#10457 closed defect (limitation)

tgz chimeraX download does not install on fedora core 37

Reported by: bennion1@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Platform Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

hello,
Unpacking the tgz file and running chimeraX from bin/
produces these results, mostly looking for libffi.so
however, I have all libffi libraries installed that exist for my repo

RPMs                                                                                     33 kB/s | 2.0 kB     00:00
Package libffi-3.4.4-1.fc37.x86_64 is already installed.
Package libffi-devel-3.4.4-1.fc37.x86_64 is already installed.


[bennion1@emer bin]$ ls
amber20    fonttools             kernprof      nib-tck2trk  pybabel          rst2html.py            sphinx-build
blockdiag  grako                 lsm2bin       nib-trk2tck  __pycache__      rst2latex.py           sphinx-quickstart
ChimeraX   html2text             nc3tonc4      normalizer   pydicom          rst2man.py             structcomp
cpuinfo    imagecodecs           nc4tonc3      parmed       pyftmerge        rst2odt_prepstyles.py  tiff2fsspec
cygdb      ipython               ncinfo        parrec2nii   pyftsubset       rst2odt.py             tiffcomment
cython     ipython3              nib-conform   pip          pygmentize       rst2pseudoxml.py       tifffile
cythonize  jupyter               nib-convert   pip3         pylupdate6       rst2s5.py              ttx
distro     jupyter-kernel        nib-dicomfs   pip3.11      pyproject-build  rst2xetex.py           wheel
docutils   jupyter-kernelspec    nib-diff      pkginfo      python3.11       rst2xml.py             wheel-filename
f2py       jupyter-migrate       nib-ls        pt2to3       pyuic6           rstpep2html.py         xparmed
f2py3      jupyter-qtconsole     nib-nifti-dx  ptdump       qtpy             sff
f2py3.11   jupyter-run           nib-roi       ptrepack     rst2html4.py     sphinx-apidoc
ffmpeg     jupyter-troubleshoot  nib-stats     pttree       rst2html5.py     sphinx-autogen
[bennion1@emer bin]$ ./ChimeraX
NOTE: available bundle cache has not been initialized yet
WARNING: Traceback (most recent call last):
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 501, in get_module
    m = importlib.import_module(self.package_name)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<frozen importlib._bootstrap>", line 1206, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1178, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1149, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 690, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 940, in exec_module
  File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/seqalign/__init__.py", line 25, in <module>
    from .cmd import (get_alignment_sequence, SeqArg, AlignmentArg, AlignSeqPairArg, SeqRegionArg,
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 318, in <module>
    from chimerax.atomic.seq_support import IdentityDenominator, percent_identity
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/atomic/__init__.py", line 33, in <module>
    from .molobject import Atom, Bond, Chain, CoordSet, Element, Pseudobond, Residue, Sequence, \
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 28, in <module>
    from .molc import CFunctions, string, cptr, pyobject, set_c_pointer, pointer, size_t
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 30, in <module>
    import ctypes
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/ctypes/__init__.py", line 8, in <module>
    from _ctypes import Union, Structure, Array
ImportError: libffi.so.6: cannot open shared object file: No such file or directory

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 386, in init_manager
    api = self._get_api(session.logger)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 520, in _get_api
    m = self.get_module()
        ^^^^^^^^^^^^^^^^^
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 503, in get_module
    raise ToolshedError("Error importing bundle %s's module: %s" % (self.name, str(e)))
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-Alignments's module: libffi.so.6: cannot open shared object file: No such file or directory

WARNING: Traceback (most recent call last):
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 501, in get_module
    m = importlib.import_module(self.package_name)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<frozen importlib._bootstrap>", line 1206, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1178, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1149, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 690, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 940, in exec_module
  File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/build_structure/__init__.py", line 14, in <module>
    from .mod import modify_atom, cn_peptide_bond
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/build_structure/mod.py", line 14, in <module>
    from chimerax.atomic import Element
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/atomic/__init__.py", line 33, in <module>
    from .molobject import Atom, Bond, Chain, CoordSet, Element, Pseudobond, Residue, Sequence, \
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 28, in <module>
    from .molc import CFunctions, string, cptr, pyobject, set_c_pointer, pointer, size_t
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 30, in <module>
    import ctypes
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/ctypes/__init__.py", line 8, in <module>
    from _ctypes import Union, Structure, Array
ImportError: libffi.so.6: cannot open shared object file: No such file or directory

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 375, in initialize
    api = self._get_api(session.logger)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 520, in _get_api
    m = self.get_module()
        ^^^^^^^^^^^^^^^^^
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 503, in get_module
    raise ToolshedError("Error importing bundle %s's module: %s" % (self.name, str(e)))
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-BuildStructure's module: libffi.so.6: cannot open shared object file: No such file or directory

WARNING: Traceback (most recent call last):
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 501, in get_module
    m = importlib.import_module(self.package_name)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<frozen importlib._bootstrap>", line 1206, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1178, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1149, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 690, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 940, in exec_module
  File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/markers/__init__.py", line 78, in <module>
    from .markers import MarkerSet, create_link, selected_markers, selected_links
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/markers/markers.py", line 25, in <module>
    from chimerax.atomic import Structure
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/atomic/__init__.py", line 33, in <module>
    from .molobject import Atom, Bond, Chain, CoordSet, Element, Pseudobond, Residue, Sequence, \
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 28, in <module>
    from .molc import CFunctions, string, cptr, pyobject, set_c_pointer, pointer, size_t
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 30, in <module>
    import ctypes
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/ctypes/__init__.py", line 8, in <module>
    from _ctypes import Union, Structure, Array
ImportError: libffi.so.6: cannot open shared object file: No such file or directory

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 375, in initialize
    api = self._get_api(session.logger)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 520, in _get_api
    m = self.get_module()
        ^^^^^^^^^^^^^^^^^
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 503, in get_module
    raise ToolshedError("Error importing bundle %s's module: %s" % (self.name, str(e)))
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-Markers's module: libffi.so.6: cannot open shared object file: No such file or directory

WARNING: Traceback (most recent call last):
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 501, in get_module
    m = importlib.import_module(self.package_name)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<frozen importlib._bootstrap>", line 1206, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1178, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1149, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 690, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 940, in exec_module
  File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/chem_group/__init__.py", line 25, in <module>
    from .chem_group import find_group
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/chem_group/chem_group.py", line 29, in <module>
    from chimerax.atomic.idatm import type_info, tetrahedral, planar, linear, single
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/atomic/__init__.py", line 33, in <module>
    from .molobject import Atom, Bond, Chain, CoordSet, Element, Pseudobond, Residue, Sequence, \
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 28, in <module>
    from .molc import CFunctions, string, cptr, pyobject, set_c_pointer, pointer, size_t
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 30, in <module>
    import ctypes
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/ctypes/__init__.py", line 8, in <module>
    from _ctypes import Union, Structure, Array
ImportError: libffi.so.6: cannot open shared object file: No such file or directory

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 375, in initialize
    api = self._get_api(session.logger)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 520, in _get_api
    m = self.get_module()
        ^^^^^^^^^^^^^^^^^
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 503, in get_module
    raise ToolshedError("Error importing bundle %s's module: %s" % (self.name, str(e)))
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ChemGroup's module: libffi.so.6: cannot open shared object file: No such file or directory

WARNING: Traceback (most recent call last):
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 501, in get_module
    m = importlib.import_module(self.package_name)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<frozen importlib._bootstrap>", line 1206, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1178, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1149, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 690, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 940, in exec_module
  File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/dist_monitor/__init__.py", line 26, in <module>
    from .cmd import SimpleMeasurable, ComplexMeasurable
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/dist_monitor/cmd.py", line 38, in <module>
    from chimerax.atomic import Atom
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/atomic/__init__.py", line 33, in <module>
    from .molobject import Atom, Bond, Chain, CoordSet, Element, Pseudobond, Residue, Sequence, \
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 28, in <module>
    from .molc import CFunctions, string, cptr, pyobject, set_c_pointer, pointer, size_t
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 30, in <module>
    import ctypes
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/ctypes/__init__.py", line 8, in <module>
    from _ctypes import Union, Structure, Array
ImportError: libffi.so.6: cannot open shared object file: No such file or directory

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 375, in initialize
    api = self._get_api(session.logger)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 520, in _get_api
    m = self.get_module()
        ^^^^^^^^^^^^^^^^^
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 503, in get_module
    raise ToolshedError("Error importing bundle %s's module: %s" % (self.name, str(e)))
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-DistMonitor's module: libffi.so.6: cannot open shared object file: No such file or directory

WARNING: QCoreApplication::postEvent: Unexpected null receiver
NOTE: Unable to import OpenGL.platform.glx.GLXPlatform: libffi.so.6: cannot open shared object file: No such file or directory
Traceback (most recent call last):
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 376, in initialize
    api._api_caller.initialize(api, session, self)
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1294, in initialize
    return cls._get_func(api, "initialize")(session, bi)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/dicom/__init__.py", line 31, in initialize
    from .ui.segmentation_mouse_mode import (
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/dicom/ui/segmentation_mouse_mode.py", line 20, in <module>
    from .segmentations import SegmentationTool
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/dicom/ui/segmentations.py", line 55, in <module>
    from ..ui.orthoplanes import Axis
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/dicom/ui/orthoplanes.py", line 51, in <module>
    from ..graphics import (
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/dicom/graphics/__init__.py", line 1, in <module>
    from .view import OrthoplaneView
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/dicom/graphics/view.py", line 6, in <module>
    from chimerax.graphics import gllist
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/graphics/gllist.py", line 71, in <module>
    wrap_opengl_routines(globals())
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/graphics/gllist.py", line 22, in wrap_opengl_routines
    from OpenGL import GL
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/OpenGL/GL/__init__.py", line 3, in <module>
    from OpenGL import error as _error
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/OpenGL/error.py", line 12, in <module>
    from OpenGL import platform, _configflags
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/OpenGL/platform/__init__.py", line 56, in <module>
    _load()
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/OpenGL/platform/__init__.py", line 50, in _load
    plugin = plugin_class()
             ^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not callable

WARNING: Traceback (most recent call last):
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 501, in get_module
    m = importlib.import_module(self.package_name)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<frozen importlib._bootstrap>", line 1206, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1178, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1149, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 690, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 940, in exec_module
  File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/swap_res/__init__.py", line 25, in <module>
    from .swap_res import swap_aa, get_rotamers
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/swap_res/swap_res.py", line 28, in <module>
    from chimerax.atomic import AtomicStructure
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/atomic/__init__.py", line 33, in <module>
    from .molobject import Atom, Bond, Chain, CoordSet, Element, Pseudobond, Residue, Sequence, \
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 28, in <module>
    from .molc import CFunctions, string, cptr, pyobject, set_c_pointer, pointer, size_t
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 30, in <module>
    import ctypes
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/ctypes/__init__.py", line 8, in <module>
    from _ctypes import Union, Structure, Array
ImportError: libffi.so.6: cannot open shared object file: No such file or directory

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 375, in initialize
    api = self._get_api(session.logger)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 520, in _get_api
    m = self.get_module()
        ^^^^^^^^^^^^^^^^^
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 503, in get_module
    raise ToolshedError("Error importing bundle %s's module: %s" % (self.name, str(e)))
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-SwapRes's module: libffi.so.6: cannot open shared object file: No such file or directory

WARNING: Traceback (most recent call last):
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 501, in get_module
    m = importlib.import_module(self.package_name)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<frozen importlib._bootstrap>", line 1206, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1178, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1149, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 690, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 940, in exec_module
  File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/atomic/__init__.py", line 33, in <module>
    from .molobject import Atom, Bond, Chain, CoordSet, Element, Pseudobond, Residue, Sequence, \
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 28, in <module>
    from .molc import CFunctions, string, cptr, pyobject, set_c_pointer, pointer, size_t
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 30, in <module>
    import ctypes
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/ctypes/__init__.py", line 8, in <module>
    from _ctypes import Union, Structure, Array
ImportError: libffi.so.6: cannot open shared object file: No such file or directory

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 375, in initialize
    api = self._get_api(session.logger)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 520, in _get_api
    m = self.get_module()
        ^^^^^^^^^^^^^^^^^
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 503, in get_module
    raise ToolshedError("Error importing bundle %s's module: %s" % (self.name, str(e)))
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-Atomic's module: libffi.so.6: cannot open shared object file: No such file or directory

ERROR: Bundle 'ChimeraX-Alignments' custom initialization failed
ERROR: Bundle 'ChimeraX-BuildStructure' custom initialization failed
ERROR: Bundle 'ChimeraX-Markers' custom initialization failed
ERROR: Bundle 'ChimeraX-ChemGroup' custom initialization failed
ERROR: Bundle 'ChimeraX-DistMonitor' custom initialization failed
ERROR: Bundle 'ChimeraX-Dicom' custom initialization failed
ERROR: Bundle 'ChimeraX-SwapRes' custom initialization failed
ERROR: Bundle 'ChimeraX-Atomic' custom initialization failed
NOTE: Unable to import OpenGL.platform.glx.GLXPlatform: libffi.so.6: cannot open shared object file: No such file or directory
Traceback (most recent call last):
  File "<frozen runpy>", line 198, in _run_module_as_main
  File "<frozen runpy>", line 88, in _run_code
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-
packages/chimerax/core/__main__.py", line 1069, in <module>
    exit_code = init(sys.argv)
                ^^^^^^^^^^^^^^
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-
packages/chimerax/core/__main__.py", line 722, in init
    sess.ui.build()
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 191, in build
    self.main_window = mw = MainWindow(self, self.session)
                            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 445, in __init__
    self.graphics_window = g = GraphicsWindow(self._stack, ui, stereo)
                               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 36, in __init__
    oc = OpenGLContext(self, ui.primaryScreen(), use_stereo = stereo)
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 60, in __init__
    _initialize_pyopengl() # Set global GL module.
    ^^^^^^^^^^^^^^^^^^^^^^
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 375, in _initialize_pyopengl
    import OpenGL.GL
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-
packages/OpenGL/GL/__init__.py", line 3, in <module>
    from OpenGL import error as _error
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-
packages/OpenGL/error.py", line 12, in <module>
    from OpenGL import platform, _configflags
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-
packages/OpenGL/platform/__init__.py", line 56, in <module>
    _load()
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-
packages/OpenGL/platform/__init__.py", line 50, in _load
    plugin = plugin_class()
             ^^^^^^^^^^^^^^
TypeError: 'NoneType' object is not callable


BUG: TypeError: 'NoneType' object is not callable

File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-
packages/OpenGL/platform/__init__.py", line 50, in _load
plugin = plugin_class()
^^^^^^^^^^^^^^

 _See log for complete Python traceback._


NOTE: Exception ignored in: <function OpenGLContext.__del__ at 0x7f140c464fe0>
Traceback (most recent call last):
  File "/home/bennion1/Downloads/chimerax-1.7/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 85, in __del__
    if not self._deleted:
           ^^^^^^^^^^^^^
AttributeError: 'OpenGLContext' object has no attribute '_deleted'

[cid:53a9550c-38ae-4239-9fd1-3365588775ff][cid:54192077-477e-4f79-af47-9ac7ba06d252][cid:2d1f31c5-8fe5-4b09-94f9-7ae2edbded1b]Biosciences and Biotechnology Division|PLS|Lawrence Livermore National Laboratory|925-422-5722

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comment:1 by Eric Pettersen, 22 months ago

Cc: Tom Goddard added
Component: UnassignedPlatform
Owner: set to Greg Couch
Platform: all
Project: ChimeraX
Status: newassigned

Reported by Brian Bennion

comment:2 by Greg Couch, 22 months ago

Resolution: limitation
Status: assignedclosed

The .tar.gz is not expected to work on Fedora 37, or really any recent version of Linux. The dependencies are frequently too old or missing.

In your case, you can try the RHEL/CentOS 9 rpm, which is based on Fedora 36. Or use the experimental flatpak version of ChimeraX. The plan is to get rid of the .tar.gz download and for users to use the flatpak instead.

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