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Opened 20 months ago
Closed 20 months ago
#14639 closed defect (nonchimerax)
Looks like Mac daily build is not notarized
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Build System | Version: | |
| Keywords: | Cc: | chimerax-programmers | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.3.1-arm64-arm-64bit
ChimeraX Version: 1.8.dev202402241727 (2024-02-24 17:27:28 UTC)
Description
When I started this Mac ChimeraX daily build it said it could not be checked for malware and would not open it. Apparently it is not notarized.
Log:
UCSF ChimeraX version: 1.8.dev202402241727 (2024-02-24)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/goddard/ucsf/presentations/paxlovid-vr-
> mar2023/data/mpro_nirmatrelvir.cxs format session
Opened eds 7rfw extended as #3, grid size 58,57,47, pixel 0.573,0.553,0.568,
shown at level 0.48, step 1, values float32
Log from Thu Mar 23 18:12:01 2023UCSF ChimeraX version: 1.6.dev202303230058
(2023-03-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/goddard/ucsf/presentations/paxlovid-vr-
> mar2023/data/mpro_nirmatrelvir.cxs format session
Opened eds 7rfw extended as #3, grid size 58,57,47, pixel 0.573,0.553,0.568,
shown at level 0.48, step 1, values float32
Opened eds 7rfw extended as #5, grid size 58,57,47, pixel 0.573,0.553,0.568,
shown at level 0.478, step 1, values float32
Log from Thu Mar 23 17:52:16 2023UCSF ChimeraX version: 1.6.dev202303230058
(2023-03-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/goddard/ucsf/presentations/paxlovid-vr-
> mar2023/data/mpro_nirmatrelvir.cxs format session
Opened eds 7rfw extended as #3, grid size 58,57,47, pixel 0.573,0.553,0.568,
shown at level 0.48, step 1, values float32
Opened eds 7rfw extended as #5, grid size 58,57,47, pixel 0.573,0.553,0.568,
shown at level 0.478, step 1, values float32
Log from Thu Mar 23 17:41:16 2023UCSF ChimeraX version: 1.6.dev202303230058
(2023-03-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/goddard/ucsf/presentations/paxlovid-vr-mar2023/data/paxlovid.cxs
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Opened eds 7rfw extended as #3, grid size 58,57,47, pixel 0.573,0.553,0.568,
shown at level 0.48, step 1, values float32
Opened eds 7rfw extended as #5, grid size 58,57,47, pixel 0.573,0.553,0.568,
shown at level 0.478, step 1, values float32
Log from Mon Mar 20 10:30:55 2023UCSF ChimeraX version: 1.6.dev202302100235
(2023-02-10)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 7tgr format mmcif fromDatabase pdb
7tgr title:
Structure of SARS-CoV-2 main protease in complex with GC376 [more info...]
Chain information for 7tgr #1
---
Chain | Description | UniProt
A | 3C-like proteinase | R1AB_SARS2 1-304
Non-standard residues in 7tgr #1
---
B1S —
(1R,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic
acid
CL — chloride ion
EDO — 1,2-ethanediol (ethylene glycol)
K — potassium ion
K36 —
(1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic
acid (GC376)
NA — sodium ion
7tgr mmCIF Assemblies
---
1| author_and_software_defined_assembly
> ui tool show "Send to Quest"
> graphics quality atomTriangles 100
> graphics quality bondTriangles 20
> graphics quality ribbonDivisions 10
> open 7tgr fromDatabase eds
Summary of feedback from opening 7tgr fetched from eds
---
note | Fetching map 7tgr from
http://www.ebi.ac.uk/pdbe/coordinates/files/7tgr.ccp4
Opened eds 7tgr as #2, grid size 204,96,80, pixel 0.562,0.551,0.574, shown at
level 0.818, step 1, values float32
> volume #2 level 0.7671
> select :166
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select ligand
62 atoms, 63 bonds, 3 residues, 1 model selected
> select sel :< 5
263 atoms, 248 bonds, 39 residues, 1 model selected
> usage volume cover
volume cover volumes [atomBox an atoms specifier] [pad a number] [box box
bounds] [x 2 floats] [y 2 floats] [z 2 floats] [fBox box bounds] [fx 2 floats]
[fy 2 floats] [fz 2 floats] [iBox box bounds] [ix 2 floats] [iy 2 floats] [iz
2 floats] [useSymmetry true or false] [cellSize cellSize] [step map step]
[modelId modelId]
— Use symmetry to extend a map to cover a region
cellSize: some integers
modelId: a model id
> volume cover #2 atomBox sel
Extended map eds 7tgr to box of size (60, 77, 95),
cell size (204, 96, 80) grid points, 4 symmetry operations,
0 points not covered by any symmetry,
maximum value difference where symmetric map copies overlap = 1.308e-06
Opened eds 7tgr extended as #3, grid size 60,77,95, pixel 0.562,0.551,0.574,
shown at step 1, values float32
> close #3
Drag select of 14 atoms, 32 residues, 9 bonds
> select clear
> select :B1S
29 atoms, 30 bonds, 1 residue, 1 model selected
> select sel :< 4
182 atoms, 179 bonds, 20 residues, 1 model selected
> select :B1S :< 3
97 atoms, 98 bonds, 9 residues, 1 model selected
> select :B1S :< 5
229 atoms, 223 bonds, 29 residues, 1 model selected
> volume cover #2 atomBox sel
Extended map eds 7tgr to box of size (58, 50, 47),
cell size (204, 96, 80) grid points, 4 symmetry operations,
0 points not covered by any symmetry,
maximum value difference where symmetric map copies overlap = 1.308e-06
Opened eds 7tgr extended as #3, grid size 58,50,47, pixel 0.562,0.551,0.574,
shown at step 1, values float32
> volume #3 level 0.6057
> volume #3 level 0.4812
> volume zone #3 nearAtoms sel & #1 range 3.44
> volume #3 level 0.3982
> volume #3 level 0.472
> select :166
9 atoms, 8 bonds, 1 residue, 1 model selected
> color :166 magenta
> color :166 orange
> color :166 byhetero
> color :B1S pink
> graphics quality bondTriangles 20
[Repeated 2 time(s)]
> save 7tgr.cxs
> close
> open 7rfw
7rfw title:
Structure of SARS-CoV-2 main protease in complex with a covalent inhibitor
[more info...]
Chain information for 7rfw #1
---
Chain | Description | UniProt
A | 3C-like proteinase | R1AB_SARS2 1-306
Non-standard residues in 7rfw #1
---
4WI —
(1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide
(PF-07321332, bound form; nirmatrelvir, bound form; Paxlovid, bound form)
7rfw mmCIF Assemblies
---
1| author_and_software_defined_assembly
> graphics quality bondTriangles 20
> graphics quality
Quality 1, atom triangles 100, bond triangles 20, ribbon divisions 10
> color :4WI pink
> color :4WI byhetero
> select ligand
68 atoms, 70 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
7 hydrogen bonds found
> color :166 orange
> color :166 byhetero
> select :21,50
15 atoms, 13 bonds, 2 residues, 1 model selected
> show sel
> color sel cyan
> color sel byhetero
> select clear
> open 7rfw fromDatabase eds
Summary of feedback from opening 7rfw fetched from eds
---
note | Fetching map 7rfw from
http://www.ebi.ac.uk/pdbe/coordinates/files/7rfw.ccp4
Opened eds 7rfw as #2, grid size 200,96,80, pixel 0.573,0.553,0.568, shown at
level 0.885, step 1, values float32
> select :4WI :<5
276 atoms, 276 bonds, 7 pseudobonds, 28 residues, 2 models selected
> volume cover #2 near sel
Expected a keyword
> volume cover #2 atomBox sel
Extended map eds 7rfw to box of size (58, 57, 47),
cell size (200, 96, 80) grid points, 4 symmetry operations,
0 points not covered by any symmetry,
maximum value difference where symmetric map copies overlap = 1.4156e-06
Opened eds 7rfw extended as #3, grid size 58,57,47, pixel 0.573,0.553,0.568,
shown at step 1, values float32
> volume #3 level 0.6537
> volume #3 level 0.5574
> volume zone #3 nearAtoms sel & #1 range 3.44
> volume #3 level 0.4804
> select clear
> volume #3 color #ffffb24e
> volume #3 color #ffffb27f
> save paxlovid.cxs
> sym #1 assembly 1
Made 2 copies for 7rfw assembly 1
> view
> hide #!4.2 models
> show #!4.2 models
> color #4.2 cornflowerblue ribbons
> color #4.2 cornflowerblue
> color #4.2:4WI pink
> color #4.2:21,50 lime
> color #4.2:166 orange lime
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #4.2:166 orange
> color #4.1:21,50 lime
> color #4 byhetero
> save paxlovid.cxs
> volume #3 color #ffffff7f
> volume #3 color #ffffff80
[Repeated 1 time(s)]
> save paxlovid.cxs
> save paxlovid.glb
> ui tool show "Send to Quest"
> save /Users/goddard/Desktop/paxlovid.glb
Running command: "/opt/homebrew/bin/adb" push
/Users/goddard/Desktop/paxlovid.glb /sdcard/Android/data/com.UCSF.Lookie/files
stdout:
adb: error: failed to get feature set: no devices/emulators found
stderr:
> save /Users/goddard/Desktop/paxlovid.glb
Running command: "/opt/homebrew/bin/adb" push
/Users/goddard/Desktop/paxlovid.glb
/sdcard/Android/data/com.UCSF.LookieAR/files
stdout:
adb: error: failed to get feature set: no devices/emulators found
stderr:
> save /Users/goddard/Desktop/paxlovid.glb
Running command: "/opt/homebrew/bin/adb" push
/Users/goddard/Desktop/paxlovid.glb
/sdcard/Android/data/com.UCSF.LookieAR/files
> volume cover #2 atomBox #4.2:4WI :< 5
Extended map eds 7rfw to box of size (58, 57, 47),
cell size (200, 96, 80) grid points, 4 symmetry operations,
0 points not covered by any symmetry,
maximum value difference where symmetric map copies overlap = 1.4156e-06
Opened eds 7rfw extended as #5, grid size 58,57,47, pixel 0.573,0.553,0.568,
shown at step 1, values float32
> select #4.2:4WI :< 5
288 atoms, 286 bonds, 7 pseudobonds, 30 residues, 4 models selected
> volume #5 color #feffff
> volume #5 color #feffff7c
> volume #5 color #feffff7d
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic
models, 1 maps.
> hide #!4.1 models
> volume zone #5 nearAtoms sel & #4.2 range 3.44
> volume #2 level 0.4977
> volume #5 level 0.4783
> show #!4.1 models
> select clear
> save paxlovid.cxs
[Repeated 1 time(s)]
> save /Users/goddard/Desktop/paxlovid.glb
Running command: "/opt/homebrew/bin/adb" push
/Users/goddard/Desktop/paxlovid.glb
/sdcard/Android/data/com.UCSF.LookieAR/files
> save paxlovid.cxs
——— End of log from Mon Mar 20 10:30:55 2023 ———
opened ChimeraX session
> graphics quality atomTriangles 100
> graphics quality ribbonDivisions 2
> graphics quality ribbonDivisions 5
> graphics quality ribbonSides 8
> graphics quality ribbonSides 4
> ~hbonds
> graphics quality ribbonSides 8
> graphics quality bondTriangles 20
> save /Users/goddard/ucsf/presentations/paxlovid-vr-
> mar2023/data/mpro_nirmatrelvir.cxs
——— End of log from Thu Mar 23 17:41:16 2023 ———
opened ChimeraX session
> color #4.2 salmon
> color #4.2:21,50 lime
> color #4.2:4WI pink
> color #4.2 byhetero
> save /Users/goddard/ucsf/presentations/paxlovid-vr-
> mar2023/data/mpro_nirmatrelvir.cxs
> save /Users/goddard/ucsf/presentations/paxlovid-vr-
> mar2023/data/mpro_nirmatrelvir.glb
> save /Users/goddard/ucsf/presentations/paxlovid-vr-
> mar2023/images/mpro_nirmatrelvir.png
> select #4.2/A:401@C11
1 atom, 1 residue, 1 model selected
> select up
68 atoms, 70 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
7 hydrogen bonds found
> ~hbonds
> color #4.2:166 orange
> color #4.2 byhetero
> select clear
> save /Users/goddard/ucsf/presentations/paxlovid-vr-
> mar2023/images/mpro_nirmatrelvir.png
> save /Users/goddard/ucsf/presentations/paxlovid-vr-
> mar2023/data/mpro_nirmatrelvir.glb
> save /Users/goddard/ucsf/presentations/paxlovid-vr-
> mar2023/data/mpro_nirmatrelvir.cxs
——— End of log from Thu Mar 23 17:52:16 2023 ———
opened ChimeraX session
> close #5
> save /Users/goddard/ucsf/presentations/paxlovid-vr-
> mar2023/data/mpro_nirmatrelvir.cxs
——— End of log from Thu Mar 23 18:12:01 2023 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac Studio
Model Identifier: Mac14,14
Model Number: Z1800003VLL/A
Chip: Apple M2 Ultra
Total Number of Cores: 24 (16 performance and 8 efficiency)
Memory: 64 GB
System Firmware Version: 10151.81.1
OS Loader Version: 10151.81.1
Software:
System Software Overview:
System Version: macOS 14.3.1 (23D60)
Kernel Version: Darwin 23.3.0
Time since boot: 13 days, 2 hours, 9 minutes
Graphics/Displays:
Apple M2 Ultra:
Chipset Model: Apple M2 Ultra
Type: GPU
Bus: Built-In
Total Number of Cores: 60
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
PHL 278B1:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
alphashape: 1.3.1
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.14.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.0.3
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.16
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.3
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.4
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.53
ChimeraX-AtomicLibrary: 12.1.14
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
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: 2.12
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: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
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: 1.8.dev202402241727
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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: 1.1.9
ChimeraX-ListInfo: 1.2.2
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: 2.7
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.2
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.15
ChimeraX-ModelPanel: 1.5
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-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.2
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
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: 1.2.1
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-Segmentations: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
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: 1.15
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.4
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-TetraScapeCommand: 0.1
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: 1.35
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-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
click: 8.1.7
click-log: 0.4.0
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.8
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.1
fonttools: 4.49.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.43
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
Jinja2: 3.1.3
jupyter-client: 8.6.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.10
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.1.0
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.2
matplotlib-inline: 0.1.6
msgpack: 1.0.7
ndindex: 1.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.2.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.9.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.3
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.2.0
pip: 24.0
pkginfo: 1.9.6
platformdirs: 4.2.0
prompt-toolkit: 3.0.43
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.3.0
pygments: 2.17.2
pynmrstar: 3.3.2
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3302
pyparsing: 3.1.1
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.2
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.2
python-dateutil: 2.8.2
pytz: 2024.1
pyzmq: 25.1.2
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
Rtree: 1.1.0
scipy: 1.12.0
setuptools: 69.1.0
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
shapely: 2.0.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.0
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.1
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.1
trimesh: 4.0.10
typing-extensions: 4.10.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.42.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
Attachments (1)
Change History (7)
comment:1 by , 20 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Build System |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Looks like Mac daily build is not notarized |
comment:2 by , 20 months ago
by , 20 months ago
| Attachment: | Screenshot 2024-02-26 at 12.17.30 PM.png added |
|---|
Mac warning dialog that ChimeraX could not be verified.
comment:4 by , 20 months ago
There are no error messages and the status code is success from the Mac ARM and Intel builds (did not check universal) and the Mac ARM build exhibits the same failure to start. So it looks like Apple's notarytool is not reporting the failure. I will try to dump everything from the "notarytool log" command to see if there are some new fields that indicate an error.
comment:5 by , 20 months ago
I added some code to capture all of the output from command "notarytool log" and it indicates nothing wrong with the notarization. I've attached all the notarization output. Copying ChimeraX from this dmg does not run apparently due to a notarization problem as shown in the attached image saying the developer cannot be verified.
We suspect the problem is because AmberTools23 has library paths outside the app tree. Eric has reverted to AmberTools20 so we should check if the daily build can be installed tomorrow without the "developer cannot be verified".
If the problem persists, it may be some problem with our Apple developer account.
comment:6 by , 20 months ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
Reverting AmberTools23 with the library paths referencing libraries outside the build yesterday has fixed today's daily build notarization.
I'm not sure why Apple's "notarytool log" reported no trouble with the notarization yesterday. Hopefully Apple will fix this.
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I strongly suspect that the root cause is AmberTools23 [because it wrongly references non-system libraries outside the app], though I don't know why the notarization process would not report a failure.