Unable to install chimerax on ubuntu 21.04

[osmelfleitas83@…]

Hello

I am trying to install chimerax on ubuntu 21.04 but I am getting this
return


Reading package lists... Done
Building dependency tree
Reading state information... Done
Note, selecting 'ucsf-chimerax' instead of
'/home/osmel/Documents/virtual_screening/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: libffi7 but it is not installable
E: Unable to correct problems, you have held broken packages.

What can I do?
Thank you very much
Osmel

[pett]

Reported by Osmel Fleitas

[Greg Couch]

Hello, that is unexpected. Can you send me the command you used to try to install ucsf-chimerax? In addition, please run the following commands and send me the output? First run:

apt-cache search libffi

And then run:

dpkg-query --list | grep libffi

And lastly, run:

cat /etc/os-release

Thanks.

[osmelfleitas83@…]

Hello

The command that I used was :
$ sudo apt-get install
~/Documents/virtual_screening/ucsf-chimerax_1.2.5-1_amd64.deb

Output
(base) osmel@osmel-Inspiron-5590:~$ apt-cache search libffi
libffi-dev - Foreign Function Interface library (development files)
libffi8ubuntu1 - Foreign Function Interface library runtime
libffi-checklib-perl - module to check availability of a library for FFI
libffi-platypus-perl - module to create Perl bindings to non-Perl libraries
with FFI
libffindex0 - library for simple index/database for huge amounts of small
files
libffindex0-dev - library for simple index/database for huge amounts of
small files (development)
libjffi-java - Java Foreign Function Interface
libjffi-jni - Java Foreign Function Interface (JNI library)

(base) osmel@osmel-Inspiron-5590:~$ dpkg-query --list | grep libffi
ii  libffi-dev:amd64
3.4~20200819gead65ca871-0ubuntu3    amd64        Foreign Function Interface
library (development files)
ii  libffi8ubuntu1:amd64
3.4~20200819gead65ca871-0ubuntu3    amd64        Foreign Function Interface
library runtime

(base) osmel@osmel-Inspiron-5590:~$  cat /etc/os-release
NAME="Ubuntu"
VERSION="20.10 (Groovy Gorilla)"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 20.10"
VERSION_ID="20.10"
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"
VERSION_CODENAME=groovy
UBUNTU_CODENAME=groovy
(base) osmel@osmel-Inspiron-5590:~$


On Tue, Jun 29, 2021 at 10:09 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[Greg Couch]

Thank you. I see that you are using Ubuntu 20.10 and that a newer version of libffi is installed. I haven't done this before, but :-) You'll need to add the --ignore-missing and/or --fix-broken options to the command line. For example:

sudo apt-get install --ignore-missing ~/Documents/virtual_screening/ucsf-chimerax_1.2.5-1_amd64.deb

And then you'll need to do one of:

(A) pretend that libffi.so.7 exists with:

sudo ln -s libffi.so.8 /usr/lib/x86_64-linux-gnu/libffi.so.7

(B) use a binary editor and change libffi.so.7 to libffi.so.8 in:

/usr/lib/ucsf-chimerax/lib/python3.8/lib-dynload/_ctypes.cpython-38-x86_64-linux-gnu.so

Or, (C) get the libffi7.so.7 debian package from a Ubuntu 20.04 repository and install it.

Option C is guaranteed to work, but personally, I'd do option B.

Please report back what you try and what works.

The long term solution is for ChimeraX to switch from being a debian package to a snap or flatpak container.

[Greg Couch]

Sorry, option C is the libffi7 package and that package provides the shared library libffi.so.7.

[osmelfleitas83@…]

Hello

I performed again the installation adding the options --ignore-missing
and/or --fix-broken and following option A (I don't know how to do option
B). Thi was the output:

(base) osmel@osmel-Inspiron-5590:~$ sudo apt-get install --ignore-missing
~/Documents/virtual_screening/ucsf-chimerax_1.2.5-1_amd64.deb
[sudo] password for osmel:
Reading package lists... Done
Building dependency tree
Reading state information... Done
Note, selecting 'ucsf-chimerax' instead of
'/home/osmel/Documents/virtual_screening/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: libffi7 but it is not installable
E: Unable to correct problems, you have held broken packages.
(base) osmel@osmel-Inspiron-5590:~$ sudo apt-get install --ignore-missing
--fix-broken  ~/Documents/virtual_screening/ucsf-chimerax_1.2.5-1_amd64.deb
Reading package lists... Done
Building dependency tree
Reading state information... Done
Note, selecting 'ucsf-chimerax' instead of
'/home/osmel/Documents/virtual_screening/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: libffi7 but it is not installable
E: Unable to correct problems, you have held broken packages.
(base) osmel@osmel-Inspiron-5590:~$ sudo ln -s libffi.so.8
/usr/lib/x86_64-linux-gnu/libffi.so.7
ln: failed to create symbolic link '/usr/lib/x86_64-linux-gnu/libffi.so.7':
File exists
(base) osmel@osmel-Inspiron-5590:~$

On Wed, Jun 30, 2021 at 8:36 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[Greg Couch]

Thinking about this more, option C is best. Download the libffi7 package from ​http://archive.ubuntu.com/ubuntu/pool/main/libf/libffi/libffi7_3.3-4_amd64.deb and install it. Then, when you install ChimeraX, all of the dependencies will be met.

[osmelfleitas83@…]

Hello

It worked
Thank you very much for the help


On Tue, Jul 13, 2021 at 10:09 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[Greg Couch]

Correct summary and description to say the problem was installing on Ubuntu 21.04.