Opened 22 months ago

Closed 22 months ago

#14493 closed defect (limitation)

ffmpeg: Symbol not found

Reported by: serhatinceer@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc: chimera-programmers
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-11.6-arm64-arm-64bit
ChimeraX Version: 1.7rc202312072052 (2023-12-07 20:52:49 UTC)
Description
movie encode /Users/serhatwin/Desktop/movie1.mp4
/Applications/ChimeraX-1.7-rc2023.12.07.app/Contents/bin/ffmpeg -r 25 -i /var/folders/09/qx10fjxn00x3wbdw21pw0s2h0000gn/T/chimovie_QgUT-%05d.ppm -vf crop=floor(in_w/2)*2:floor(in_h/2)*2:0:0 -y -vcodec libx264 -f mp4 -pix_fmt yuv420p -crf 20 /Users/serhatwin/Desktop/movie1.mp4 stdout: stderr: dyld: Symbol not found: __ZNSt3__113basic_filebufIcNS_11char_traitsIcEEE4openEPKcj Referenced from: /Applications/ChimeraX-1.7-rc2023.12.07.app/Contents/bin/ffmpeg (which was built for Mac OS X 12.0) Expected in: /usr/lib/libc++.1.dylib An error occurred during encoding. See Reply Log for details. Error during MPEG encoding: ----------------------------- Exit value: -6 Error message: stdout: stderr: dyld: Symbol not found: __ZNSt3__113basic_filebufIcNS_11char_traitsIcEEE4openEPKcj Referenced from: /Applications/ChimeraX-1.7-rc2023.12.07.app/Contents/bin/ffmpeg (which was built for Mac OS X 12.0) Expected in: /usr/lib/libc++.1.dylib

Log:
UCSF ChimeraX version: 1.7rc202312072052 (2023-12-07)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/serhatwin/Desktop/PROTOCOL/Results/Multimer/Lisc/GDF_GRE_Lisc_new/relaxed_model_1_multimer_v3_pred_4.pdb

Chain information for relaxed_model_1_multimer_v3_pred_4.pdb #1  
---  
Chain | Description  
A B C D | No description available  
E F | No description available  


> movie record

> turn y 2 180

> wait 180

> movie encode /Users/serhatwin/Desktop/movie1.mp4

/Applications/ChimeraX-1.7-rc2023.12.07.app/Contents/bin/ffmpeg -r 25 -i
/var/folders/09/qx10fjxn00x3wbdw21pw0s2h0000gn/T/chimovie_QgUT-%05d.ppm -vf
crop=floor(in_w/2)*2:floor(in_h/2)*2:0:0 -y -vcodec libx264 -f mp4 -pix_fmt
yuv420p -crf 20 /Users/serhatwin/Desktop/movie1.mp4  
stdout:  

stderr:  
dyld: Symbol not found:
__ZNSt3__113basic_filebufIcNS_11char_traitsIcEEE4openEPKcj  
Referenced from:
/Applications/ChimeraX-1.7-rc2023.12.07.app/Contents/bin/ffmpeg (which was
built for Mac OS X 12.0)  
Expected in: /usr/lib/libc++.1.dylib  


An error occurred during encoding. See Reply Log for details.  

Error during MPEG encoding:  
\-----------------------------  
Exit value: -6  
Error message:  
stdout:  

stderr:  
dyld: Symbol not found:
__ZNSt3__113basic_filebufIcNS_11char_traitsIcEEE4openEPKcj  
Referenced from:
/Applications/ChimeraX-1.7-rc2023.12.07.app/Contents/bin/ffmpeg (which was
built for Mac OS X 12.0)  
Expected in: /usr/lib/libc++.1.dylib  


\-----------------------------  


> log metadata #1

The model has no metadata

> log chains #1

Chain information for relaxed_model_1_multimer_v3_pred_4.pdb #1  
---  
Chain | Description  
A B C D | No description available  
E F | No description available  


> log

> log metadata #1

The model has no metadata

> log metadata

The model has no metadata

> color bychain

> show cartoons

> hide cartoons

> hide atoms

> show cartoons

> save /Users/serhatwin/Desktop/image1.png supersample 3

> set bgColor white

> set bgColor #ffffff00

> view orient

[Repeated 2 time(s)]

> ui mousemode right "rotate slab"

[Repeated 2 time(s)]

> volume region all imageMode "full region"

No volumes specified  

> view

[Repeated 1 time(s)]

> view orient

> lighting simple

> lighting soft

> lighting full

> lighting soft

> lighting full

> lighting soft

> lighting full

> save /Users/serhatwin/Desktop/image1.png supersample 3

> save /Users/serhatwin/Desktop/image2.png supersample 3

> save /Users/serhatwin/Desktop/image3.png supersample 3

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/serhatwin/Desktop/movie1.mp4

/Applications/ChimeraX-1.7-rc2023.12.07.app/Contents/bin/ffmpeg -r 25 -i
/var/folders/09/qx10fjxn00x3wbdw21pw0s2h0000gn/T/chimovie_QgUT-%05d.ppm -vf
crop=floor(in_w/2)*2:floor(in_h/2)*2:0:0 -y -vcodec libx264 -f mp4 -pix_fmt
yuv420p -crf 20 /Users/serhatwin/Desktop/movie1.mp4  
stdout:  

stderr:  
dyld: Symbol not found:
__ZNSt3__113basic_filebufIcNS_11char_traitsIcEEE4openEPKcj  
Referenced from:
/Applications/ChimeraX-1.7-rc2023.12.07.app/Contents/bin/ffmpeg (which was
built for Mac OS X 12.0)  
Expected in: /usr/lib/libc++.1.dylib  


An error occurred during encoding. See Reply Log for details.  

Error during MPEG encoding:  
\-----------------------------  
Exit value: -6  
Error message:  
stdout:  

stderr:  
dyld: Symbol not found:
__ZNSt3__113basic_filebufIcNS_11char_traitsIcEEE4openEPKcj  
Referenced from:
/Applications/ChimeraX-1.7-rc2023.12.07.app/Contents/bin/ffmpeg (which was
built for Mac OS X 12.0)  
Expected in: /usr/lib/libc++.1.dylib  


\-----------------------------  





OpenGL version: 4.1 Metal - 71.7.1
OpenGL renderer: Apple M1
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 Air
     Model Identifier: MacBookAir10,1
     Chip: Apple M1
     Total Number of Cores: 8 (4 performance and 4 efficiency)
     Memory: 8 GB
     System Firmware Version: 6723.140.2
     OS Loader Version: 6723.140.2

Software:

   System Software Overview:

     System Version: macOS 11.6 (20G165)
     Kernel Version: Darwin 20.6.0
     Time since boot: 15:26

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:
       C27F390:
         Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
         UI Looks like: 1920 x 1080 @ 60.00Hz
         Main Display: Yes
         Mirror: On
         Mirror Status: Master Mirror
         Online: Yes
         Rotation: Supported
         Automatically Adjust Brightness: Yes
       Color LCD:
         Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
         UI Looks like: 1920 x 1080 @ 60.00Hz
         Mirror: On
         Mirror Status: Hardware Mirror
         Online: Yes
         Automatically Adjust Brightness: No
         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: 1.5.13
   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: 12.1.3
   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: 1.3.2
   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: 1.7rc202312072052
   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: 1.1.3
   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: 1.1.8
   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: 2.6
   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: 1.5.13
   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: 1.13.1
   ChimeraX-PDB: 2.7.3
   ChimeraX-PDBBio: 1.0.1
   ChimeraX-PDBLibrary: 1.0.3
   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: 1.12.3
   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-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
   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: 4.46.0
   funcparserlib: 2.0.0a0
   glfw: 2.6.3
   grako: 3.16.5
   h5py: 3.10.0
   html2text: 2020.1.16
   idna: 3.6
   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: 4.9.0
   pickleshare: 0.7.5
   Pillow: 10.0.1
   pip: 23.0
   pkginfo: 1.9.6
   platformdirs: 4.1.0
   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: 25.1.2
   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: 6.4
   traitlets: 5.9.0
   typing-extensions: 4.9.0
   tzdata: 2023.3
   urllib3: 2.1.0
   wcwidth: 0.2.12
   webcolors: 1.12
   wheel: 0.38.4
   wheel-filename: 1.4.1
   widgetsnbextension: 4.0.9

Change History (2)

comment:1 by Eric Pettersen, 22 months ago

Component: Unassigned → Input/Output
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ffmpeg: Symbol not found

Reported by Serhat Inceer

comment:2 by Greg Couch, 22 months ago

Cc: chimera-programmers added
Resolution: → limitation
Status: assigned → closed

You are running macOS 11.6. And in the error log, it says:

/Applications/ChimeraX-1.7-rc2023.12.07.app/Contents/bin/ffmpeg (which was built for Mac OS X 12.0)

So, unfortunately, you'll need to update your system to macOS 12 to use ffmpeg.

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