id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1672 Library linking failure after ISOLDE install arnaud.basle@… Conrad Huang "{{{ 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 from ..molobject import Restraint_Change_Tracker File ""/home/CAMPUS/namlb/.local/share/ChimeraX/0.8/site- packages/chimerax/isolde/molobject.py"", line 42, in _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 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 }}} " defect closed normal Tool Shed fixed Tristan Croll Linux64 (X11) ChimeraX