Opened 7 years ago

Closed 6 years ago

#1672 closed defect (fixed)

Library linking failure after ISOLDE install

Reported by: arnaud.basle@… Owned by: Conrad Huang
Priority: normal Milestone:
Component: Tool Shed Version:
Keywords: Cc: Tristan Croll
Blocked By: Blocking:
Notify when closed: Platform: Linux64 (X11)
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-4.15.0-20-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 0.8 (2018-12-17)
Description
It seems ISOLDE install for "just me" as user but then get this error when opening ISOLDE in tools general

Log:
Startup Messages  
---  
note | Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/__init__.py", line 338, in __init__  
self.init_available_from_cache(logger)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/__init__.py", line 445, in  
init_available_from_cache  
abc.load_from_cache()  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/available.py", line 61, in load_from_cache  
b = _build_bundle(d)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/available.py", line 242, in _build_bundle  
keywords = _extract_extra_keywords(keywords)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/installed.py", line 270, in  
_extract_extra_keywords  
all_kwds = [k.strip() for k in kwds.split(',')]  
AttributeError: 'list' object has no attribute 'split'  
  
UCSF ChimeraX version: 0.8 (2018-12-17)  
How to cite UCSF ChimeraX  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/ui/gui.py",
line 706, in _about  
with open(fn) as f:  
FileNotFoundError: [Errno 2] No such file or directory: '/usr/lib/ucsf-
chimerax/lib/python3.6/site-packages/chimerax/ui/about.html'  
  
FileNotFoundError: [Errno 2] No such file or directory: '/usr/lib/ucsf-
chimerax/lib/python3.6/site-packages/chimerax/ui/about.html'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/ui/gui.py",
line 706, in _about  
with open(fn) as f:  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/ui/gui.py",
line 706, in _about  
with open(fn) as f:  
FileNotFoundError: [Errno 2] No such file or directory: '/usr/lib/ucsf-
chimerax/lib/python3.6/site-packages/chimerax/ui/about.html'  
  
FileNotFoundError: [Errno 2] No such file or directory: '/usr/lib/ucsf-
chimerax/lib/python3.6/site-packages/chimerax/ui/about.html'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/ui/gui.py",
line 706, in _about  
with open(fn) as f:  
  
See log for complete Python traceback.  
  
Downloading bundle ChimeraX_ISOLDE-1.0b2-cp36-cp36m-linux_x86_64.whl  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/ui/widgets/htmlview.py", line 386, in download_finished  
session=self.session)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 548, in install_bundle  
results = self._pip_install(bundle, per_user=per_user, reinstall=reinstall)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 845, in _pip_install  
results = self._run_pip(command)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 872, in _run_pip  
raise RuntimeError(s)  
RuntimeError: ERROR:  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/__init__.py", line 338, in __init__  
self.init_available_from_cache(logger)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/__init__.py", line 445, in  
init_available_from_cache  
abc.load_from_cache()  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/available.py", line 61, in load_from_cache  
b = _build_bundle(d)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/available.py", line 242, in _build_bundle  
keywords = _extract_extra_keywords(keywords)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/installed.py", line 270, in  
_extract_extra_keywords  
all_kwds = [k.strip() for k in kwds.split(',')]  
AttributeError: 'list' object has no attribute 'split'  
  
  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing ./Downloads/ChimeraX_ISOLDE-1.0b2-cp36-cp36m-linux_x86_64.whl  
Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=0.7 in
/usr/lib/ucsf-chimerax/lib/python3.6/site-packages (from ChimeraX-
ISOLDE==1.0b2) (1.0)  
Collecting ChimeraX-Clipper>=0.3 (from ChimeraX-ISOLDE==1.0b2)  
Using cached
https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxclipper/releases/0.3.1/ChimeraX_Clipper-0.3.1-cp36-cp36m-linux_x86_64.whl  
Requirement already satisfied, skipping upgrade: ChimeraX-Core==0.8 in
/usr/lib/ucsf-chimerax/lib/python3.6/site-packages (from ChimeraX-
ISOLDE==1.0b2) (0.8)  
Requirement already satisfied, skipping upgrade: ChimeraX-UI>=1.0 in
/usr/lib/ucsf-chimerax/lib/python3.6/site-packages (from ChimeraX-
Atomic>=0.7->ChimeraX-ISOLDE==1.0b2) (1.0)  
Installing collected packages: ChimeraX-Clipper, ChimeraX-ISOLDE  
Could not install packages due to an EnvironmentError: [Errno 13] Permission
denied: '/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/ChimeraX_Clipper-0.3.1.dist-info'  
Consider using the `--user` option or check the permissions.  
  
You are using pip version 18.1, however version 19.0.1 is available.  
You should consider upgrading via the 'pip install --upgrade pip' command.  
  
  
RuntimeError: ERROR:  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/__init__.py", line 338, in __init__  
self.init_available_from_cache(logger)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/__init__.py", line 445, in  
init_available_from_cache  
abc.load_from_cache()  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/available.py", line 61, in load_from_cache  
b = _build_bundle(d)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/available.py", line 242, in _build_bundle  
keywords = _extract_extra_keywords(keywords)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/installed.py", line 270, in  
_extract_extra_keywords  
all_kwds = [k.strip() for k in kwds.split(',')]  
AttributeError: 'list' object has no attribute 'split'  
  
  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing ./Downloads/ChimeraX_ISOLDE-1.0b2-cp36-cp36m-linux_x86_64.whl  
Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=0.7 in
/usr/lib/ucsf-chimerax/lib/python3.6/site-packages (from ChimeraX-
ISOLDE==1.0b2) (1.0)  
Collecting ChimeraX-Clipper>=0.3 (from ChimeraX-ISOLDE==1.0b2)  
Using cached
https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxclipper/releases/0.3.1/ChimeraX_Clipper-0.3.1-cp36-cp36m-linux_x86_64.whl  
Requirement already satisfied, skipping upgrade: ChimeraX-Core==0.8 in
/usr/lib/ucsf-chimerax/lib/python3.6/site-packages (from ChimeraX-
ISOLDE==1.0b2) (0.8)  
Requirement already satisfied, skipping upgrade: ChimeraX-UI>=1.0 in
/usr/lib/ucsf-chimerax/lib/python3.6/site-packages (from ChimeraX-
Atomic>=0.7->ChimeraX-ISOLDE==1.0b2) (1.0)  
Installing collected packages: ChimeraX-Clipper, ChimeraX-ISOLDE  
Could not install packages due to an EnvironmentError: [Errno 13] Permission
denied: '/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/ChimeraX_Clipper-0.3.1.dist-info'  
Consider using the `--user` option or check the permissions.  
  
You are using pip version 18.1, however version 19.0.1 is available.  
You should consider upgrading via the 'pip install --upgrade pip' command.  
  
  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 872, in _run_pip  
raise RuntimeError(s)  
  
See log for complete Python traceback.  
  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 6613, resource id:
11480320, major code: 40 (TranslateCoords), minor code: 0  

Downloading bundle ChimeraX_ISOLDE-1.0b2-cp36-cp36m-linux_x86_64.whl  
Successfully installed ChimeraX-Clipper-0.3.1 ChimeraX-ISOLDE-1.0b2  
Installed ChimeraX-Clipper (0.3.1)  
Installed ChimeraX-ISOLDE (1.0b2)  

'clip' is a prefix of an existing command 'clipper'  

> toolshed show ISOLDE

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/info.py", line 579, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 1188, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "/home/CAMPUS/namlb/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/__init__.py", line 31, in start_tool  
return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/tools.py", line 214, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File "/home/CAMPUS/namlb/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/tool.py", line 159, in __init__  
self.isolde = isolde.Isolde(self)  
File "/home/CAMPUS/namlb/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 315, in __init__  
self._start_gui(gui)  
File "/home/CAMPUS/namlb/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 443, in _start_gui  
self._populate_menus_and_update_params()  
File "/home/CAMPUS/namlb/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 532, in
_populate_menus_and_update_params  
self._update_model_list(None, None, force=True)  
File "/home/CAMPUS/namlb/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/isolde.py", line 919, in _update_model_list  
from .restraints import MDFF_Mgr  
File "/home/CAMPUS/namlb/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/restraints/__init__.py", line 11, in <module>  
from ..molobject import Restraint_Change_Tracker  
File "/home/CAMPUS/namlb/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/molobject.py", line 42, in <module>  
_c_functions = CFunctions(os.path.splitext(libfile)[0])  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/atomic/molc.py", line 23, in __init__  
self._c_lib = ctypes_open(library_path)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/atomic/molc.py", line 261, in ctypes_open  
lib = ctypes.PyDLL(lib_path)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/ctypes/__init__.py", line 348, in
__init__  
self._handle = _dlopen(self._name, mode)  
OSError: /home/CAMPUS/namlb/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/libmolc.so: undefined symbol:
_ZNK10atomstruct7Residue9find_atomERKN6chutil7CStringILi5EILc65ELc116ELc111ELc109ELc32ELc78ELc97ELc109ELc101EEEE  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/ui/gui.py",
line 941, in <lambda>  
run(ses, "toolshed show %s" % quote_if_necessary(tool_name)))  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2587, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/commands/toolshed.py", line 337, in toolshed_show  
bi.start_tool(session, tool_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/info.py", line 585, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
/home/CAMPUS/namlb/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/libmolc.so: undefined symbol:
_ZNK10atomstruct7Residue9find_atomERKN6chutil7CStringILi5EILc65ELc116ELc111ELc109ELc32ELc78ELc97ELc109ELc101EEEE  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in
bundle ChimeraX-ISOLDE:  
/home/CAMPUS/namlb/.local/share/ChimeraX/0.8/site-
packages/chimerax/isolde/libmolc.so: undefined symbol:
_ZNK10atomstruct7Residue9find_atomERKN6chutil7CStringILi5EILc65ELc116ELc111ELc109ELc32ELc78ELc97ELc109ELc101EEEE  
  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/info.py", line 585, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 340.107
OpenGL renderer: Quadro FX 580/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (6)

comment:1 by Tristan Croll, 7 years ago

Cc: Tristan Croll added
Platform: → Linux64 (X11)
Project: → ChimeraX
Summary: ChimeraX bug report submission → Library linking failure after ISOLDE install

I've seen this behaviour a couple of times on some Linux machines: when ChimeraX is run from a symlink, for some reason ToolShed bundles can't find the main ChimeraX library directory. Could you try running ChimeraX directly from its executable (which I think on your machine would be /usr/lib/ucsf-chimerax/bin/ChimeraX) and see if it works that way?

comment:2 by Eric Pettersen, 7 years ago

Component: Unassigned → Tool Shed
Owner: set to Conrad Huang
Status: new → assigned

in reply to:  3 ; comment:3 by arnaud.basle@…, 7 years ago 

Hi,

Yes I think it works when starting directly the executable and choosing 
"just me".

When selecting "all users" it fails with the error below.

RuntimeError: ERROR: Traceback (most recent call last):   File 
"/usr/lib/ucsf-chimerax/lib/python3.6/site- 
packages/chimerax/core/toolshed/__init__.py", line 338, in __init__ 
     self.init_available_from_cache(logger)   File 
"/usr/lib/ucsf-chimerax/lib/python3.6/site- 
packages/chimerax/core/toolshed/__init__.py", line 445, in 
init_available_from_cache     abc.load_from_cache()   File 
"/usr/lib/ucsf-chimerax/lib/python3.6/site- 
packages/chimerax/core/toolshed/available.py", line 61, in 
load_from_cache     b = _build_bundle(d)   File 
"/usr/lib/ucsf-chimerax/lib/python3.6/site- 
packages/chimerax/core/toolshed/available.py", line 242, in 
_build_bundle     keywords = _extract_extra_keywords(keywords)   File 
"/usr/lib/ucsf-chimerax/lib/python3.6/site- 
packages/chimerax/core/toolshed/installed.py", line 270, in 
_extract_extra_keywords     all_kwds = [k.strip() for k in 
kwds.split(',')] AttributeError: 'list' object has no attribute 'split' 
Looking in indexes: https://pypi.org/simple, 
https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing 
/home/CAMPUS/namlb/Downloads/ChimeraX_ISOLDE-1.0b2-cp36-cp36m-linux_x86_64.whl 
Requirement already satisfied, skipping upgrade: ChimeraX-Core==0.8 in 
/usr/lib/ucsf-chimerax/lib/python3.6/site-packages (from 
ChimeraX-ISOLDE==1.0b2) (0.8) Requirement already satisfied, skipping 
upgrade: ChimeraX-Clipper>=0.3 in 
/home/CAMPUS/namlb/.local/share/ChimeraX/0.8/site-packages (from 
ChimeraX-ISOLDE==1.0b2) (0.3.1) Requirement already satisfied, skipping 
upgrade: ChimeraX-Atomic>=0.7 in 
/usr/lib/ucsf-chimerax/lib/python3.6/site-packages (from 
ChimeraX-ISOLDE==1.0b2) (1.0) Requirement already satisfied, skipping 
upgrade: ChimeraX-UI>=1.0 in 
/usr/lib/ucsf-chimerax/lib/python3.6/site-packages (from 
ChimeraX-Atomic>=0.7->ChimeraX-ISOLDE==1.0b2) (1.0) Installing collected 
packages: ChimeraX-ISOLDE Found existing installation: ChimeraX-ISOLDE 
1.0b2 Uninstalling ChimeraX-ISOLDE-1.0b2: Successfully uninstalled 
ChimeraX-ISOLDE-1.0b2 Rolling back uninstall of ChimeraX-ISOLDE Could 
not install packages due to an EnvironmentError: [Errno 13] Permission 
denied: 
'/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/ChimeraX_ISOLDE-1.0b2.dist-info' 
Consider using the `--user` option or check the permissions. You are 
using pip version 18.1, however version 19.0.1 is available. You should 
consider upgrading via the 'pip install --upgrade pip' command. File 
"/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/core/toolshed/__init__.py", 
line 872, in _run_pip raise RuntimeError(s) See log for complete Python 
traceback.

I have tried "sudo ChimeraX" in case I need permissions for all users 
but then ChimeraX does not open at all:

RuntimeError: ERROR: Traceback (most recent call last):   File 
"/usr/lib/ucsf-chimerax/lib/python3.6/site- 
packages/chimerax/core/toolshed/__init__.py", line 338, in __init__ 
     self.init_available_from_cache(logger)   File 
"/usr/lib/ucsf-chimerax/lib/python3.6/site- 
packages/chimerax/core/toolshed/__init__.py", line 445, in 
init_available_from_cache     abc.load_from_cache()   File 
"/usr/lib/ucsf-chimerax/lib/python3.6/site- 
packages/chimerax/core/toolshed/available.py", line 61, in 
load_from_cache     b = _build_bundle(d)   File 
"/usr/lib/ucsf-chimerax/lib/python3.6/site- 
packages/chimerax/core/toolshed/available.py", line 242, in 
_build_bundle     keywords = _extract_extra_keywords(keywords)   File 
"/usr/lib/ucsf-chimerax/lib/python3.6/site- 
packages/chimerax/core/toolshed/installed.py", line 270, in 
_extract_extra_keywords     all_kwds = [k.strip() for k in 
kwds.split(',')] AttributeError: 'list' object has no attribute 'split' 
Looking in indexes: https://pypi.org/simple, 
https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing 
/home/CAMPUS/namlb/Downloads/ChimeraX_ISOLDE-1.0b2-cp36-cp36m-linux_x86_64.whl 
Requirement already satisfied, skipping upgrade: ChimeraX-Core==0.8 in 
/usr/lib/ucsf-chimerax/lib/python3.6/site-packages (from 
ChimeraX-ISOLDE==1.0b2) (0.8) Requirement already satisfied, skipping 
upgrade: ChimeraX-Clipper>=0.3 in 
/home/CAMPUS/namlb/.local/share/ChimeraX/0.8/site-packages (from 
ChimeraX-ISOLDE==1.0b2) (0.3.1) Requirement already satisfied, skipping 
upgrade: ChimeraX-Atomic>=0.7 in 
/usr/lib/ucsf-chimerax/lib/python3.6/site-packages (from 
ChimeraX-ISOLDE==1.0b2) (1.0) Requirement already satisfied, skipping 
upgrade: ChimeraX-UI>=1.0 in 
/usr/lib/ucsf-chimerax/lib/python3.6/site-packages (from 
ChimeraX-Atomic>=0.7->ChimeraX-ISOLDE==1.0b2) (1.0) Installing collected 
packages: ChimeraX-ISOLDE Found existing installation: ChimeraX-ISOLDE 
1.0b2 Uninstalling ChimeraX-ISOLDE-1.0b2: Successfully uninstalled 
ChimeraX-ISOLDE-1.0b2 Rolling back uninstall of ChimeraX-ISOLDE Could 
not install packages due to an EnvironmentError: [Errno 13] Permission 
denied: 
'/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/ChimeraX_ISOLDE-1.0b2.dist-info' 
Consider using the `--user` option or check the permissions. You are 
using pip version 18.1, however version 19.0.1 is available. You should 
consider upgrading via the 'pip install --upgrade pip' command. File 
"/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/core/toolshed/__init__.py", 
line 872, in _run_pip raise RuntimeError(s)

  Cheers,

Arnaud

On 01/02/2019 14:56, ChimeraX wrote:

comment:4 by Tristan Croll, 7 years ago

I think the second traceback you copied in is the wrong one (looks identical to the first?). But it turns out I also get (two slightly different) tracebacks when I try to run the ChimeraX 0.8 or daily build CentOS rpms as root.

ChimeraX 0.8: 

sudo chimerax --nogui

0.00% done: Initializing core
Traceback (most recent call last):  
  File "/opt/UCSF/ChimeraX/lib/python3.6/runpy.py", line 193, in
_run_module_as_main  
    "__main__", mod_spec)  
  File "/opt/UCSF/ChimeraX/lib/python3.6/runpy.py", line 85, in _run_code  
    exec(code, run_globals)  
  File "/opt/UCSF/ChimeraX/lib/python3.6/site-packages/ChimeraX_main.py", line
807, in <module>  
    exit_code = init(sys.argv)  
  File "/opt/UCSF/ChimeraX/lib/python3.6/site-packages/ChimeraX_main.py", line
544, in init  
    check_available=opts.get_available_bundles)  
  File "/opt/UCSF/ChimeraX/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 1283, in init  
    _toolshed = Toolshed(*args, **kw)  
  File "/opt/UCSF/ChimeraX/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 366, in __init__  
    settings.toolshed_last_check = now.isoformat()  
  File "/opt/UCSF/ChimeraX/lib/python3.6/site-
packages/chimerax/core/settings.py", line 190, in __setattr__  
    ConfigFile.__setattr__(self, name, value)  
  File "/opt/UCSF/ChimeraX/lib/python3.6/site-
packages/chimerax/core/configfile.py", line 365, in __setattr__  
    ConfigFile.save(self)  
  File "/opt/UCSF/ChimeraX/lib/python3.6/site-
packages/chimerax/core/configfile.py", line 314, in save  
    with SaveTextFile(self._filename) as f:  
  File "/opt/UCSF/ChimeraX/lib/python3.6/site-
packages/chimerax/core/safesave.py", line 162, in __init__  
    SaveFile.__init__(self, filename, open=open_text, critical=critical)  
  File "/opt/UCSF/ChimeraX/lib/python3.6/site-
packages/chimerax/core/safesave.py", line 69, in __init__  
    raise OSError(errno.ENOTDIR, os.strerror(errno.ENOTDIR), save_dir)  
NotADirectoryError: [Errno 20] Not a directory:
'/non/existent/directory/.config/ChimeraX'  
  

NotADirectoryError: [Errno 20] Not a directory:
'/non/existent/directory/.config/ChimeraX'  
  
File "/opt/UCSF/ChimeraX/lib/python3.6/site-
packages/chimerax/core/safesave.py", line 69, in __init__  
raise OSError(errno.ENOTDIR, os.strerror(errno.ENOTDIR), save_dir)  
  
 _See log for complete Python traceback._  
  

Updating list of available bundles failed: expected str, bytes or os.PathLike object, not NoneType

sudo chimerax-daily --nogui

0.00% done: Initializing core
Traceback (most recent call last):  
  File "/opt/UCSF/ChimeraX-daily/lib/python3.7/runpy.py", line 193, in
_run_module_as_main  
    "__main__", mod_spec)  
  File "/opt/UCSF/ChimeraX-daily/lib/python3.7/runpy.py", line 85, in
_run_code  
    exec(code, run_globals)  
  File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/ChimeraX_main.py", line 807, in <module>  
    exit_code = init(sys.argv)  
  File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/ChimeraX_main.py", line 544, in init  
    check_available=opts.get_available_bundles)  
  File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1364, in init  
    _toolshed = Toolshed(*args, **kw)  
  File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 349, in __init__  
    if not available.has_cache_file(self._cache_dir):  
  File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/available.py", line 81, in has_cache_file  
    return os.path.exists(os.path.join(cache_dir, _CACHE_FILE))  
  File "/bin/../../opt/UCSF/ChimeraX-daily/lib/python3.7/posixpath.py", line
80, in join  
    a = os.fspath(a)  
TypeError: expected str, bytes or os.PathLike object, not NoneType  
  

TypeError: expected str, bytes or os.PathLike object, not NoneType  
  
File "/bin/../../opt/UCSF/ChimeraX-daily/lib/python3.7/posixpath.py", line 80,
in join  
a = os.fspath(a)  
  
 _See log for complete Python traceback._

comment:5 by Tristan Croll, 7 years ago

You can bypass the code causing the error by editing line 120 of /usr/lib/ucsf-chimerax/lib/python3.6/site-packages/ChimeraX_main.py to:

    opts.get_available_bundles = False

That allows me to get a GUI with sudo chimerax, and you should be able to install for everyone from there. Once done, just revert the line to 

    opts.get_available_bundles = True

comment:6 by Greg Couch, 6 years ago

Resolution: → fixed
Status: assigned → closed

Fixed by requiring all Linux binary bundles be built on the same platform, currently CentOS 7.

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