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Opened 6 years ago
Closed 6 years ago
#2375 closed defect (nonchimerax)
Shell tab-completion attempts import of non-Python libs
| Reported by: | Tristan Croll | Owned by: | Eric Pettersen |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | General Controls | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-3.10.0-957.12.2.el7.x86_64-x86_64-with-centos-7.6.1810-Core
ChimeraX Version: 0.91 (2019-08-27)
Description
A bit weird... tab-completing "from chimerax.clipper." in the shell seems to have led to it trying to import all the non-python compiled libraries in the Clipper directory (lib_symmetry, libccp4, libclipper etc. are all C++-only libraries).
Log:
UCSF ChimeraX version: 0.91 (2019-08-27)
© 2016-2019 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 6cdx structureFactors true
Summary of feedback from opening 6cdx fetched from pdb
---
notes | Fetching compressed mmCIF 6cdx from
http://files.rcsb.org/download/6cdx.cif
Fetching CCD 4LT from http://ligand-expo.rcsb.org/reports/4/4LT/4LT.cif
Fetching compressed 6cdx structure factors from
http://files.rcsb.org/download/6cdx-sf.cif
Resolution: 1.000002419435916
6cdx title:
High-resolution crystal structure of fluoropropylated cystine knot, binding to
alpha-5 beta-6 integrin [more info...]
Chain information for 6cdx
---
Chain | Description
1.3/A 1.3/B | cystine knot (fluoropropylated)
Non-standard residues in 6cdx #1.3
---
4LT — (2R)-2-fluoropropanoic acid
6cdx mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> toolshed show Shell
/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/IPython/core/history.py:226: UserWarning: IPython History requires
SQLite, your history will not be saved
warn("IPython History requires SQLite, your history will not be saved")
Module chimerax.clipper.lib_symmetry not importable in path
['/run/media/tic20/storage/structure_dump/3io0',
'/home/tic20/.local/share/ChimeraX/0.91/site-packages', '/opt/UCSF/ChimeraX-
daily/lib/python37.zip', '/opt/UCSF/ChimeraX-daily/lib/python3.7',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/lib-dynload', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages/PyOpenGL-3.1.3b2-py3.7.egg',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/PyOpenGL_accelerate-3.1.3b1-py3.7-linux-x86_64.egg',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/tables-3.4.4-py3.7-linux-x86_64.egg', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages/numexpr-2.7.0-py3.7-linux-x86_64.egg',
'/home/tic20/chimerax_start', '/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/IPython/extensions'].
Module chimerax.clipper.libccp4 not importable in path
['/run/media/tic20/storage/structure_dump/3io0',
'/home/tic20/.local/share/ChimeraX/0.91/site-packages', '/opt/UCSF/ChimeraX-
daily/lib/python37.zip', '/opt/UCSF/ChimeraX-daily/lib/python3.7',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/lib-dynload', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages/PyOpenGL-3.1.3b2-py3.7.egg',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/PyOpenGL_accelerate-3.1.3b1-py3.7-linux-x86_64.egg',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/tables-3.4.4-py3.7-linux-x86_64.egg', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages/numexpr-2.7.0-py3.7-linux-x86_64.egg',
'/home/tic20/chimerax_start', '/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/IPython/extensions'].
Module chimerax.clipper.libclipper not importable in path
['/run/media/tic20/storage/structure_dump/3io0',
'/home/tic20/.local/share/ChimeraX/0.91/site-packages', '/opt/UCSF/ChimeraX-
daily/lib/python37.zip', '/opt/UCSF/ChimeraX-daily/lib/python3.7',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/lib-dynload', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages/PyOpenGL-3.1.3b2-py3.7.egg',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/PyOpenGL_accelerate-3.1.3b1-py3.7-linux-x86_64.egg',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/tables-3.4.4-py3.7-linux-x86_64.egg', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages/numexpr-2.7.0-py3.7-linux-x86_64.egg',
'/home/tic20/chimerax_start', '/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/IPython/extensions'].
Module chimerax.clipper.libclipper_cx not importable in path
['/run/media/tic20/storage/structure_dump/3io0',
'/home/tic20/.local/share/ChimeraX/0.91/site-packages', '/opt/UCSF/ChimeraX-
daily/lib/python37.zip', '/opt/UCSF/ChimeraX-daily/lib/python3.7',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/lib-dynload', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages/PyOpenGL-3.1.3b2-py3.7.egg',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/PyOpenGL_accelerate-3.1.3b1-py3.7-linux-x86_64.egg',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/tables-3.4.4-py3.7-linux-x86_64.egg', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages/numexpr-2.7.0-py3.7-linux-x86_64.egg',
'/home/tic20/chimerax_start', '/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/IPython/extensions'].
Module chimerax.clipper.libfftw2xc not importable in path
['/run/media/tic20/storage/structure_dump/3io0',
'/home/tic20/.local/share/ChimeraX/0.91/site-packages', '/opt/UCSF/ChimeraX-
daily/lib/python37.zip', '/opt/UCSF/ChimeraX-daily/lib/python3.7',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/lib-dynload', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages/PyOpenGL-3.1.3b2-py3.7.egg',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/PyOpenGL_accelerate-3.1.3b1-py3.7-linux-x86_64.egg',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/tables-3.4.4-py3.7-linux-x86_64.egg', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages/numexpr-2.7.0-py3.7-linux-x86_64.egg',
'/home/tic20/chimerax_start', '/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/IPython/extensions'].
Module chimerax.clipper.libfftw_mkl_core not importable in path
['/run/media/tic20/storage/structure_dump/3io0',
'/home/tic20/.local/share/ChimeraX/0.91/site-packages', '/opt/UCSF/ChimeraX-
daily/lib/python37.zip', '/opt/UCSF/ChimeraX-daily/lib/python3.7',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/lib-dynload', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages/PyOpenGL-3.1.3b2-py3.7.egg',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/PyOpenGL_accelerate-3.1.3b1-py3.7-linux-x86_64.egg',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/tables-3.4.4-py3.7-linux-x86_64.egg', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages/numexpr-2.7.0-py3.7-linux-x86_64.egg',
'/home/tic20/chimerax_start', '/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/IPython/extensions'].
Module chimerax.clipper.libmmdb2 not importable in path
['/run/media/tic20/storage/structure_dump/3io0',
'/home/tic20/.local/share/ChimeraX/0.91/site-packages', '/opt/UCSF/ChimeraX-
daily/lib/python37.zip', '/opt/UCSF/ChimeraX-daily/lib/python3.7',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/lib-dynload', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages/PyOpenGL-3.1.3b2-py3.7.egg',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/PyOpenGL_accelerate-3.1.3b1-py3.7-linux-x86_64.egg',
'/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/tables-3.4.4-py3.7-linux-x86_64.egg', '/opt/UCSF/ChimeraX-
daily/lib/python3.7/site-packages/numexpr-2.7.0-py3.7-linux-x86_64.egg',
'/home/tic20/chimerax_start', '/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/IPython/extensions'].
OpenGL version: 3.3.0 NVIDIA 415.27
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Change History (5)
comment:1 by , 6 years ago
| Component: | Unassigned → General Controls |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Shell tab-completion attempts import of non-Python libs |
comment:2 by , 6 years ago
| Status: | accepted → feedback |
|---|
follow-up: 3 comment:3 by , 6 years ago
Not really... I guess I could see about moving them into a dedicated directory off the Python search path. I’ve just never seen this message printed to the log before.
comment:4 by , 6 years ago
I just saw in the "tables" package where they put the hdf libraries in a ".libs" subdirectory, so the non-Python stuff is not actually on sys.path.
comment:5 by , 6 years ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | feedback → closed |
I don't think there's anything I can do about this.
Note:
See TracTickets
for help on using tickets.
They are libraries with the same extension (.so) as importable Python libraries, in a directory in the Python path. I don't know how the shell would be able to tell they're _not_ Python libs without trying to import them. Do you have some kind of suggestion here?