitor 1 no description >>>>> INFO:: monitor 1 connection unit-0 >>>>> INFO:: monitor 1 refresh rate 120 mHz >>>>> INFO:: monitor 1 scale_factor 2 >>>>> INFO:: monitor 1 scale 2 >>>>> INFO:: GL Version: 4.1 Metal - 89.4 >>>>> INFO:: GL Shading Language Version: 4.10 >>>>> INFO:: GL Renderer: Apple M2 Max >>>>> INFO:: GL Vendor: Apple >>>>> WARNING:: validation failed: texture-meshes.shader validation status 0 >>>>> Shader compile texture-meshes.shader validation-failed >>>>> WARNING:: validation failed: outline-of-active-residue.shader validation >>>>> status 0 >>>>> Shader compile outline-of-active-residue.shader validation-failed >>>>> WARNING:: validation failed: map.shader validation status 0 >>>>> Shader compile map.shader validation-failed >>>>> WARNING:: validation failed: draw-map-cap.shader validation status 0 >>>>> Shader compile draw-map-cap.shader validation-failed >>>>> WARNING:: validation failed: model.shader validation status 0 >>>>> Shader compile model.shader validation-failed >>>>> WARNING:: validation failed: central-cube.shader validation status 0 >>>>> Shader compile central-cube.shader validation-failed >>>>> WARNING:: validation failed: central-cube.shader validation status 0 >>>>> Shader compile central-cube.shader validation-failed >>>>> WARNING:: validation failed: hud-text.shader validation status 0 >>>>> Shader compile hud-text.shader validation-failed >>>>> WARNING:: validation failed: hud-bars.shader validation status 0 >>>>> Shader compile hud-bars.shader validation-failed >>>>> WARNING:: validation failed: hud-labels.shader validation status 0 >>>>> Shader compile hud-labels.shader validation-failed >>>>> WARNING:: validation failed: hud-image-texture.shader validation status 0 >>>>> Shader compile hud-image-texture.shader validation-failed >>>>> WARNING:: validation failed: atom-label.shader validation status 0 >>>>> Shader compile atom-label.shader validation-failed >>>>> WARNING:: validation failed: moleculestotriangles.shader validation >>>>> status 0 >>>>> Shader compile moleculestotriangles.shader validation-failed >>>>> WARNING:: validation failed: lines.shader validation status 0 >>>>> Shader compile lines.shader validation-failed >>>>> WARNING:: validation failed: lines-pulse.shader validation status 0 >>>>> Shader compile lines-pulse.shader validation-failed >>>>> WARNING:: validation failed: rama-balls.shader validation status 0 >>>>> Shader compile rama-balls.shader validation-failed >>>>> WARNING:: validation failed: particles.shader validation status 0 >>>>> Shader compile particles.shader validation-failed >>>>> WARNING:: validation failed: instanced-objects.shader validation status 0 >>>>> Shader compile instanced-objects.shader validation-failed >>>>> WARNING:: validation failed: extra-distance-restraints.shader validation >>>>> status 0 >>>>> Shader compile extra-distance-restraints.shader validation-failed >>>>> WARNING:: validation failed: hud-geometry-tooltip-text.shader validation >>>>> status 0 >>>>> Shader compile hud-geometry-tooltip-text.shader validation-failed >>>>> WARNING:: validation failed: residue-markers.shader validation status 0 >>>>> Shader compile residue-markers.shader validation-failed >>>>> WARNING:: validation failed: ligand-view.shader validation status 0 >>>>> Shader compile ligand-view.shader validation-failed >>>>> WARNING:: validation failed: model-as-mesh.shader validation status 0 >>>>> Shader compile model-as-mesh.shader validation-failed >>>>> WARNING:: validation failed: symmetry-atoms-lines.shader validation >>>>> status 0 >>>>> Shader compile symmetry-atoms-lines.shader validation-failed >>>>> WARNING:: validation failed: hud-bars.shader validation status 0 >>>>> Shader compile hud-bars.shader validation-failed >>>>> WARNING:: validation failed: rama-plot-axes-and-ticks.shader validation >>>>> status 0 >>>>> Shader compile rama-plot-axes-and-ticks.shader validation-failed >>>>> WARNING:: validation failed: rama-plot-phi-psi-markers.shader validation >>>>> status 0 >>>>> Shader compile rama-plot-phi-psi-markers.shader validation-failed >>>>> WARNING:: validation failed: hud-lines.shader validation status 0 >>>>> Shader compile hud-lines.shader validation-failed >>>>> WARNING:: validation failed: background-image.shader validation status 0 >>>>> Shader compile background-image.shader validation-failed >>>>> WARNING:: validation failed: meshes.shader validation status 0 >>>>> Shader compile meshes.shader validation-failed >>>>> WARNING:: validation failed: texture-meshes.shader validation status 0 >>>>> Shader compile texture-meshes.shader validation-failed >>>>> WARNING:: validation failed: residue-markers-for-ssao.shader validation >>>>> status 0 >>>>> Shader compile residue-markers-for-ssao.shader validation-failed >>>>> WARNING:: validation failed: meshes-with-shadows.shader validation status >>>>> 0 >>>>> Shader compile meshes-with-shadows.shader validation-failed >>>>> WARNING:: validation failed: meshes-for-shadow-map.shader validation >>>>> status 0 >>>>> Shader compile meshes-for-shadow-map.shader validation-failed >>>>> WARNING:: validation failed: instanced-meshes-for-shadow-map.shader >>>>> validation status 0 >>>>> Shader compile instanced-meshes-for-shadow-map.shader validation-failed >>>>> WARNING:: validation failed: meshes-for-ssao.shader validation status 0 >>>>> Shader compile meshes-for-ssao.shader validation-failed >>>>> WARNING:: validation failed: instanced-meshes-for-ssao.shader validation >>>>> status 0 >>>>> Shader compile instanced-meshes-for-ssao.shader validation-failed >>>>> WARNING:: validation failed: texture-meshes-for-ssao.shader validation >>>>> status 0 >>>>> Shader compile texture-meshes-for-ssao.shader validation-failed >>>>> WARNING:: validation failed: texture-meshes-with-shadows.shader >>>>> validation status 0 >>>>> Shader compile texture-meshes-with-shadows.shader validation-failed >>>>> WARNING:: validation failed: texture-meshes-shadow-map.shader validation >>>>> status 0 >>>>> Shader compile texture-meshes-shadow-map.shader validation-failed >>>>> WARNING:: validation failed: shadow-map-image-texture.shader validation >>>>> status 0 >>>>> Shader compile shadow-map-image-texture.shader validation-failed >>>>> WARNING:: validation failed: 9.ssao_geometry.shader validation status 0 >>>>> Shader compile 9.ssao_geometry.shader validation-failed >>>>> WARNING:: validation failed: 9.ssao.shader validation status 0 >>>>> Shader compile 9.ssao.shader validation-failed >>>>> WARNING:: validation failed: 9.ssao_blur.shader validation status 0 >>>>> Shader compile 9.ssao_blur.shader validation-failed >>>>> WARNING:: validation failed: instanced-meshes-with-shadows.shader >>>>> validation status 0 >>>>> Shader compile instanced-meshes-with-shadows.shader validation-failed >>>>> WARNING:: validation failed: effects.shader validation status 0 >>>>> Shader compile effects.shader validation-failed >>>>> WARNING:: validation failed: blur-x.shader validation status 0 >>>>> Shader compile blur-x.shader validation-failed >>>>> WARNING:: validation failed: blur-y.shader validation status 0 >>>>> Shader compile blur-y.shader validation-failed >>>>> WARNING:: validation failed: depth-of-field.shader validation status 0 >>>>> Shader compile depth-of-field.shader validation-failed >>>>> WARNING:: validation failed: rotation-centre-cross-hairs-for-ssao.shader >>>>> validation status 0 >>>>> Shader compile rotation-centre-cross-hairs-for-ssao.shader >>>>> validation-failed >>>>> DEBUG:: in setup_python_with_coot_modules() pkgpydirectory: >>>>> /opt/homebrew/Cellar/coot/1.1.15/share/coot/../../lib/python3.12/site-packages/coot >>>>> DEBUG:: in setup_python_with_coot_modules() pydirectory: >>>>> /opt/homebrew/Cellar/coot/1.1.15/share/coot/../../lib/python3.12/site-packages >>>>> DEBUG:: in setup_python_with_coot_modules() appending to sys path: >>>>> /opt/homebrew/Cellar/coot/1.1.15/share/coot/../../lib/python3.12/site-packages >>>>> DEBUG:: in setup_python_with_coot_modules() appending to sys path: >>>>> /opt/homebrew/Cellar/coot/1.1.15/share/coot/../../lib/python3.12/site-packages/coot >>>>> DEBUG:: in setup_python_with_coot_modules() sys imported >>>>> DEBUG:: in setup_python_with_coot_modules() PyImport_ImportModule() coot: >>>>> 0x15a8bcae0 >>>>> DEBUG:: in setup_python_with_coot_modules() PyImport_ImportModule() >>>>> coot_utils: 0x178d438d0 >>>>> >>>>> (MacCoot:93628): GLib-GIRepository-WARNING **: 06:00:12.139: Failed to >>>>> load shared library 'libgobject-2.0.0.dylib' referenced by the typelib: >>>>> dlopen(libgobject-2.0.0.dylib, 0x0009): tried: 'libgobject-2.0.0.dylib' >>>>> (no such file), >>>>> '/System/Volumes/Preboot/Cryptexes/OSlibgobject-2.0.0.dylib' (no such >>>>> file), '/usr/lib/libgobject-2.0.0.dylib' (no such file, not in dyld >>>>> cache), 'libgobject-2.0.0.dylib' (no such file) >>>>> >>>>> (MacCoot:93628): GLib-GIRepository-WARNING **: 06:00:12.145: Failed to >>>>> load shared library 'libglib-2.0.0.dylib' referenced by the typelib: >>>>> dlopen(libglib-2.0.0.dylib, 0x0009): tried: 'libglib-2.0.0.dylib' (no >>>>> such file), '/System/Volumes/Preboot/Cryptexes/OSlibglib-2.0.0.dylib' (no >>>>> such file), '/usr/lib/libglib-2.0.0.dylib' (no such file, not in dyld >>>>> cache), 'libglib-2.0.0.dylib' (no such file) >>>>> Traceback (most recent call last): >>>>> File >>>>> "/opt/homebrew/Cellar/[email protected]/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/coot/coot_gui.py", >>>>> line 39, in <module> >>>>> from gi.repository import Gtk, GObject >>>>> File "<frozen importlib._bootstrap>", line 1360, in _find_and_load >>>>> File "<frozen importlib._bootstrap>", line 1331, in >>>>> _find_and_load_unlocked >>>>> File "<frozen importlib._bootstrap>", line 921, in _load_unlocked >>>>> File "<frozen importlib._bootstrap>", line 813, in module_from_spec >>>>> File >>>>> "/opt/homebrew/Cellar/[email protected]/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/gi/importer.py", >>>>> line 146, in create_module >>>>> importlib.import_module('gi.repository.' + dep.split("-")[0]) >>>>> File >>>>> "/opt/homebrew/Cellar/[email protected]/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/importlib/__init__.py", >>>>> line 90, in import_module >>>>> return _bootstrap._gcd_import(name[level:], package, level) >>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>> File "<frozen importlib._bootstrap>", line 1387, in _gcd_import >>>>> File "<frozen importlib._bootstrap>", line 1360, in _find_and_load >>>>> File "<frozen importlib._bootstrap>", line 1331, in >>>>> _find_and_load_unlocked >>>>> File "<frozen importlib._bootstrap>", line 921, in _load_unlocked >>>>> File "<frozen importlib._bootstrap>", line 813, in module_from_spec >>>>> File >>>>> "/opt/homebrew/Cellar/[email protected]/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/gi/importer.py", >>>>> line 146, in create_module >>>>> importlib.import_module('gi.repository.' + dep.split("-")[0]) >>>>> File >>>>> "/opt/homebrew/Cellar/[email protected]/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/importlib/__init__.py", >>>>> line 90, in import_module >>>>> return _bootstrap._gcd_import(name[level:], package, level) >>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>> File "<frozen importlib._bootstrap>", line 1387, in _gcd_import >>>>> File "<frozen importlib._bootstrap>", line 1360, in _find_and_load >>>>> File "<frozen importlib._bootstrap>", line 1331, in >>>>> _find_and_load_unlocked >>>>> File "<frozen importlib._bootstrap>", line 921, in _load_unlocked >>>>> File "<frozen importlib._bootstrap>", line 813, in module_from_spec >>>>> File >>>>> "/opt/homebrew/Cellar/[email protected]/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/gi/importer.py", >>>>> line 146, in create_module >>>>> importlib.import_module('gi.repository.' + dep.split("-")[0]) >>>>> File >>>>> "/opt/homebrew/Cellar/[email protected]/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/importlib/__init__.py", >>>>> line 90, in import_module >>>>> return _bootstrap._gcd_import(name[level:], package, level) >>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>> File "<frozen importlib._bootstrap>", line 1387, in _gcd_import >>>>> File "<frozen importlib._bootstrap>", line 1360, in _find_and_load >>>>> File "<frozen importlib._bootstrap>", line 1331, in >>>>> _find_and_load_unlocked >>>>> File "<frozen importlib._bootstrap>", line 921, in _load_unlocked >>>>> File "<frozen importlib._bootstrap>", line 813, in module_from_spec >>>>> File >>>>> "/opt/homebrew/Cellar/[email protected]/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/gi/importer.py", >>>>> line 146, in create_module >>>>> importlib.import_module('gi.repository.' + dep.split("-")[0]) >>>>> File >>>>> "/opt/homebrew/Cellar/[email protected]/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/importlib/__init__.py", >>>>> line 90, in import_module >>>>> return _bootstrap._gcd_import(name[level:], package, level) >>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>> File "<frozen importlib._bootstrap>", line 1387, in _gcd_import >>>>> File "<frozen importlib._bootstrap>", line 1360, in _find_and_load >>>>> File "<frozen importlib._bootstrap>", line 1331, in >>>>> _find_and_load_unlocked >>>>> File "<frozen importlib._bootstrap>", line 921, in _load_unlocked >>>>> File "<frozen importlib._bootstrap>", line 813, in module_from_spec >>>>> File >>>>> "/opt/homebrew/Cellar/[email protected]/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/gi/importer.py", >>>>> line 147, in create_module >>>>> dynamic_module = load_overrides(introspection_module) >>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>> File >>>>> "/opt/homebrew/Cellar/[email protected]/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/gi/overrides/__init__.py", >>>>> line 98, in load_overrides >>>>> override_mod = importlib.import_module(override_package_name) >>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>> File >>>>> "/opt/homebrew/Cellar/[email protected]/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/importlib/__init__.py", >>>>> line 90, in import_module >>>>> return _bootstrap._gcd_import(name[level:], package, level) >>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>> File >>>>> "/opt/homebrew/Cellar/[email protected]/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/gi/overrides/GLib.py", >>>>> line 37, in <module> >>>>> from gi import _option as option >>>>> File >>>>> "/opt/homebrew/Cellar/[email protected]/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/gi/_option.py", >>>>> line 41, in <module> >>>>> OPTION_CONTEXT_ERROR_QUARK = >>>>> GLib.quark_to_string(GLib.option_error_quark()) >>>>> >>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>> gi._error.GError: gi-invoke-error-quark: Could not locate >>>>> g_option_error_quark: dlopen(libglib-2.0.0.dylib, 0x0009): tried: >>>>> 'libglib-2.0.0.dylib' (no such file), >>>>> '/System/Volumes/Preboot/Cryptexes/OSlibglib-2.0.0.dylib' (no such file), >>>>> '/usr/lib/libglib-2.0.0.dylib' (no such file, not in dyld cache), >>>>> 'libglib-2.0.0.dylib' (no such file) (1) >>>>> DEBUG:: in setup_python_with_coot_modules() PyImport_ImportModule() for >>>>> gui_module: 0x0 >>>>> Load python config script >>>>> /Users/xbrazzolotto/.config/Coot/coot_preferences.py >>>>> Traceback (most recent call last): >>>>> File "/Users/xbrazzolotto/.config/Coot/coot_preferences.py", line 16, in >>>>> <module> >>>>> coot.set_use_primary_mouse_button_for_rotation(0) >>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>> AttributeError: module 'coot' has no attribute >>>>> 'set_use_primary_mouse_button_for_rotation' >>>>> WARNING:: no molecule for imol = 0 >>>>> WARNING:: atom with name " CA " alt-loc "empty", res-no: 52, ins-code "", >>>>> chain: "A" not found in molecule 0 >>>>> >>>>> >>>>> Best >>>>> Xavier >>>>> >>>>> To unsubscribe from the COOT list, click the following link: >>>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 >>>> >>> >> > ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of 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