Unable to Install Chimerax on Ubuntu 24.04 due to Package Dependencies

[minamothersole@…]

Hello,

I am unable to install ChimeraX on my personal Ubuntu 24.04 system due to
package dependencies that are supposedly not installable. Please see
screenshot of my terminal. Is there any work around?

Much appreciated,

Mina

Screenshot from 2024-08-26 13-44-53.png​

[minamothersole@…]

Added by email2trac

[pett]

Reported by Mina Mothersole

[Greg Couch]

Very weird. I was able to install on Ubuntu 24.04 without any problems. We need to figure out why libgdk-pixbuf-2.0-0, libosmesa6, and libxcb-cursor0 won't install.

Please run "sudo apt install libosmesa6" and copy & paste the error. I can't select text from a screenshot.

[minamothersole@…]

Hello,

Please see attached screenshot with error message.

Mina

On Tue, Aug 27, 2024 at 10:37 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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Screenshot from 2024-08-27 14-05-29.png​

[minamothersole@…]

Added by email2trac

[minamothersole@…]

The error message reads:
"E: Unable to locate package libosmesa6"

On Tue, Aug 27, 2024 at 2:06 PM Mina Mothersole <minamothersole@gmail.com>
wrote:

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>> #15824: Unable to Install Chimerax on Ubuntu 24.04 due to Package
>> Dependencies
>> ---------------------------------------+------------------------
>>           Reporter:  minamothersole@…  |      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          |
>> ---------------------------------------+------------------------
>> Comment (by Greg Couch):
>>
>>  Very weird.  I was able to install on Ubuntu 24.04 without any problems.
>>  We need to figure out why libgdk-pixbuf-2.0-0, libosmesa6, and libxcb-
>>  cursor0 won't install.
>>
>>  Please run "sudo apt install libosmesa6" and copy & paste the error.  I
>>  can't select text from a screenshot.
>> --
>> Ticket URL: <
>> https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/15824#comment:2>
>> ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
>> ChimeraX Issue Tracker
>>
>

[Zach Pearson]

Has it been a while since you ran apt update?

[Greg Couch]

Please do not send screenshots. Instead copy and paste the text.

If libosmesa6 can not be found, then there is something seriously wrong with your setup. What is the contents of /etc/apt/sources.list.d/ubuntu.sources?

[minamothersole@…]

I put "sudo -l /etc/apt/sources.list.d/ubuntu.sources"  and the output was
"sudo: /etc/apt/sources.list.d/ubuntu.sources: command not found". And I
sudo apt update every time I open the terminal so it's been updated
recently.

On Tue, Aug 27, 2024 at 2:22 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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[Greg Couch]

Try "sudo cat /etc/apt/sources.list.d/ubuntu.sources"

[Greg Couch]

Might as well confirm which version of Linux you're running. Also include the output of "cat /etc/os-release".

[minamothersole@…]

Types: deb
URIs: http://ca.archive.ubuntu.com/ubuntu/
Suites: noble noble-updates noble-proposed
Components: main universe
Signed-By: /usr/share/keyrings/ubuntu-archive-keyring.gpg
Enabled: no

On Wed, Aug 28, 2024 at 1:03 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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[minamothersole@…]

PRETTY_NAME="Ubuntu 24.04 LTS"
NAME="Ubuntu"
VERSION_ID="24.04"
VERSION="24.04 LTS (Noble Numbat)"
VERSION_CODENAME=noble
ID=ubuntu
ID_LIKE=debian
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="
https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
UBUNTU_CODENAME=noble
LOGO=ubuntu-logo

On Wed, Aug 28, 2024 at 1:06 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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[Greg Couch]

So /etc/os-release matches what I have.

Your /etc/apt/sources.list.d/ubuntu.sources looks like it should work. For comparison, I have more components enabled. If you have Nvidia graphics, you will need the restricted component to install the proprietary driver that ChimeraX needs.

Types: deb
URIs: http://us.archive.ubuntu.com/ubuntu/
Suites: noble noble-updates noble-backports
Components: main restricted universe multiverse
Signed-By: /usr/share/keyrings/ubuntu-archive-keyring.gpg

Types: deb
URIs: http://security.ubuntu.com/ubuntu/
Suites: noble-security
Components: main restricted universe multiverse
Signed-By: /usr/share/keyrings/ubuntu-archive-keyring.gpg

Run the "software-properties-gtk" program to enable additional Ubuntu Software sources. I don't understand now, but it could be a US vs CA difference. If you change the URLs to ​http://us.archive.ubuntu.com/ubuntu instead of ca.archive.ubuntu.com, it might fix things. It should be done autmatically, but you might need to do a "sudo apt update" to update the package metadata. After that the "apt-cache show libosmesa6" should give you details about the libosmesa6 package.

[minamothersole@…]

I'm sorry, how do I change the URL in the terminal? Thank you for your
assistance with this.

On Wed, Aug 28, 2024 at 1:49 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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[Greg Couch]

Use your favorite text editor. For example, I use vim, so I'd "sudo vi /etc/apt/sources.list.d/ubuntu.sources". If you don't know vim, nano is easier, so "sudo nano /etc/apt/sources.list.d/ubuntu.sources".

But before you do that, let's figure out if you have problems contacting the Ubuntu servers. What happens when you do "sudo apt update"? If it succeeds, then "apt-cache show libosmesa6" would tell you about the libosmesa6 package, and that dependency should be resolvable when you install ChimeraX.

[minamothersole@…]

For "sudo apt update": "All packages are up to date."
For "apt-cache show libosmesa6": "N: Unable to locate package libosmesa6 E:
No packages found"

I have changed the URIs to the US version. I tried repeating the previous
steps but it still came up with the same error message of "No packages
found" for libosmesa6.

On Thu, Aug 29, 2024 at 2:30 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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