Opened 7 months ago
Closed 7 months ago
#17079 closed defect (fixed)
Scipy symbol not found
Reported by: | Owned by: | Zach Pearson | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Build System | Version: | |
Keywords: | Cc: | Tom Goddard | |
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: macOS-12.2-arm64-arm-64bit ChimeraX Version: 1.10.dev202503110047 (2025-03-11 00:47:19 UTC) Description Replace this text with list of actions that caused this problem to occur Log: UCSF ChimeraX version: 1.10.dev202503110047 (2025-03-11) © 2016-2025 Regents of the University of California. All rights reserved. > open "/Users/victoriaeverodonnell/Library/CloudStorage/Box-Box/WCM > Lab/Ever/ABCg2/ABCg2 structures/g2_af3_dox_rosace .cxs" Log from Tue Feb 11 11:11:54 2025 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9rc202412100036 (2024-12-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open "/Users/everodonnell/Documents/ABCg2/ABCg2 > structures/abcg2_af3_docking/abcg2_dox_model.cif" Chain information for abcg2_dox_model.cif #1 --- Chain | Description A B | . Computing secondary structure > select /a 5087 atoms, 5194 bonds, 655 residues, 1 model selected > hide sel atoms > select /b 5087 atoms, 5194 bonds, 655 residues, 1 model selected > hide sel atoms > select /a 5087 atoms, 5194 bonds, 655 residues, 1 model selected > ui tool show "Color Actions" > color sel slate gray > set bgColor white > lighting soft > graphics silhouettes true > select clear > cartoon style modeHelix tube sides 20 > open open /Users/everodonnell/Documents/ABCg2/abcg2_effect_rosace_.csv chain > /A 'open' has no suffix > open /Users/everodonnell/Documents/ABCg2/abcg2_effect_rosace_.csv chain /A Summary of feedback from opening /Users/everodonnell/Documents/ABCg2/abcg2_effect_rosace_.csv --- note | Plotted 12260 mutations with abund_se on x-axis and abundace on y-axis Opened deep mutational scan data for 12262 mutations of 632 residues with score names abund_se, abundace, dox, dox_se, mtx, mtx_se, position, sn38, sn38_se, surface, surface_se. Assigned scores to 632 of 655 residues of chain /A. > mutationscores define dox_only fromScoreName dox ranges "(dox >= > 0.324153098295916) and mtx <= 0.327670003560941 and sn38 <= > 0.789315769551341" combine sum Defined score dox_only having range 0.326 to 6.79 for 116 residues using 166 mutations Set attribute dox_only for 116 residues of chain /A > ui tool show "Render/Select by Attribute" > color byattribute r:dox_only target sabc palette > 0.326224,white:1.2732,#f794d0:6.79293,#e50a8f 10331 atoms, 1315 residues, atom dox_only range 0.326 to 6.79 > ui tool show "Render/Select by Attribute" > select ::dox_only>=0.326223663 & ::dox_only<=6.792931777 962 atoms, 898 bonds, 116 residues, 1 model selected > show sel atoms > select clear > select /a :542 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear > select /a :288 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 79 atoms, 81 bonds, 10 residues, 1 model selected > select up 5087 atoms, 5194 bonds, 655 residues, 1 model selected > select down 79 atoms, 81 bonds, 10 residues, 1 model selected > select down 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > select /a :450 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear > select /a :449 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear > select /a :641 8 atoms, 7 bonds, 1 residue, 1 model selected > style sel sphere Changed 8 atom styles > transparency [percentage] target r Missing or invalid "percent" argument: Expected a number > transparency 50 target r > ui mousemode right distance > distance /A:482@NH2 /A:641@CD1 Distance between /A ARG 482 NH2 and LEU 641 CD1: 12.411Å > color #2.1 black models > select clear > select /a :650 11 atoms, 11 bonds, 1 residue, 1 model selected > save "/Users/everodonnell/Desktop/g2_af3_dox_rosace .cxs" ——— End of log from Tue Feb 11 11:11:54 2025 ——— > view name session-start opened ChimeraX session Traceback (most recent call last): File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/triggerset.py", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/structure.py", line 1940, in _update_graphics_if_needed s[i].update_graphics_if_needed() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/structure.py", line 380, in update_graphics_if_needed self._create_ribbon_graphics() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/structure.py", line 690, in _create_ribbon_graphics ribbons_drawing.compute_ribbons(self) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/ribbon.py", line 630, in compute_ribbons _make_ribbon_graphics(structure, self) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/ribbon.py", line 142, in _make_ribbon_graphics centers = _arc_helix_geometry(coords, xs_mgr, displays, start, end, geometry) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/ribbon.py", line 1010, in _arc_helix_geometry hc = HelixCylinder(coords[start:end]) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/sse.py", line 196, in __init__ self._straight_optimize() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/sse.py", line 409, in _straight_optimize opt = OptLine(self.coords, centroid, axis) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/sse.py", line 36, in __init__ from scipy.optimize import minimize File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/scipy/optimize/__init__.py", line 414, in <module> from ._optimize import * File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/scipy/optimize/_optimize.py", line 35, in <module> from scipy.linalg import cholesky, issymmetric, LinAlgError File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/scipy/linalg/__init__.py", line 203, in <module> from ._misc import * File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/scipy/linalg/_misc.py", line 3, in <module> from .blas import get_blas_funcs File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/scipy/linalg/blas.py", line 213, in <module> from scipy.linalg import _fblas ImportError: dlopen(/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/scipy/linalg/_fblas.cpython-311-darwin.so, 0x0002): Symbol not found: _caxpy$NEWLAPACK Referenced from: /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/scipy/linalg/_fblas.cpython-311-darwin.so Expected in: /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate Error processing trigger "graphics update": ImportError: dlopen(/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/scipy/linalg/_fblas.cpython-311-darwin.so, 0x0002): Symbol not found: _caxpy$NEWLAPACK Referenced from: /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/scipy/linalg/_fblas.cpython-311-darwin.so Expected in: /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/scipy/linalg/blas.py", line 213, in from scipy.linalg import _fblas See log for complete Python traceback. OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: MacBookAir10,1 Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 7429.81.3 OS Loader Version: 7429.81.3 Software: System Software Overview: System Version: macOS 12.2 (21D49) Kernel Version: Darwin 21.3.0 Time since boot: 1 day 46 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 7 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.2.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.2.0 build: 1.2.2.post1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.1 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.19.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.1 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.5 ChimeraX-AtomicLibrary: 14.1.13 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 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: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10.dev202503110047 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 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: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.5.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 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: 2.1.7 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.15 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 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-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.7 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: 1.1.2 ChimeraX-ProfileGrids: 1.0.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 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: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.44 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 coverage: 7.6.12 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.13 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.17.0 fonttools: 4.56.0 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h5py: 3.13.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.0.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.4.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.1.0 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 24.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.6 pluggy: 1.5.0 prompt_toolkit: 3.0.50 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.32 Pygments: 2.18.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.1 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.3.5 pytest-cov: 6.0.0 python-dateutil: 2.9.0.post0 pytz: 2025.1 pyzmq: 26.2.1 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 75.8.2 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.1.3 sphinx-autodoc-typehints: 3.0.1 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2025.1 urllib3: 2.3.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.13
Change History (3)
comment:1 by , 7 months ago
Cc: | added |
---|---|
Component: | Unassigned → Build System |
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → Scipy symbol not found |
comment:2 by , 7 months ago
Looking at the build log I see
2025-03-12T07:11:51.6689520Z Collecting scipy==1.14.0 (from -r app_requirements.txt (line 59))
2025-03-12T07:11:51.6804230Z Downloading scipy-1.14.0-cp311-cp311-macosx_14_0_arm64.whl.metadata (60 kB)
So we're getting the macOS 14 version of scipy. Evidently macOS 14 ships with a new version of BLAS? See also: https://github.com/numpy/numpy/issues/25026
Anyway, I'll just have to ensure the right version is installed nightly.
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This is similar to #17006, except that this report is on macOS 12, not 11, and scipy supposedly works on macOS 12.