bundles missing in the Linux build?

[s.dallangelo@…]

The following bug report has been submitted:
Platform:        Linux-4.15.0-96-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 0.94 (2020-04-14)
Description
trying to build a peptide wit build sequence tool(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.94.dev202004140658 (2020-04-14)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show "Build Structure"

No rotamer libraries installed  
No rotamer libraries installed  
No rotamer libraries installed  
No rotamer libraries installed  

> help help:quickstart

> toolshed show Rotamers

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 621, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1614, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/swap_res/__init__.py", line 37, in start_tool  
return prep_rotamers_dialog(session, tool_name)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/swap_res/tool.py", line 22, in prep_rotamers_dialog  
_prd = PrepRotamersDialog(session, rotamers_tool_name)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/swap_res/tool.py", line 44, in __init__  
self._lib_change_cb)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/options/options.py", line 58, in __init__  
self._make_widget(**kw)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/rotamers/manager.py", line 82, in _make_widget  
callback=self.make_callback)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/rotamers/manager.py", line 67, in library_name_menu  
lib_name = self.default_command_library_name  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/rotamers/manager.py", line 108, in
default_command_library_name  
raise LimitationError("No rotamer libraries installed")  
chimerax.core.errors.LimitationError: No rotamer libraries installed  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1375, in <lambda>  
run(ses, "toolshed show %s" % StringArg.unparse(tool_name)))  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/toolshed.py", line 339, in toolshed_show  
bi.start_tool(session, name)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 627, 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 Rotamers in
bundle ChimeraX-SwapRes:  
No rotamer libraries installed  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Rotamers in
bundle ChimeraX-SwapRes:  
No rotamer libraries installed  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 627, 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 (Core Profile) Mesa 19.2.8
OpenGL renderer: llvmpipe (LLVM 9.0, 256 bits)
OpenGL vendor: VMware, Inc.
Manufacturer: Hewlett-Packard
Model: HP Z440 Workstation
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
CPU: 8 Intel(R) Xeon(R) CPU E5-1630 v4 @ 3.70GHz
Cache Size: 10240 KB
Graphics:
	02:00.0 VGA compatible controller [0300]: NVIDIA Corporation GM107GL [Quadro K620] [10de:13bb] (rev a2)
	Subsystem: Hewlett-Packard Company GM107GL [Quadro K620] [103c:1098]
	Kernel driver in use: nvidia

[Eric Pettersen]

Greg,

This error implies that the Dunbrack, Dynameomics, and Richardson bundles (all under bundles/rotamer_libs in the source) didn't get installed on Linux somehow? I do not get this error on Mac (I do get a later error, which I have pushed a fix for). Can you download a Linux daily build and see if chimerax.atomic.rotamers.libs.dunbrack exists?

--Eric

Reported by Sergio Dall'Angelo

[Eric Pettersen]

Reporter address bouncing.

[Greg Couch]

In  meeting, will look later.  The only case were the files would be 
missing that I can quickly think of is if the files are not part of the 
bundle's wheel.

[Greg Couch]

Confirmed that there are no chimerax.atomic.rotamers.libs in the Linux daily build. It was due to a bug in the build process and has been fixed.

For developers:

It is because the rotamer_libs Makefile's sync target was not SUBDIRS aware, so the wheels were not being saved. The segger bundle has a similar problem. I've fixed both of them. This bug would have prevented the bundles from being in the toolshed.