Opened 2 years ago
Closed 2 years ago
#10457 closed defect (limitation)
tgz chimeraX download does not install on fedora core 37
| Reported by: | 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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Attachments (3)
Change History (5)
by , 2 years ago
| Attachment: | Outlook-bdyggrlc.png added |
|---|
comment:1 by , 2 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Platform |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
Reported by Brian Bennion
comment:2 by , 2 years ago
| Resolution: | → limitation |
|---|---|
| Status: | assigned → closed |
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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