chimerax 1.0 installation

[Muyuan.Chen@…]

Hi,
I had chimeraX 0.8 on my linux machine since it came out and it has been working well. Recently I am trying to upgrade to a later release but keep getting freetype related errors:

chimerax-1.0/bin/ChimeraX: symbol lookup error: chimerax-1.0/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5XcbQpa.so.5: undefined symbol: FT_Get_Font_Format

Any suggestions on how to make it work?

Thanks,
Muyuan

[Greg Couch]

What version of Linux are you running?

[Muyuan.Chen@…]

Ubuntu 16.04.

[Greg Couch]

So I can't reproduce this. I installed Ubuntu 16.04 in a virtual machine did a "sudo apt-get upgrade" to get it up to date. Then I downloaded the ucsf_chimerax_1.0_amd64.deb for Ubuntu 16.04 and ran "sudo apt-get install ./ucsf_chimerax_1.0_amd64.deb" to install it. Then I ran "chimerax" and it started up with no problems.

How did you install ChimeraX?

[Muyuan.Chen@…]

I tried both Ubuntu installer and Linux tar file and get the same error. I assume there are some libraries on my machine that have conflict with chimerax.
Since chimerax 0.8 still works, I am not that eager to figure it out...

________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, August 31, 2020 6:49:16 PM
Cc: Chen, Muyuan <Muyuan.Chen@bcm.edu>; gregc@cgl.ucsf.edu <gregc@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #3670: chimerax 1.0 installation

#3670: chimerax 1.0 installation
------------------------------------+------------------------
          Reporter:  Muyuan.Chen@…  |      Owner:  Greg Couch
              Type:  defect         |     Status:  accepted
          Priority:  normal         |  Milestone:
         Component:  Platform       |    Version:
        Resolution:                 |   Keywords:
        Blocked By:                 |   Blocking:
Notify when closed:                 |   Platform:  all
           Project:  ChimeraX       |
------------------------------------+------------------------

Comment (by Greg Couch):

 So I can't reproduce this.  I installed Ubuntu 16.04 in a virtual machine
 did a "sudo apt-get upgrade" to get it up to date.  Then I downloaded the
 ucsf_chimerax_1.0_amd64.deb for Ubuntu 16.04 and ran "sudo apt-get install
 ./ucsf_chimerax_1.0_amd64.deb" to install it.  Then I ran "chimerax" and
 it started up with no problems.

 How did you install ChimeraX?

--
Ticket URL: <https://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_trac_ChimeraX_ticket_3670-23comment-3A4&d=DwIGaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=zPLILKgdfwMpudxhWtXchY3IRd-K8CjwG2fmrCioqH0&m=WL2l_NNFM0nAXB1E-R1qQuVXE59wRzbBnIDo291WXD4&s=oEyTh0CIo2i8y7hAQG94LQobGDJTloa0MjxgvQukAG4&e= >
ChimeraX <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimerax_&d=DwIGaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=zPLILKgdfwMpudxhWtXchY3IRd-K8CjwG2fmrCioqH0&m=WL2l_NNFM0nAXB1E-R1qQuVXE59wRzbBnIDo291WXD4&s=hxWC3augno2J8zf0ippZgCQK9QRnRtI68zoyk8VtYK4&e= >
ChimeraX Issue Tracker

[Greg Couch]

Installing the .deb should get all of the necessary system libraries installed.

Do you have the LD_LIBRARY_PATH environment variable set? If so, if you unset it, does ChimeraX 1.0 work then? If so, please try the ChimeraX 1.1 release candidate. I put a fix into the daily build and the release candidate that avoids problems with LD_LIBRARY_PATH being set.

[Muyuan.Chen@…]

I thought the deb should handle the dependency too but it doesn’t. LD Library path is empty. It seems everything is linked to a correct so file when I ldd libqt5xcbqpa...

________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, August 31, 2020 7:21:21 PM
Cc: Chen, Muyuan <Muyuan.Chen@bcm.edu>; gregc@cgl.ucsf.edu <gregc@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #3670: chimerax 1.0 installation

#3670: chimerax 1.0 installation
------------------------------------+------------------------
          Reporter:  Muyuan.Chen@…  |      Owner:  Greg Couch
              Type:  defect         |     Status:  accepted
          Priority:  normal         |  Milestone:
         Component:  Platform       |    Version:
        Resolution:                 |   Keywords:
        Blocked By:                 |   Blocking:
Notify when closed:                 |   Platform:  all
           Project:  ChimeraX       |
------------------------------------+------------------------

Comment (by Greg Couch):

 Installing the .deb should get all of the necessary system libraries
 installed.

 Do you have the LD_LIBRARY_PATH environment variable set?  If so, if you
 unset it, does ChimeraX 1.0 work then?  If so, please try the ChimeraX 1.1
 release candidate.  I put a fix into the daily build and the release
 candidate that avoids problems with LD_LIBRARY_PATH being set.

--
Ticket URL: <https://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_trac_ChimeraX_ticket_3670-23comment-3A6&d=DwIGaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=zPLILKgdfwMpudxhWtXchY3IRd-K8CjwG2fmrCioqH0&m=iWs7w4yAnYW3LWlOobtUukgpCnMTUPy9LWc3OIHr3Ks&s=JEu4jWQulDPHu3aHCm0EBYWPbBQ77QVEBmPeWzUjqx8&e= >
ChimeraX <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimerax_&d=DwIGaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=zPLILKgdfwMpudxhWtXchY3IRd-K8CjwG2fmrCioqH0&m=iWs7w4yAnYW3LWlOobtUukgpCnMTUPy9LWc3OIHr3Ks&s=mYcJ4xqzcQOWXgHVVUooYHFkdK0fHw08B2kTeWk7sd0&e= >
ChimeraX Issue Tracker

[Greg Couch]

Still try out the release candidate. The changes also protect against incompatible system Qt libraries.

[Greg Couch]

Fixed in ChimeraX 1.1.