installation issue

[francois.hoh@…]

Hi


I tried on my lab top and same error with or without ./


Building dependency tree... Done
Reading state information... Done
E: Unable to locate package ucsf-chimerax_1.4ubuntu22.04_amd64.deb
E: Couldn't find any package by glob 'ucsf-chimerax_1.4ubuntu22.04_amd64.deb'
E: Couldn't find any package by regex 'ucsf-chimerax_1.4ubuntu22.04_amd64.deb'

in attached , my labtop config

Thank's

Untitled 1.pdf​

[francois.hoh@…]

Added by email2trac

[Greg Couch]

So your error of "E: Unable to locate package ucsf-chimerax_1.4ubuntu22.04_amd64.deb" means that you forgot to use ./ucsf-chimerax_1.4ubuntu22.04_amd64.deb (because it complained about a package name instead of a file name). But the ./ only works if ucsf-chimerax_1.4ubuntu22.04_amd64.deb is in the current directory. Make sure you give the full path to it. The example on the ChimeraX download page says to use "~/Downloads/ucsf-chimerax_1.4ubuntu22.04_amd64.deb" because web browsers normally download files to the ~/Downloads directory.

Here's the beginning what I expect that you would see (except in French instead of English, and your username, not gregc):

$ sudo apt-get install ./usfcsf-chimerax_1.4ubuntu22.04_amd64.deb
[sudo] password for gregc:
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
Note, selecting 'ucsf-chimerax' instead of './ucsf-chimerax_1.4ubuntu22.04_amd64.deb'
Suggested packages:
  opencl-icd
The following NEW packages will be installed:
  ucsf-chimerax
0 upgraded, 1 newly installed, 0 to remove and 14 not upgraded.

And the end there is an information message that can be ignored:

N: Download is performed unsandboxed as root as file '/home/gregc/Downloads/ucsf-chimerax_1.4ubuntu22.04_amd64.deb' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied)

[francois.hoh@…]

As writen in my request:

I tried on my lab top and same error with or without ./


So



________________________________
De : ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Envoyé : mardi 27 septembre 2022 02:15:20
Cc : HOH Francois; gregc@cgl.ucsf.edu
Objet : Re: [ChimeraX] #7679: installation issue

#7679: installation issue
-------------------------------------+------------------------
          Reporter:  francois.hoh@…  |      Owner:  Greg Couch
              Type:  defect          |     Status:  closed
          Priority:  normal          |  Milestone:
         Component:  Platform        |    Version:
        Resolution:  nonchimerax     |   Keywords:
        Blocked By:                  |   Blocking:
Notify when closed:                  |   Platform:  all
           Project:  ChimeraX        |
-------------------------------------+------------------------
Changes (by Greg Couch):

 * status:  assigned => closed
 * resolution:   => nonchimerax


Comment:

 So your error of "E: Unable to locate package ucsf-
 chimerax_1.4ubuntu22.04_amd64.deb" means that you forgot to use ./ucsf-
 chimerax_1.4ubuntu22.04_amd64.deb (because it complained about a package
 name instead of a file name).  But the ./ only works if ucsf-
 chimerax_1.4ubuntu22.04_amd64.deb is in the current directory.  Make sure
 you give the full path to it.  The example on the ChimeraX download page
 says to use "~/Downloads/ucsf-chimerax_1.4ubuntu22.04_amd64.deb" because
 web browsers normally download files to the ~/Downloads directory.

 Here's the beginning what I expect that you would see (except in French
 instead of English, and your username, not gregc):
 {{{
 $ sudo apt-get install ./ucsf-chimerax_1.4ubuntu22.04_amd64.deb
 [sudo] password for gregc:
 Reading package lists... Done
 Building dependency tree... Done
 Reading state information... Done
 Note, selecting 'ucsf-chimerax' instead of './ucsf-
 chimerax_1.4ubuntu22.04_amd64.deb'
 Suggested packages:
   opencl-icd
 The following NEW packages will be installed:
   ucsf-chimerax
 0 upgraded, 1 newly installed, 0 to remove and 14 not upgraded.
 }}}
 And the end there is an information message that can be ignored:
 {{{
 N: Download is performed unsandboxed as root as file
 '/home/gregc/Downloads/ucsf-chimerax_1.4ubuntu22.04_amd64.deb' couldn't be
 accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied)
 }}}

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7679#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Greg Couch]

So you should see a different error messages with "apt-get install ./ucsf-chimerax_1.4ubuntu22.04_amd64.deb".

The next step is for you to show a colleague what you are doing. Or, if that doesn't work, we can have a zoom meeting where you share your screen so I can see exactly how it fails.

Double check that you are in the right directory to use ./. That is

$ ls -l ./ucsf-chimerax_1.4ubuntu22.04_amd64.deb
-rw-r--r--. 1 chimera chimdev 333624574 Jun 10 02:54 ucsf-chimerax_1.4ubuntu22.04_amd64.deb

$ sudo apt-get install ./ucsf-chimerax_1.4ubuntu22.04_amd64.deb

[francois.hoh@…]

Hi


So, the first issue is fixed, but another error :

==

fhoh@fhoh-Precision-Tower-7810:~/PROG$ sudo apt-get install ./ucsf-chimerax_1.4ubuntu22.04_amd64.deb
[sudo] Mot de passe de fhoh :
Désolé, essayez de nouveau.
[sudo] Mot de passe de fhoh :
Lecture des listes de paquets... Fait
Construction de l'arbre des dépendances... Fait
Lecture des informations d'état... Fait
Note : sélection de « ucsf-chimerax » au lieu de « ./ucsf-chimerax_1.4ubuntu22.04_amd64.deb »
ucsf-chimerax est déjà la version la plus récente (1.4ubuntu22.04).
0 mis à jour, 0 nouvellement installés, 0 à enlever et 238 non mis à jour.
1 partiellement installés ou enlevés.
Après cette opération, 0 o d'espace disque supplémentaires seront utilisés.
Souhaitez-vous continuer ? [O/n] o
Paramétrage de ucsf-chimerax-daily (2022.09.23ubuntu22.04) ...
Install desktop menu and associated mime types
Traceback (most recent call last):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/__main__.py", line 723, in init
    run(sess, cmd)
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38, in run
    results = command.run(text, log=log, return_json=return_json)
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897, in run
    result = ci.function(session, **kw_args)
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/linux/cmd.py", line 23, in linux_xdg_install
    install(session, verbose=verbose, system=system)
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/linux/_xdg.py", line 430, in install
    install_icons(session, info, verbose)
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/linux/_xdg.py", line 288, in install_icons
    shutil.copyfile(path, os.path.join(p2, '%s.svg' % info.name))
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/shutil.py", line 264, in copyfile
    with open(src, 'rb') as fsrc:
FileNotFoundError: [Errno 2] Aucun fichier ou dossier de ce type: '/usr/share/ChimeraX-icon.svg'
dpkg: erreur de traitement du paquet ucsf-chimerax-daily (--configure) :
 installed ucsf-chimerax-daily package post-installation script subprocess returned error exit status 70
Des erreurs ont été rencontrées pendant l'exécution :
 ucsf-chimerax-daily
E: Sub-process /usr/bin/dpkg returned an error code (1)

====================================================

Thank's


FH



________________________________
De : ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Envoyé : jeudi 29 septembre 2022 02:29:38
Cc : HOH Francois; gregc@cgl.ucsf.edu
Objet : Re: [ChimeraX] #7679: installation issue

#7679: installation issue
-------------------------------------+------------------------
          Reporter:  francois.hoh@…  |      Owner:  Greg Couch
              Type:  defect          |     Status:  closed
          Priority:  normal          |  Milestone:
         Component:  Platform        |    Version:
        Resolution:  nonchimerax     |   Keywords:
        Blocked By:                  |   Blocking:
Notify when closed:                  |   Platform:  all
           Project:  ChimeraX        |
-------------------------------------+------------------------

Comment (by Greg Couch):

 So you should see a different error messages with "apt-get install ./ucsf-
 chimerax_1.4ubuntu22.04_amd64.deb".

 The next step is for you to show a colleague what you are doing.  Or, if
 that doesn't work, we can have a zoom meeting where you share your screen
 so I can see exactly how it fails.

 Double check that you are in the right directory to use ./.  That is
 {{{
 $ ls -l ./ucsf-chimerax_1.4ubuntu22.04_amd64.deb
 -rw-r--r--. 1 chimera chimdev 333624574 Jun 10 02:54 ucsf-
 chimerax_1.4ubuntu22.04_amd64.deb

 $ sudo apt-get install ./ucsf-chimerax_1.4ubuntu22.04_amd64.deb
 }}}

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7679#comment:4>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker