Installation problems on Debian "Bullseye"

[kostrewa@…]

Dear ChimeraX developers,

I am responsible for Linux software at the Gene Center of the University 
of Munich.

I am trying to install the production release version 1.2.5-1 of 
ChimeraX on a fresh Debian "Bullseye". Unfortunately, neither the 
generic version, nor installation of any of the deb packages work.

If you want, I can send you the details for all versions that I've 
tried. However, I thought, I rather give you the details for the Ubuntu 
20.04 version, which should be closest to Debian "Bullseye".

Trying to install the downloaded package as root results in the 
following error message:

# apt install ./ucsf-chimerax_1.2.5-1_amd64.deb
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
Note, selecting 'ucsf-chimerax' instead of 
'./ucsf-chimerax_1.2.5-1_amd64.deb'
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
  ucsf-chimerax : Depends: libllvm10 but it is not installable
E: Unable to correct problems, you have held broken packages.

Debian "Bullseye" unfortunately has libllvm versions 9 and 11 in its 
repository, but not version 10:

# apt search --names-only libllvm
Sorting... Done
Full Text Search... Done

<snip>

libllvm11/stable,now 1:11.0.1-2 amd64 [installed,automatic]
   Modular compiler and toolchain technologies, runtime library

libllvm9/stable,now 1:9.0.1-16.1 amd64 [installed,automatic]
   Modular compiler and toolchain technologies, runtime library

</snip>

If you need more information, I would be happy to send it to you!

Best regards,

Dirk Kostrewa.

-- 

*******************************************************
Dirk Kostrewa
Gene Center Munich
Department of Biochemistry, AG Hopfner
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:    +49-89-2180-76998
E-mail: kostrewa@genzentrum.lmu.de
         dirk.kostrewa@lmu.de
WWW:    www.genzentrum.lmu.de
*******************************************************Dea

[pett]

Reported by Dirk Kostrewa

[Greg Couch]

Unfortunately, we have currently limited our Linux support to Ubuntu LTS releases and RHEL/CentOS. That said, if you can get ChimeraX to install without the broken dependency on libllvm10, the only feature you'll lose is the offscreen rendering support (chimerax --offscreen). So an untested way of installing the ucsf-chimerax package would be to use dpkg directly with "dpkg -i --ignore-depends=libllvm10 ucsf-chimerax....". That won't automatically install the dependencies, so you'll need to install those separately. You can see all of dependencies by looking at the Depends: line in the output from "dpkg -I ucsf-chimera....".

[kostrewa@…]

Dear Greg Couch,

this is great! There were only a handful of dependencies missing, and 
ChimeraX runs fine without libllvm10.

Many thanks!

Best regards,

Dirk Kostrewa.

On 10/19/21 7:47 AM, ChimeraX wrote:

[kostrewa@…]

Dear ChimeraX developers,


unfortunately, installing ChimeraX with "dpkg -i --ignore-depends=libllvm10 ./ucsf-chimerax_1.2.5-1_amd64.deb" leads to a broken package system on Debian "Bullseye", which only becomes visible the next time an installation or upgrade is tried:



# apt -y upgrade
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
You might want to run 'apt --fix-broken install' to correct these.
The following packages have unmet dependencies:
 ucsf-chimerax : Depends: libllvm10 but it is not installable
E: Unmet dependencies. Try 'apt --fix-broken install' with no packages (or specify a solution).


The proposed command "apt --fix-broken install' just removes ucsf-chimerax, again.


I know of other structural biology sites where Debian is used for running Linux in a productive manner. It would be great if you could also provide a Debian package of your great ChimeraX, or if change the libllvm dependency to either libllvm9 or libllvm11, both of which are available in the Debian repositories (but not libllvm10 for reasons unknown to me).


Best regards,


Dirk Kostrewa.

--

*******************************************************
Dirk Kostrewa
Gene Center Munich
Department of Biochemistry, AG Hopfner
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:    +49-89-2180-76998
E-mail: kostrewa@genzentrum.lmu.de
        dirk.kostrewa@lmu.de
WWW:    www.genzentrum.lmu.de
        strubio.userweb.mwn.de
*******************************************************

________________________________
Von: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Gesendet: Dienstag, 19. Oktober 2021 09:35
An: gregc@cgl.ucsf.edu; Kostrewa, Dirk
Cc: chimera-programmers@cgl.ucsf.edu
Betreff: Re: [ChimeraX] #5422: Installation problems on Debian "Bullseye"

#5422: Installation problems on Debian "Bullseye"
---------------------------------+------------------------
          Reporter:  kostrewa@…  |      Owner:  Greg Couch
              Type:  defect      |     Status:  closed
          Priority:  normal      |  Milestone:
         Component:  Platform    |    Version:
        Resolution:  limitation  |   Keywords:
        Blocked By:              |   Blocking:
Notify when closed:              |   Platform:  all
           Project:  ChimeraX    |
---------------------------------+------------------------

Comment (by kostrewa@…):

 {{{
 Dear Greg Couch,

 this is great! There were only a handful of dependencies missing, and
 ChimeraX runs fine without libllvm10.

 Many thanks!

 Best regards,

 Dirk Kostrewa.

 On 10/19/21 7:47 AM, ChimeraX wrote:
 }}}

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5422#comment:3>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Greg Couch]

For Debian 11, you might be able to use the llbllvm10 package from the 
Ubuntu repository.  See https://packages.ubuntu.com/focal/libllvm10.  An 
alternative to installing the ChimeraX package would be to extract the 
files from package and put those somewhere.  The usr/lib/ucsf-chimerax 
directory can be put anywere.  Its bin directory should not be put on 
your path, instead you should make a symbolic link to 
usr/lib/ucsf-chimerax/bin/ChimeraX.


Our long term plan is to make a flatpak for ChimeraX.  And then perhaps 
we can have just one Linux distribution, or just a couple.


     -- Greg


On 10/21/2021 6:12 AM, Kostrewa, Dirk wrote: