![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Timeline
Jan 13, 2021:
- 7:09 PM 2021-1-14 edited by
- (diff)
- 7:02 PM Ticket #4136 (Crash in QOpenGLContext.create() on Windows) created by
- […]
- 6:00 PM Ticket #4134 (Modeller job fault / server error) closed by
- duplicate: Duplicate of #4135
- 5:32 PM Ticket #3596 (Implement Coulombic surface coloring) closed by
- fixed: Coulombic now also handles non-standard residues (only on Mac right …
- 3:33 PM Ticket #4135 (Modeller job fault / server error) created by
- […]
- 3:25 PM Ticket #4134 (Modeller job fault / server error) created by
- […]
- 2:23 PM 2021-1-14 edited by
- (diff)
- 1:37 PM 2021-1-14 edited by
- (diff)
- 10:37 AM Ticket #4133 (Graphics is white) closed by
- nonchimerax: Probably your graphics driver is not adequate. The Qt window toolkit …
- 10:34 AM Ticket #4131 (Graphics hardware encountered an error and was reset) closed by
- nonchimerax: Usual Apple Intel graphics driver crash.
- 7:51 AM Ticket #4133 (Graphics is white) created by
- […]
- 1:54 AM Ticket #4132 (Build fails "no such option: --extra-index-url") closed by
- fixed
Jan 12, 2021:
- 9:18 PM Ticket #4132 (Build fails "no such option: --extra-index-url") created by
- Looks like your change to handling of ChimeraX.exe options broke the …
- 9:05 PM Ticket #4130 (Enable offscreen rendering on macOS) closed by
- fixed: Made new prereqs/osmesa that can install libOSmesa for Mac or Linux. …
- 7:42 PM Ticket #4131 (Graphics hardware encountered an error and was reset) created by
- […]
- 4:20 PM Ticket #4130 (Enable offscreen rendering on macOS) created by
- Provide OSMesa in macOS ChimeraX builds for offscreen rendering with …
- 1:48 PM Ticket #4127 (atomic_lib compilation warning "ChimeraX_main.py: option -I not recognized") closed by
- fixed: Changed ChimeraX's sys.argv parsing to recognize all Python options. …
- 11:07 AM Ticket #4129 (macOS notarization fails, lxml wheel uses pre-macOS 10.9) closed by
- fixed: Reverted to pip installing lxml from source code on macOS.
- 11:03 AM Ticket #4129 (macOS notarization fails, lxml wheel uses pre-macOS 10.9) created by
- Job: cac3f9f4-947d-4e93-8b04-bff3827e316f Status: Invalid Summary: …
- 10:47 AM 2021-1-14 created by
- 10:43 AM DeveloperMeetings edited by
- (diff)
- 9:42 AM Ticket #4128 (save JPEG with transparent background: cannot write mode RGBA as JPEG) closed by
- duplicate: Fixed (only) in the daily build.
Jan 11, 2021:
- 5:16 PM Ticket #4128 (save JPEG with transparent background: cannot write mode RGBA as JPEG) created by
- […]
- 3:42 PM Ticket #4127 (atomic_lib compilation warning "ChimeraX_main.py: option -I not recognized") created by
- make install on atomic_lib on macOS 10.15 gives strange warnings about …
- 9:26 AM Ticket #4126 (Execution of 'Structure' object's 'atoms' property raised AttributeError) closed by
- can't reproduce
Jan 9, 2021:
Jan 8, 2021:
- 5:56 PM Ticket #4124 (sequences from structure chains not closed when structure closed) closed by
- fixed: With delattr moved from Cython to Python, needed to also make …
- 5:08 PM Ticket #4123 (sequence selection region stays when structure is closed) closed by
- fixed: Deleting structures with selections in them wasn't firing 'selection …
- 4:34 PM Ticket #4121 (Surface cap not transparent) closed by
- fixed: Fixed. I made coloring the a volume surface or changing its …
- 4:30 PM Ticket #4125 (Command argument quoting not working for single quotes) created by
- […]
- 1:26 PM Ticket #4124 (sequences from structure chains not closed when structure closed) created by
- e.g. open 1www seq chain /Y close Also same problem for …
- 1:25 PM Ticket #4123 (sequence selection region stays when structure is closed) created by
- open uniprot:cah1_human open 1bzm .... select with mouse on structure, …
- 8:51 AM Ticket #4122 (End of simulation: 'PositionRestraintMgr' object has no attribute ...) created by
- […]
- 5:03 AM Ticket #4121 (Surface cap not transparent) created by
- […] Screenshot_1.png
Jan 7, 2021:
- 8:49 PM WikiStart edited by
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- 8:48 PM WikiStart edited by
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- 8:46 PM WikiStart edited by
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- 8:43 PM WikiStart edited by
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- 8:42 PM WikiStart edited by
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- 8:41 PM WikiStart edited by
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- 8:39 PM WikiStart edited by
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- 8:38 PM WikiStart edited by
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- 8:37 PM WikiStart edited by
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- 8:35 PM WikiStart edited by
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- 8:26 PM WikiStart edited by
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- 8:23 PM WikiStart edited by
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- 8:21 PM WikiStart edited by
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- 8:11 PM WikiStart edited by
- (diff)
- 8:05 PM Ticket #4120 (Support PySide2 and PyQt5 with a shim qt module) created by
- At Jan 7, 2021 group meeting we decided to look into using the …
- 7:51 PM Ticket #4119 (Migrate from Qt 5 to Qt 6) created by
- Qt 6.0 was released in December of 2020 although some modules were not …
- 5:27 PM WikiStart edited by
- (diff)
- 5:12 PM Ticket #4095 (VR initialization failure) closed by
- nonchimerax: Gabriel was able to get Oculus Rift working with ChimeraX.
- 5:10 PM Ticket #4118 (Add offscreen rendering support for macOS using XQuartz libOSMesa.dylib) closed by
- wontfix: Unfortunately XQuartz was last updated in 2016 and the …
- 5:07 PM Ticket #4118 (Add offscreen rendering support for macOS using XQuartz libOSMesa.dylib) created by
- Would be nice to have offscreen rendering when using ChimeraX as a …
- 5:01 PM Ticket #4117 (Chimera documentation mistakenly used with ChimeraX) closed by
- not a bug
- 4:53 PM 2021-1-7 edited by
- (diff)
- 2:21 PM 2021-1-7 edited by
- (diff)
- 2:19 PM 2021-1-7 edited by
- (diff)
- 2:16 PM 2021-1-7 edited by
- (diff)
- 1:43 PM Ticket #4117 (Chimera documentation mistakenly used with ChimeraX) created by
- […] Untitled.png
- 10:59 AM Ticket #4116 (prevent duplicate pending bundle submissions) created by
- When a pending bundle submission is made with the same name and …
- 10:59 AM Ticket #4114 (Crash in garbage collection during new-object allocation) closed by
- can't reproduce
- 10:55 AM Ticket #4113 (Toolshed using internal UI API) closed by
- duplicate
- 10:28 AM Ticket #4115 (Crash in garbage collection during new-object allocation) created by
- […]
- 2:03 AM Ticket #4114 (Crash in garbage collection during new-object allocation) created by
- […]
Jan 6, 2021:
- 10:43 PM Ticket #4113 (Toolshed using internal UI API) created by
- […]
- 6:45 PM 2021-1-7 edited by
- (diff)
- 6:43 PM 2021-1-7 edited by
- (diff)
- 5:41 PM 2021-1-7 edited by
- (diff)
- 3:16 PM Ticket #4112 (swapaa may be using probability as dominant criterion) closed by
- not a bug: You have to supply "ignoreOtherModels true" to the swapaa command. …
- 12:59 PM Ticket #4112 (swapaa may be using probability as dominant criterion) created by
- unless I am confused. Here is the example: open 6pt2 del /B,D hide …
- 10:59 AM 2021-1-7 edited by
- (diff)
- 10:56 AM 2021-1-7 created by
- 10:53 AM WikiStart edited by
- (diff)
- 10:52 AM DeveloperMeetings edited by
- (diff)
- 10:51 AM DeveloperMeetings edited by
- (diff)
Jan 5, 2021:
- 9:35 PM Ticket #4111 (Cannot install Maestro file reader from Toolshed on macOS Big Sur) closed by
- fixed: Version 1.8.1 of the maestro bundle, with the fixed dependency, is on …
- 4:54 PM Ticket #4111 (Cannot install Maestro file reader from Toolshed on macOS Big Sur) created by
- […]
- 11:38 AM Ticket #4105 (Amber Solvate not responding) closed by
- nonchimerax: Hi Sam, Since the solvation tool in Amber is designed to be used in …
- 11:25 AM Ticket #4110 (Crash performing @selector(onOkClicked)) created by
- […]
- 11:06 AM Ticket #4108 (Log chain table selection selects nothing) closed by
- fixed: Chain-selection table entry now handles circular permutations.
- 9:13 AM Ticket #4109 (Save dialog: 'SaveModelOptionWidget' object has no attribute '_name') closed by
- duplicate: Hi Ryan, Thanks for reporting this problem. It has been fixed in the …
- 4:30 AM Ticket #4109 (Save dialog: 'SaveModelOptionWidget' object has no attribute '_name') created by
- […]
Jan 4, 2021:
- 6:56 PM Ticket #4108 (Log chain table selection selects nothing) created by
- […]
- 5:12 PM Ticket #4103 ('Ribbon' object has no attribute '_flip_mode') closed by
- fixed: You are using old ChimeraX version 0.93. The current version is …
- 4:48 PM Ticket #4099 (No matching residues in matchmaker sequence alignment) closed by
- fixed: When adding the code to show the RMSD header in the alignment, managed …
- 3:20 PM Ticket #4107 (Toolshed offers to install bundle that requires core<=1.1 in ChimeraX ...) created by
- […]
- 3:11 PM Ticket #4106 (Toolshed install of StrudelScore fails, apparently wheel file has ...) created by
- […]
- 3:07 PM Ticket #4100 (glUniformMatrix4fv: invalid operation) closed by
- can't reproduce: This was an OpenGL graphics error in glUniformMatrix4fv (Invalid …
- 2:20 PM Ticket #4104 (Toolshed error in "already installed" message) closed by
- duplicate: Duplicate of #3795
- 1:37 PM Ticket #4105 (Amber Solvate not responding) created by
- […]
- 1:32 PM Ticket #4104 (Toolshed error in "already installed" message) created by
- […]
- 1:31 PM Ticket #4103 ('Ribbon' object has no attribute '_flip_mode') created by
- […]
- 10:08 AM Ticket #4102 (Excessive logging of already satisfied dependencies) created by
- […]
- 9:31 AM Ticket #3929 (Added NH2 saved after TER) closed by
- not a bug: Presumably the same as #3892; fixed by using struct_edit.add_bond() in …
- 9:30 AM Ticket #3892 (chain merge not reordering residues) closed by
- not a bug: Ah. I have now added text to various doc strings to mention using …
Dec 31, 2020:
- 4:23 PM ChangeLog edited by
- (diff)
- 2:17 PM Ticket #4101 (Problem downloading ChimeraX: "The URL you used has expired") created by
- […]
- 1:25 PM Ticket #4100 (glUniformMatrix4fv: invalid operation) created by
- […]
- 11:57 AM Ticket #4098 (Session file not recognized) closed by
- not a bug: Turns out the extension should have been .cxc
- 4:20 AM Ticket #4099 (No matching residues in matchmaker sequence alignment) created by
- […]
Dec 30, 2020:
- 5:08 PM Ticket #3055 (Add ParmEd to ChimeraX's standard bundles) closed by
- fixed: Installed ParmEd as a prereq. It adds 4.6M to the distribution (on Mac).
- 4:25 PM Ticket #4084 (Wrong numpy parsing in Coulombic C++ module) closed by
- fixed: Thanks, have fixed that up. I found the documentation in the various …
- 9:58 AM Ticket #4098 (Session file not recognized) created by
- […]
- 9:44 AM Ticket #4097 (Error in error message reinstalling bundle) closed by
- duplicate
- 8:22 AM Ticket #4097 (Error in error message reinstalling bundle) created by
- […]
Dec 29, 2020:
Dec 28, 2020:
- 5:34 PM Ticket #4095 (VR initialization failure) created by
- […]
- 4:00 PM Ticket #4091 (Python shell autocomplete: _queue.Empty) closed by
- fixed: ipython implicitly relies on the 'jedi' module for auto-completion, …
- 3:57 PM Ticket #4094 (Python shell autocomplete: _queue.Empty) closed by
- duplicate: Duplicate of #4091; adding Tom to recipient list for that ticket
- 12:58 PM Ticket #4094 (Python shell autocomplete: _queue.Empty) created by
- […]
- 10:24 AM 2020-12-17 edited by
- (diff)
- 9:37 AM Ticket #4092 (Toolshed using internal UI API) closed by
- duplicate
- 9:34 AM Ticket #4090 (Toolshed using internal UI API) closed by
- duplicate
- 9:32 AM Ticket #4089 (Nucleotides: point is None) closed by
- duplicate: I believe this was fixed awhile ago.
- 9:29 AM Ticket #4088 (Crash moving window) closed by
- can't reproduce
- 6:56 AM Ticket #4093 (OpenMM crash uploading OpenCL array) created by
- […]
- 12:06 AM Ticket #4092 (Toolshed using internal UI API) created by
- […]
Dec 27, 2020:
Dec 26, 2020:
- 7:15 PM Ticket #4090 (Toolshed using internal UI API) created by
- […]
- 12:03 PM Ticket #4089 (Nucleotides: point is None) created by
- […]
Dec 23, 2020:
- 8:00 PM Ticket #4088 (Crash moving window) created by
- […]
- 5:45 PM Ticket #4087 (Wide tool can nuke graphics window) created by
- Opening the attached alignment on the right side of the main window …
- 5:20 PM Ticket #4075 (Error saving tool position of stacked tool) closed by
- fixed: Fixed. PyQt returned an int for which side the tool was on, whereas …
- 10:12 AM Ticket #4086 (MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ...) closed by
- fixed: Hi Roberto, Thanks for reporting this problem. It has been fixed in …
- 2:53 AM Ticket #4086 (MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ...) created by
- […]
Dec 22, 2020:
- 10:03 PM Ticket #4085 (Webcam command broken by pyside2) created by
- […]
- 10:00 PM Ticket #4068 (Programmer documentation missing atomic and map_data classes) closed by
- fixed: Fixed. Took out the LD_LIBRARY_PATH fix that allowed Sphinx to import …
- 9:54 PM Ticket #4073 (Need reliable linking for python C++ modules using libarrays) closed by
- fixed: Fixed. Made all 21 C++ Python modules that depend on libarrays call …
- 6:18 PM Ticket #4084 (Wrong numpy parsing in Coulombic C++ module) created by
- The code in Coulombic esp.cpp in potential_at_points() for parsing …
- 4:16 PM Ticket #4080 (drag-select rectangle invisible on gray background) closed by
- fixed: Fixed. Made the selection drag box always green against any …
- 1:01 PM Ticket #4083 (need some way to see association when model color is white) created by
- If the model color is white and I associate it with a sequence, you …
- 11:55 AM Ticket #4082 (over-selection when clicking feature regions in Sequence Viewer) closed by
- fixed: The code to form a "concise residue spec" from a set of residues was wrong.
- 10:21 AM ChangeLog edited by
- (diff)
- 10:01 AM Ticket #4079 (Crash rendering scene graph) closed by
- can't reproduce
- 9:14 AM Ticket #4082 (over-selection when clicking feature regions in Sequence Viewer) created by
- open uniprot:pdcd1_human open 3bp5 sequence associate /A pdcd1_human …
- 8:38 AM Ticket #4081 (Sequence Viewer assoc dialog incorrectly says not associated) created by
- Opening the attached cxc file fetches uniprot sequences and associates …
- 8:30 AM Ticket #4080 (drag-select rectangle invisible on gray background) created by
- The drag-select rectangle shows as a green line against black …
- 12:15 AM Ticket #4079 (Crash rendering scene graph) created by
- […]
Dec 21, 2020:
- 6:34 PM Ticket #4078 (Testing bug reporter improved error message code) closed by
- fixed: Working.
- 6:31 PM Ticket #4076 (Bug report with bug-reporter failure(!)) closed by
- fixed: Fixed. The bug reporter traceback was from submitting the bug with no …
- 6:27 PM Ticket #4078 (Testing bug reporter improved error message code) created by
- […]
- 4:51 PM Ticket #840 (Make 2d labels a model shown in Model Panel) closed by
- fixed: This was implemented long ago.
- 3:29 PM Ticket #4077 (labels with onTop false have silhouette edge rectangles) created by
- with labels onTop false and graphics silhouette true, all of the 3D …
- 1:59 PM ChangeLog edited by
- (diff)
- 1:48 PM Ticket #4074 (ValueError after closing one session and opening another) closed by
- can't reproduce: Unfortunately the problem (Sequence Viewer showing alignment not …
- 10:17 AM Ticket #4072 (ValueError after closing one session and opening another) closed by
- duplicate: Now in ticket #4074
Dec 20, 2020:
Dec 18, 2020:
- 10:01 PM Ticket #4075 (Error saving tool position of stacked tool) created by
- […]
- 7:30 PM Ticket #4074 (ValueError after closing one session and opening another) created by
- […]
- 6:14 PM Ticket #4073 (Need reliable linking for python C++ modules using libarrays) created by
- About 35 modules of ChimeraX have C++ code that uses the arrays module …
- 3:29 PM Ticket #4072 (ValueError after closing one session and opening another) created by
- […]
- 12:54 PM Ticket #4065 (Opening .nc file: No module named 'Scientific') closed by
- fixed: Fixed netcdf map reader. It was never ported from Chimera 1 and was …
- 11:44 AM Ticket #4071 (Sphinx doesn't like indentation of some code comments) created by
- Make install in docs/devel is issuing warnings from Sphinx that …
- 11:31 AM Ticket #4070 (Error in save error message) closed by
- duplicate
- 11:17 AM Ticket #4070 (Error in save error message) created by
- […]
- 10:22 AM Ticket #4069 (Toolshed using internal UI API) closed by
- duplicate
- 1:55 AM Ticket #4069 (Toolshed using internal UI API) created by
- […]
Dec 17, 2020:
- 9:27 PM Ticket #4066 (Meeting name case sensitive) closed by
- fixed: Fixed. New code that checks a joiners initial message to make sure …
- 7:38 PM 2020-12-17 edited by
- (diff)
- 6:40 PM Ticket #4068 (Programmer documentation missing atomic and map_data classes) created by
- Lots of ChimeraX APIs such as Atoms are Atom are not in the …
- 4:18 PM NeteSOW edited by
- (diff)
- 2:21 PM NeteSOW edited by
- (diff)
- 12:15 PM Ticket #3716 (Error within error message) closed by
- duplicate: Duplicate of #3896.
- 12:14 PM Ticket #3874 (Error in error message reinstalling bundle) closed by
- duplicate: Duplicate of #3896
- 11:18 AM 2020-12-17 edited by
- (diff)
- 11:18 AM 2020-12-17 edited by
- (diff)
- 11:09 AM Ticket #4067 (ChimeraX distribution is too big, over 1 Gbyte uncompressed) created by
- We need to look into trimming ChimeraX bloat. It is absolutely …
- 9:43 AM Ticket #4066 (Meeting name case sensitive) created by
- […]
- 9:26 AM Ticket #4064 (Opening .nc file: No module named 'Scientific') closed by
- duplicate: Duplicate of #4065
- 9:18 AM 2020-12-17 edited by
- (diff)
- 2:29 AM Ticket #4065 (Opening .nc file: No module named 'Scientific') created by
- […]
- 2:24 AM Ticket #4064 (Opening .nc file: No module named 'Scientific') created by
- […]
Dec 16, 2020:
- 11:26 AM Ticket #4060 (VR meeting: LZ4F_decompress failed with code: ERROR_frameSize_wrong) closed by
- can't reproduce: I think we can only wait and see if this error occurs again. Phil, …
- 11:20 AM Ticket #4062 (Toolshed using internal UI API) closed by
- duplicate: Fixed in daily build. Duplicate of #3905.
- 11:18 AM Ticket #4061 (Coulombic: local variable 'cmap' referenced before assignment) closed by
- fixed
- 10:49 AM Ticket #4063 (Selection: Attempt to call an undefined function glBlitFramebuffer) closed by
- can't reproduce: I don't think this error message about not finding the standard OpenGL …
- 10:40 AM Ticket #4059 (Crash popping up menu, two screens, macOS) closed by
- duplicate: Duplicate. Supposedly fixed in Qt 5.15.2 which we updated to two days …
- 9:53 AM Ticket #4063 (Selection: Attempt to call an undefined function glBlitFramebuffer) created by
- […] 5F19_-_WT_-_minimized_-_All.pdb
- 9:38 AM Ticket #4057 (Toolshed using internal UI API) closed by
- duplicate
- 9:00 AM Ticket #4062 (Toolshed using internal UI API) created by
- […]
- 7:04 AM Ticket #4061 (Coulombic: local variable 'cmap' referenced before assignment) created by
- […]
- 6:23 AM Ticket #4060 (VR meeting: LZ4F_decompress failed with code: ERROR_frameSize_wrong) created by
- […]
Dec 15, 2020:
- 10:26 PM Ticket #4059 (Crash popping up menu, two screens, macOS) created by
- […]
- 6:53 PM Ticket #4058 (Volume Viewer: RuntimeWarning: overflow encountered in log) closed by
- fixed: Fixed. I changed the volume viewer code to use float64 for counts …
- 5:41 PM Ticket #4058 (Volume Viewer: RuntimeWarning: overflow encountered in log) created by
- […]
- 4:36 PM Ticket #4057 (Toolshed using internal UI API) created by
- […]
- 3:40 PM Ticket #3974 (Something broke in the PBD look up) closed by
- can't reproduce: Are you certain that there isn't some other output file from Robetta …
- 12:47 PM 2020-12-17 edited by
- (diff)
- 10:15 AM 2020-12-17 created by
- 10:11 AM DeveloperMeetings edited by
- (diff)
- 9:24 AM Ticket #4056 (Toolshed internal UI API) closed by
- duplicate: Already fixed I believe.
- 8:06 AM Ticket #4056 (Toolshed internal UI API) created by
- […]
Dec 14, 2020:
- 4:32 PM Ticket #3853 (Bug in chimeraX 1.1 version) closed by
- can't reproduce: No response from request for more information.
- 3:06 PM Ticket #4055 (Problem with open-command providers after bundle reinstall) created by
- […]
- 3:00 PM Ticket #4010 (Adding second residue to Chain makes new Chain) closed by
- fixed: Apparently already fixed in the daily build. However, the daily build …
- 1:47 PM Ticket #4054 (Cannot make a tool undockable) closed by
- fixed: Fixed. Bug introduced when converting PyQt5 to PySide2. Dockable and …
- 1:26 PM Ticket #4052 (Crash destroying/disconnecting screen) closed by
- duplicate: Crash when second screen disconnected. I guess ChimeraX was on an …
- 1:22 PM Ticket #4050 (Crash changing screens) closed by
- duplicate: Duplicate of #3682. Fixed in daily builds.
- 12:46 PM Ticket #4054 (Cannot make a tool undockable) created by
- […]
- 12:02 PM Ticket #3383 (Redirect Python logging to the ChimeraX log) closed by
- fixed: Removed the explicit (and less flexible) support for Python logging …
- 11:36 AM Ticket #4049 (Crash posting popup menu on dual monitor) closed by
- can't reproduce
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