Opened 4 years ago

Closed 4 years ago

#4709 closed defect (fixed)

can't install chimerax

Reported by: francisco.murphy@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Platform Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

[murphy@eva02 Downloads]$ sudo rpm -i
./ucsf-chimerax-1.2.5-1.el8.x86_64.rpm
[sudo] password for murphy:
error: Failed dependencies:
fftw-libs-single is needed by ucsf-chimerax-1.2.5-1.el8.x86_64
mesa-libOSMesa is needed by ucsf-chimerax-1.2.5-1.el8.x86_64
[murphy@eva02 Downloads]$ sudo dnf install
./ucsf-chimerax-1.2.5-1.el8.x86_64.rpm
Last metadata expiration check: 2:29:59 ago on Mon 31 May 2021 07:01:27 PM
CDT.
Dependencies resolved.
================================================================================
 Package               Arch        Version              Repository
Size
================================================================================
Installing:
 ucsf-chimerax         x86_64      1.2.5-1.el8          @commandline
 307 M
Upgrading:
 mesa-libGL            x86_64      21.1.1-1.fc34        updates
171 k
 mesa-libglapi         x86_64      21.1.1-1.fc34        updates
 55 k
Installing dependencies:
 fftw-libs-single      x86_64      3.3.8-10.fc34        fedora
 953 k
 mesa-libOSMesa        x86_64      21.1.1-1.fc34        updates
3.1 M

Transaction Summary
================================================================================
Install  3 Packages
Upgrade  2 Packages

Total size: 311 M
Total download size: 4.3 M
Is this ok [y/N]: y
Downloading Packages:
(1/4): fftw-libs-single-3.3.8-10.fc34.x86_64.rp 588 kB/s | 953 kB     00:01

(2/4): mesa-libGL-21.1.1-1.fc34.x86_64.rpm       83 kB/s | 171 kB     00:02

(3/4): mesa-libglapi-21.1.1-1.fc34.x86_64.rpm   112 kB/s |  55 kB     00:00

(4/4): mesa-libOSMesa-21.1.1-1.fc34.x86_64.rpm  1.1 MB/s | 3.1 MB     00:02

--------------------------------------------------------------------------------
Total                                           1.1 MB/s | 4.3 MB     00:03

Running transaction check
Transaction check succeeded.
Running transaction test
The downloaded packages were saved in cache until the next successful
transaction.
You can remove cached packages by executing 'dnf clean packages'.
Error: Transaction test error:
  file /usr/lib/.build-id/34/aac32bb4d3c0f44e72e57cf253a871240a1154 from
install of ucsf-chimerax-1.2.5-1.el8.x86_64 conflicts with file from
package rstudio-1.4.1106-1.x86_64
  file /usr/lib/.build-id/80/916a3578c4abf8d9433986b7ca87ee58797eb5 from
install of ucsf-chimerax-1.2.5-1.el8.x86_64 conflicts with file from
package rstudio-1.4.1106-1.x86_64
  file /usr/lib/.build-id/ea/6a2369dae8e186543b5e0fa413cb7ee7058c84 from
install of ucsf-chimerax-1.2.5-1.el8.x86_64 conflicts with file from
package rstudio-1.4.1106-1.x86_64

[murphy@eva02 Downloads]$ dnf clean packages
0 files removed
[murphy@eva02 Downloads]$ sudo dnf install
./ucsf-chimerax-1.2.5-1.el8.x86_64.rpm
Last metadata expiration check: 2:30:45 ago on Mon 31 May 2021 07:01:27 PM
CDT.
Dependencies resolved.
================================================================================
 Package               Arch        Version              Repository
Size
================================================================================
Installing:
 ucsf-chimerax         x86_64      1.2.5-1.el8          @commandline
 307 M
Upgrading:
 mesa-libGL            x86_64      21.1.1-1.fc34        updates
171 k
 mesa-libglapi         x86_64      21.1.1-1.fc34        updates
 55 k
Installing dependencies:
 fftw-libs-single      x86_64      3.3.8-10.fc34        fedora
 953 k
 mesa-libOSMesa        x86_64      21.1.1-1.fc34        updates
3.1 M

Transaction Summary
================================================================================
Install  3 Packages
Upgrade  2 Packages

Total size: 311 M
Is this ok [y/N]: y
Downloading Packages:
[SKIPPED] fftw-libs-single-3.3.8-10.fc34.x86_64.rpm: Already downloaded

[SKIPPED] mesa-libOSMesa-21.1.1-1.fc34.x86_64.rpm: Already downloaded

[SKIPPED] mesa-libGL-21.1.1-1.fc34.x86_64.rpm: Already downloaded

[SKIPPED] mesa-libglapi-21.1.1-1.fc34.x86_64.rpm: Already downloaded

Running transaction check
Transaction check succeeded.
Running transaction test
The downloaded packages were saved in cache until the next successful
transaction.
You can remove cached packages by executing 'dnf clean packages'.
Error: Transaction test error:
  file /usr/lib/.build-id/34/aac32bb4d3c0f44e72e57cf253a871240a1154 from
install of ucsf-chimerax-1.2.5-1.el8.x86_64 conflicts with file from
package rstudio-1.4.1106-1.x86_64
  file /usr/lib/.build-id/80/916a3578c4abf8d9433986b7ca87ee58797eb5 from
install of ucsf-chimerax-1.2.5-1.el8.x86_64 conflicts with file from
package rstudio-1.4.1106-1.x86_64
  file /usr/lib/.build-id/ea/6a2369dae8e186543b5e0fa413cb7ee7058c84 from
install of ucsf-chimerax-1.2.5-1.el8.x86_64 conflicts with file from
package rstudio-1.4.1106-1.x86_64
[murphy@eva02 Downloads]$ sudo dnf install chimerax-daily.rpm
[sudo] password for murphy:
Last metadata expiration check: 2:38:26 ago on Mon 31 May 2021 07:01:27 PM
CDT.
Dependencies resolved.
=======================================================================================================================
 Package                          Architecture        Version
           Repository                 Size
=======================================================================================================================
Installing:
 ucsf-chimerax-daily              x86_64              2021.05.29-1.el8
            @commandline              292 M
Upgrading:
 mesa-libGL                       x86_64              21.1.1-1.fc34
           updates                   171 k
 mesa-libglapi                    x86_64              21.1.1-1.fc34
           updates                    55 k
Installing dependencies:
 fftw-libs-single                 x86_64              3.3.8-10.fc34
           fedora                    953 k
 mesa-libOSMesa                   x86_64              21.1.1-1.fc34
           updates                   3.1 M

Transaction Summary
=======================================================================================================================
Install  3 Packages
Upgrade  2 Packages

Total size: 297 M
Is this ok [y/N]: y
Downloading Packages:
[SKIPPED] fftw-libs-single-3.3.8-10.fc34.x86_64.rpm: Already downloaded

[SKIPPED] mesa-libOSMesa-21.1.1-1.fc34.x86_64.rpm: Already downloaded

[SKIPPED] mesa-libGL-21.1.1-1.fc34.x86_64.rpm: Already downloaded

[SKIPPED] mesa-libglapi-21.1.1-1.fc34.x86_64.rpm: Already downloaded

Running transaction check
Transaction check succeeded.
Running transaction test
The downloaded packages were saved in cache until the next successful
transaction.
You can remove cached packages by executing 'dnf clean packages'.
Error: Transaction test error:
  file /usr/lib/.build-id/34/aac32bb4d3c0f44e72e57cf253a871240a1154 from
install of ucsf-chimerax-daily-2021.05.29-1.el8.x86_64 conflicts with file
from package rstudio-1.4.1106-1.x86_64
  file /usr/lib/.build-id/80/916a3578c4abf8d9433986b7ca87ee58797eb5 from
install of ucsf-chimerax-daily-2021.05.29-1.el8.x86_64 conflicts with file
from package rstudio-1.4.1106-1.x86_64
  file /usr/lib/.build-id/ea/6a2369dae8e186543b5e0fa413cb7ee7058c84 from
install of ucsf-chimerax-daily-2021.05.29-1.el8.x86_64 conflicts with file
from package rstudio-1.4.1106-1.x86_64
[murphy@eva02 Downloads]$ sudo dnf install
ucsf-chimerax-1.2.5-1.el7.x86_64.rpm
Last metadata expiration check: 2:38:46 ago on Mon 31 May 2021 07:01:27 PM
CDT.
Error:
 Problem: conflicting requests
  - nothing provides libgfortran4 needed by ucsf-chimerax-1.2.5-1.el7.x86_64
  - nothing provides mesa-private-llvm needed by
ucsf-chimerax-1.2.5-1.el7.x86_64
(try to add '--skip-broken' to skip uninstallable packages)
[murphy@eva02 Downloads]$ uname -a
Linux eva02 5.11.21-300.fc34.x86_64 #1 SMP Fri May 14 17:43:38 UTC 2021
x86_64 x86_64 x86_64 GNU/Linux


Thanks

Attachments (1)

rstudioproblem.txt​ (27.0 KB ) - added by francisco.murphy@… 4 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (5)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Platform
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned

comment:2 by Greg Couch, 4 years ago

Status: assigned → feedback

Which version of Fedora are you running?

The fact that the CentOS 7 rpm failed to install is expected. Use the CentOS 8 rpm. And having to use dnf instead of rpm to install is expected. The transaction test error message is not useful. Maybe if you change the order you'll get a better error message? That is, remove rstudio, install ChimeraX, then install rstudio.

And can you send me the dependencies from the rstudio rpm? Run "rpm -qpR rstudio.rpm" to get its dependencies. I will do the same with the ChimeraX rpm (you can too to see what they are).

in reply to:  3 ; comment:3 by francisco.murphy@…, 4 years ago 

Dear Greg
For the record... I tried the centOS8, the centOS7 and the daily versions,
all of them failed with the same error message.

I am running Fedora 34.

Today I followed your advice: removed rstudio, installed chimeraX (centos8
version), then reinstalled rstudio. It seems that both programs work. But
it works only if the rstudio version installed is the one from the Fedora
repositories, not from rstudio itself. See attached txt.

Thanks for your help.


El mar, 1 de jun. de 2021 a la(s) 13:07, ChimeraX (
ChimeraX-bugs-admin@cgl.ucsf.edu) escribió:

rstudioproblem.txt​

by francisco.murphy@…, 4 years ago

Attachment: rstudioproblem.txt​ added

Added by email2trac

comment:4 by Greg Couch, 4 years ago

Resolution: → fixed
Status: feedback → closed

Okay, I think I understand what's going on now. Both rstudio and ChimeraX have the same packaging bug with embedded shared libraries that creates the conflict. With the current ChimeraX rpm you have a few solutions: (1) as you found, use the rstudio from the Fedora repository, (2) install ChimeraX in a different location -- for example into /usr/local with rpm -i --relocate /usr=/usr/local ucsf-chimerax-1.2.5-1.el8.x86_64 -- this works because ChimeraX is a relocatable package, or, (3) install rstudio somewhere else if it is a relocatable package.

I will also put a workaround that will appear in the next daily build.

Googling, this is a weird bug. It has to do with two different packages that have the same shared library but in different locations. In ChimeraX's case, the libraries from from the embedded PyQt5 (that is newer than what is in CentoS 8). The libraries are libicudata.so.56, libicuuc.so.56, and libicui18n.so.56. Since parts of ChimeraX overlap with system packages, this problem could easily occur again. So I've disabled the generation of the /usr/lib/.build-id files that caused the conflict.

Note: See TracTickets for help on using tickets.