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#15058 closed defect (worksforme)
Errors upgrading/installing ChimeraX
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Platform | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.4.0-176-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
I cannot insall the ubuntu 20.04 daily build. It seems as if I must have deleted something in the past when the problem has started.
See the the attached reply message I get upon installation.
Thanks for your help.
Boaz
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 3.3.0 NVIDIA 470.239.06
OpenGL renderer: Quadro T2000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=mate
XDG_SESSION_DESKTOP=mate
XDG_CURRENT_DESKTOP=MATE
DISPLAY=:1
Manufacturer: Dell Inc.
Model: Precision 5540
OS: Ubuntu 20.04 Focal Fossa
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 Intel(R) Core(TM) i7-9850H CPU @ 2.60GHz
Cache Size: 12288 KB
Memory:
total used free shared buff/cache available
Mem: 15Gi 1.4Gi 12Gi 53Mi 1.1Gi 13Gi
Swap: 2.0Gi 0B 2.0Gi
Graphics:
00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics 630 (Mobile) [8086:3e9b] (rev 02)
DeviceName: Onboard IGD
Subsystem: Dell UHD Graphics 630 (Mobile) [1028:0906]
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 23.2
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
File attachment: problem_installing_daily_20.04.out
Attachments (1)
Change History (14)
by , 18 months ago
| Attachment: | problem_installing_daily_20.04.out added |
|---|
comment:1 by , 18 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Platform |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Errors upgrading/installing ChimeraX |
Reported by Boaz Shaanan
comment:2 by , 18 months ago
Hi Chimerax friends,
I am not sure whether any solution has been found for my problem in upgrading to a new daily 20.04 Chimerax version. I reported this problem through the bug report system of my working 1.7 version and attached a file with the printout of the failed attempt to upgrade the daily version. I see that a bug ticket has been opened but nothing since then. Please let me know.
Many thanks,
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: bshaanan@bgu.ac.il
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, 29 April 2024 21:23
To: gregc@cgl.ucsf.edu <gregc@cgl.ucsf.edu>; בעז שאנן <bshaanan@bgu.ac.il>
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #15058: Errors upgrading/installing ChimeraX (was: ChimeraX bug report submission)
#15058: Errors upgrading/installing ChimeraX
---------------------------------+------------------------
Reporter: bshaanan@… | Owner: Greg Couch
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Platform | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
---------------------------------+------------------------
Changes (by pett):
* cc: Tom Goddard (added)
* component: Unassigned => Platform
* owner: (none) => Greg Couch
* platform: => all
* project: => ChimeraX
* status: new => assigned
* summary: ChimeraX bug report submission => Errors upgrading/installing
ChimeraX
Comment:
Reported by Boaz Shaanan
--
Ticket URL: <https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%2f%2fwww.rbvi.ucsf.edu%2ftrac%2fChimeraX%2fticket%2f15058%23comment%3a1&umid=77FFF165-1740-5C06-BFC6-86A5DE42B30B&auth=701951cf8dfb7cd99762e0f5be252082d875f1cf-3d401ba2eaa1f6144578e37ddf9c4066e815341e>
ChimeraX <https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%2f%2fwww.rbvi.ucsf.edu%2fchimerax%2f&umid=77FFF165-1740-5C06-BFC6-86A5DE42B30B&auth=701951cf8dfb7cd99762e0f5be252082d875f1cf-8fcb6e8baa11a1e112fb1feca35e4ba9d1b36675>
ChimeraX Issue Tracker
comment:3 by , 18 months ago
| Resolution: | → worksforme |
|---|---|
| Status: | assigned → closed |
Tt looks like the /usr/bin/chimerax-daily symbolic link was removed by hand before the update was done. And that broke the uninstaller. Check what "ls -l /usr/bin/chimerax-daily" gives. If the ucsf-chimerax-daily package is installed (run "dkpg-query --list ucsf-chimerax-daily"), then the ls -l will give:
lrwxrwxrwx 1 root root 46 May 1 08:14 /usr/bin/chimerax-daily -> ../../usr/lib/ucsf-chimerax-daily/bin/ChimeraX
but with a different date. Recreate that link and try again.
comment:4 by , 18 months ago
I should point out that, technically, Ubuntu 20.04 is not supported by the Qt 6.6 toolkit that we using for ChimeraX 1.8 (and the current daily builds). So you should consider upgrading your system. That said, since we're not compiling against Qt, we're just using prebuilt binaries, I don't expect there to be a problem. But I recommend upgrading to Ubuntu 24.04.1 when it comes out in August 2024.
comment:5 by , 18 months ago
OK, but this is weird. Up until now all the daily updates for 20.4 worked fine. So does the 1.7 "official" version. Has anything changed recently? Also, what's the status with regard to 22.04?
Thanks,
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben Gurion University
Beer Sheva, Israel
On May 2, 2024 07:27, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:
#15058: Errors upgrading/installing ChimeraX
---------------------------------+------------------------
Reporter: bshaanan@… | Owner: Greg Couch
Type: defect | Status: closed
Priority: normal | Milestone:
Component: Platform | Version:
Resolution: worksforme | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
---------------------------------+------------------------
Comment (by Greg Couch):
I should point out that, technically, Ubuntu 20.04 is not supported by the
Qt 6.6 toolkit that we using for ChimeraX 1.8 (and the current daily
builds). So you should consider upgrading your system. That said, since
we're not compiling against Qt, we're just using prebuilt binaries, I
don't expect there to be a problem. But I recommend upgrading to Ubuntu
24.04.1 when it comes out in August 2024.
--
Ticket URL: <https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%2f%2fwww.rbvi.ucsf.edu%2ftrac%2fChimeraX%2fticket%2f15058%23comment%3a4&umid=37CA0C24-1771-0306-8B2D-28E9A780FCEB&auth=701951cf8dfb7cd99762e0f5be252082d875f1cf-f7637458d7a95e03974f3a1316697f2b6514e808>
ChimeraX <https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%2f%2fwww.rbvi.ucsf.edu%2fchimerax%2f&umid=37CA0C24-1771-0306-8B2D-28E9A780FCEB&auth=701951cf8dfb7cd99762e0f5be252082d875f1cf-40e9a491d5fac30b326319a254fe107926ae2ab7>
ChimeraX Issue Tracker
comment:6 by , 18 months ago
I expect the updates for 20.4 to work without any problems. But it is officially no longer supported by the Qt Company. See https://doc.qt.io/archives/qt-6.6/supported-platforms.html. And the reason why I expect it to work is that ChimeraX uses the prebuilt binaries from the Qt Company that work on RHEL 8. And RHEL 8 uses GLIBC 2.28, which is older than Ubuntu 20.04's GLIBC 2.31.
comment:7 by , 18 months ago
Dear friends,
I am sorry to bother you again with my problem. Here is what I tried.
1. Following your advice I ran the following steps:
ls -l /usr/bin/chimerax-daily
lrwxrwxrwx 1 root root 46 May 4 20:00 /usr/bin/chimerax-daily -> ../../usr/lib/ucsf-chimerax-daily/bin/ChimeraX
Then dpkg-query gives this:
<SweetB [20:15] ~>dpkg-query --list ucsf-chimerax-daily
Desired=Unknown/Install/Remove/Purge/Hold
| Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
|/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad
||/ Name Version Architecture Description
+++-===================-=====================-============-=================================
ii ucsf-chimerax-daily 2024.03.26ubuntu20.04 amd64 molecular visualization
Suggesting that the installation was incomplete. Indeed Chimerax is missing from
../../usr/lib/ucsf-chimerax-daily/bin , I've no idea why.
<SweetB [20:24] ~>ll ../../usr/lib/ucsf-chimerax-daily/bin/
total 52
drwxr-xr-x 3 root root 4096 Mar 26 19:22 .
drwxr-xr-x 8 root root 4096 Aug 8 2023 ..
drwxr-xr-x 4 root root 4096 Aug 24 2021 amber20
-rwxr-xr-x 1 root root 36600 Mar 26 12:17 python3.11
-rwxr-xr-x 1 root root 1757 Mar 26 11:55 structcomp
1.
I cannot install any new daily now. If I try the daily version of 3 May I get:
sudo apt install ~/Downloads/chimerax-daily.deb
[sudo] password for bshaanan:
Reading package lists... Done
Building dependency tree
Reading state information... Done
Note, selecting 'ucsf-chimerax-daily' instead of '/home/boaz/Downloads/chimerax-daily.deb'
The following packages will be upgraded:
ucsf-chimerax-daily
1 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
Need to get 0 B/400 MB of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 /home/boaz/Downloads/chimerax-daily.deb ucsf-chimerax-daily amd64 2024.05.04ubuntu20.04 [400 MB]
(Reading database ... 422410 files and directories currently installed.)
Preparing to unpack .../Downloads/chimerax-daily.deb ...
Deregister desktop menu and associated mime types
/var/lib/dpkg/info/ucsf-chimerax-daily.prerm: 4: chimerax-daily: not found
dpkg: warning: old ucsf-chimerax-daily package pre-removal script subprocess returned error exit status 127
dpkg: trying script from the new package instead ...
Deregister desktop menu and associated mime types
/var/lib/dpkg/tmp.ci/prerm: 4: chimerax-daily: not found
dpkg: error processing archive /home/boaz/Downloads/chimerax-daily.deb (--unpack):
new ucsf-chimerax-daily package pre-removal script subprocess returned error exit status 127
Errors were encountered while processing:
/home/boaz/Downloads/chimerax-daily.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)
1.
I apologize for the mess I created, but is there an easy way to sort it out? Is it possible to un-install for the current incomplete chimerax-daily and start with a new chimerax-daily, as if it's the first ever daily on this computer?
1.
FYI, Chimerax (daily and 1.7) work fine under 20.04, I have it installed on another (slower) laptop which I don't often use.
Thanks a lot for you help and patience.
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: bshaanan@bgu.ac.il
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Thursday, 2 May 2024 10:18
To: בעז שאנן <bshaanan@bgu.ac.il>; gregc@cgl.ucsf.edu <gregc@cgl.ucsf.edu>
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #15058: Errors upgrading/installing ChimeraX
#15058: Errors upgrading/installing ChimeraX
---------------------------------+------------------------
Reporter: bshaanan@… | Owner: Greg Couch
Type: defect | Status: closed
Priority: normal | Milestone:
Component: Platform | Version:
Resolution: worksforme | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
---------------------------------+------------------------
Comment (by Greg Couch):
I expect the updates for 20.4 to work without any problems. But it is
officially no longer supported by the Qt Company. See
https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%2f%2fdoc.qt.io%2farchives%2fqt%2d6.6%2fsupported%2dplatforms.html&umid=50407E4B-1773-6B06-801F-405C752FEC55&auth=701951cf8dfb7cd99762e0f5be252082d875f1cf-2908f58900c938815590569ea22a0692d7092814. And the
reason why I expect it to work is that ChimeraX uses the prebuilt binaries
from the Qt Company that work on RHEL 8. And RHEL 8 uses GLIBC 2.28,
which is older than Ubuntu 20.04's GLIBC 2.31.
--
Ticket URL: <https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%2f%2fwww.rbvi.ucsf.edu%2ftrac%2fChimeraX%2fticket%2f15058%23comment%3a6&umid=50407E4B-1773-6B06-801F-405C752FEC55&auth=701951cf8dfb7cd99762e0f5be252082d875f1cf-8f4a9d2e7638b3cbf313296a641b819706875192>
ChimeraX <https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%2f%2fwww.rbvi.ucsf.edu%2fchimerax%2f&umid=50407E4B-1773-6B06-801F-405C752FEC55&auth=701951cf8dfb7cd99762e0f5be252082d875f1cf-0e71c094ad723b8184eefd1f40e5312694857705>
ChimeraX Issue Tracker
comment:8 by , 18 months ago
Bizarre, it looks like the uninstall is incomplete. Or perhaps the installation was incomplete. Regardless, you'll need to forcibly remove the ucsf-chimerax-daily rpm.
Use the rpm command, "rpm -e ucsf-chimerax-daily" to remove it. If that doesn't work, do "rpm -e --justdb ucsf-chimerax-daily" to remove the knowledge that ucsf-chimerax-daily was installed. And after that remove the installed files by hand: "rm -rf /usr/bin/chimerax-daily /usr/libexec/UCSF-ChimeraX-daily /usr/share/man/man1/chimerax-daily.1.gz /usr/share/doc/ucsf-chimerax-daily-*"
comment:9 by , 18 months ago
Indeed, bizarre it is. Thanks Greg for the prompt reply. I'll follow your instructions and let you know the outcome.
Cheers
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben Gurion University
Beer Sheva, Israel
On May 7, 2024 21:18, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:
#15058: Errors upgrading/installing ChimeraX
---------------------------------+------------------------
Reporter: bshaanan@… | Owner: Greg Couch
Type: defect | Status: closed
Priority: normal | Milestone:
Component: Platform | Version:
Resolution: worksforme | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
---------------------------------+------------------------
Comment (by Greg Couch):
Bizarre, it looks like the uninstall is incomplete. Or perhaps the
installation was incomplete. Regardless, you'll need to forcibly remove
the ucsf-chimerax-daily rpm.
Use the rpm command, "rpm -e ucsf-chimerax-daily" to remove it. If that
doesn't work, do "rpm -e --justdb ucsf-chimerax-daily" to remove the
knowledge that ucsf-chimerax-daily was installed. And after that remove
the installed files by hand: "rm -rf /usr/bin/chimerax-daily /usr/libexec
/UCSF-ChimeraX-daily /usr/share/man/man1/chimerax-daily.1.gz
/usr/share/doc/ucsf-chimerax-daily-*"
--
Ticket URL: <https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%2f%2fwww.rbvi.ucsf.edu%2ftrac%2fChimeraX%2fticket%2f15058%23comment%3a8&umid=8343ACD3-17E1-3706-B0B4-6C842CE85E69&auth=701951cf8dfb7cd99762e0f5be252082d875f1cf-2eda8ae82a296b6e7fd2f19d933a6c95e701ec4a>
ChimeraX <https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%2f%2fwww.rbvi.ucsf.edu%2fchimerax%2f&umid=8343ACD3-17E1-3706-B0B4-6C842CE85E69&auth=701951cf8dfb7cd99762e0f5be252082d875f1cf-da7af1c3214fd6de9d50cabb28a66fa604b9fef4>
ChimeraX Issue Tracker
comment:10 by , 18 months ago
Oops. The final rm command for RHEL-based systems not Ubuntu. For Ubuntu, it is: "rm -rf /usr/bin/chimerax-daily /usr/lib/ucsf-chimerax-daily /usr/share/doc/ucsf-chimerax-daily /usr/share/man/man1/chimearx-daily.1.gz"
comment:11 by , 18 months ago
Thanks for this correction.
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben Gurion University
Beer Sheva, Israel
On May 8, 2024 01:16, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:
#15058: Errors upgrading/installing ChimeraX
---------------------------------+------------------------
Reporter: bshaanan@… | Owner: Greg Couch
Type: defect | Status: closed
Priority: normal | Milestone:
Component: Platform | Version:
Resolution: worksforme | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
---------------------------------+------------------------
Comment (by Greg Couch):
Oops. The final rm command for RHEL-based systems not Ubuntu. For
Ubuntu, it is: "rm -rf /usr/bin/chimerax-daily /usr/lib/ucsf-chimerax-
daily /usr/share/doc/ucsf-chimerax-daily /usr/share/man/man1/chimearx-
daily.1.gz"
--
Ticket URL: <https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%2f%2fwww.rbvi.ucsf.edu%2ftrac%2fChimeraX%2fticket%2f15058%23comment%3a10&umid=9ADE4318-17E4-8A06-8ACB-740E5FF8EF29&auth=701951cf8dfb7cd99762e0f5be252082d875f1cf-22a9281ca46fbb7ac79f9bace38db64c8e408089>
ChimeraX <https://imsva91-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%2f%2fwww.rbvi.ucsf.edu%2fchimerax%2f&umid=9ADE4318-17E4-8A06-8ACB-740E5FF8EF29&auth=701951cf8dfb7cd99762e0f5be252082d875f1cf-af3a6a323e8ec948d497ab1ce963c254b167b425>
ChimeraX Issue Tracker
comment:12 by , 18 months ago
Hi Greg, Finally, success: I put the problem to rest for a few days and tried again today. After this step: sudo rm /var/lib/dpkg/info/ucsf-chimerax-daily.* the installation of the new daily build worked. Don't ask me why thesed devils were still lurking after the cleaning you suggested. Many thanks for your tremendous help. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan@bgu.ac.il
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