[chimerax-users] ProblemI am attempting he installation of ChmimeraX Installing ChimeraX on Debian mv-10

Fri Oct 8 13:37:45 PDT 2021

Indeed, using dpkg instead of apt or apt-get is most likely the reason it did not work. This is because in Debian and its derivatives, dpkg is the low-level program with the only task of installing a given (set of) deb package(s) into the system. But dpkg by itself has no dependency resolution mechanism, which is what apt (or apt-get) is doing (and these, if I understand correctly, internally defer all the installation tasks to dpkg once they are done resolving dependencies).

Guillaume

On 8 Oct 2021, at 22:10, Tom Goddard via ChimeraX-users <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>> wrote:

The ChimeraX download page says to install using

sudo apt-get install ~/Downloads/ucsf-chimerax_1.2.5-1_amd64.deb

So it might be worth trying that instead of what you tried "sudo dpkg -i ucsf-chimerax_1.2.5-1_amd64.deb".

Tom

On Oct 8, 2021, at 12:59 PM, Tom Goddard via ChimeraX-users <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>> wrote:

Hi Stephen,

Ok, sorry I don't use Linux much so I don't know why the package manager won't install those dependencies.  Our Linux expert Greg is back from vacation next Wednesday and would have suggestions I am sure.  But in the meantime the mailing list message I linked to suggested a fix to a reported Qt xcb load problem that involved installing some missing package and you could try what it suggests.  I know Greg strongly discourages using the "generic Linux" ChimeraX distribution because this kind of missing library problem you describe is common since Linux distros vary so much in what system libraries they include.

Tom

On Oct 8, 2021, at 12:50 PM, Stephen P. Molnar via ChimeraX-users <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>> wrote:

That was a quick reply. Many thanks.

However:

comp at AbNormal:~/Downloads/ChimeraX$ sudo dpkg -i ucsf-chimerax_1.2.5-1_amd64.deb
Selecting previously unselected package ucsf-chimerax.
(Reading database ... 509458 files and directories currently installed.)
Preparing to unpack ucsf-chimerax_1.2.5-1_amd64.deb ...
Unpacking ucsf-chimerax (1.2.5-1) ...
dpkg: dependency problems prevent configuration of ucsf-chimerax:
ï¿½ucsf-chimerax depends on libgfortran3; however:
ï¿½ Package libgfortran3 is not installed.
ï¿½ucsf-chimerax depends on libllvm3.8; however:
ï¿½ Package libllvm3.8 is not installed.
ï¿½ucsf-chimerax depends on libssl1.0.0; however:
ï¿½ Package libssl1.0.0 is not installed.

dpkg: error processing package ucsf-chimerax (--install):
ï¿½dependency problems - leaving unconfigured
Processing triggers for man-db (2.8.5-2) ...
Errors were encountered while processing:
ï¿½ucsf-chimerax

On 10/08/2021 03:22 PM, Tom Goddard wrote:
Hi Stephen,

ï¿½ Our linux ChimeraX expert is on vacation but here is an idea. ï¿½The problem is that the Qt window toolkit can't start and that is almost surely a missing system library, probably one that the Qt xcb plugin shared library needs. ï¿½I see a ChimeraX mailing list discussion of this problem here

https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-June/002339.html

Supposedly the ChimeraX 1.2.5-1 builds on the download page solved that issue. ï¿½If you are using the "generic Linux" ChimeraX distribution I'd suggest instead using the Ubuntu 18.04 ChimeraX version which is a .deb file for debian 10 according to the ChimeraX download page. ï¿½The advantage of using the .deb distribution is that it uses the Debian package manager to assure the needed libraries are installed, while the "generic Linux" ChimeraX .tar.gz file tries to include ï¿½the needed libraries but not always successfully since different linux distros include different system libraries.

Tom

On Oct 8, 2021, at 12:04 PM, Stephen P. Molnar via ChimeraX-users <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>> wrote:

I am attempting the installation of ChimeraC-1.2.5(chimerax-1.2.5-rc-2021.05.24) on my up to date Debian v-1064 bit platform. I ï¿½open the tar.gz package without any difficulties, but when I attempt to execute ChmieraX i get the following:

comp at AbNormal:~/Apps/chimerax-1.2.5-rc-2021.05.24/bin$<mailto:comp at AbNormal:~/Apps/chimerax-1.2.5-rc-2021.05.24/bin$> ./ChimeraX
qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, xcb.

Fatal Python error: Aborted

Current thread 0x00007fcb3dafd740 (most recent call first):
ï¿½File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/chimerax/ui/gui.py", line 157 in __init__
ï¿½File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/ChimeraX_main.py", line 577 in init
ï¿½File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/ChimeraX_main.py", line 1015 in <module>
ï¿½File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/runpy.py", line 87 in _run_code
ï¿½File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/runpy.py", line 194 in _run_module_as_main
Aborted
comp at AbNormal:~/Apps/chimerax-1.2.5-rc-2021.05.24/bin$<mailto:comp at AbNormal:~/Apps/chimerax-1.2.5-rc-2021.05.24/bin$>

xcb is installed, but the Debian v-10 default version of python is 3.7. Is this the problem?

Is there a solution? Reinstalling did not fix the problem.

Thanks in advance.

--
Stephen P. Molnar, Ph.D.
www.molecular-modeling.net<http://www.molecular-modeling.net/>
614.312.7528 (c)
Skype: ï¿½smolnar1

_______________________________________________
ChimeraX-users mailing list
ChimeraX-users at cgl.ucsf.edu<mailto:ChimeraX-users at cgl.ucsf.edu>
Manage subscription:
https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

--
Stephen P. Molnar, Ph.D.
www.molecular-modeling.net<http://www.molecular-modeling.net/>
614.312.7528 (c)
Skype:  smolnar1

_______________________________________________
ChimeraX-users mailing list
ChimeraX-users at cgl.ucsf.edu<mailto:ChimeraX-users at cgl.ucsf.edu>
Manage subscription:
https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

_______________________________________________
ChimeraX-users mailing list
ChimeraX-users at cgl.ucsf.edu<mailto:ChimeraX-users at cgl.ucsf.edu>
Manage subscription:
https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

_______________________________________________
ChimeraX-users mailing list
ChimeraX-users at cgl.ucsf.edu<mailto:ChimeraX-users at cgl.ucsf.edu>
Manage subscription:
https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/

E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20211008/e4d06d55/attachment-0001.html>