[phenixbb] Problems installing 1.10.1 on RHEL 6.3

Billy Poon bkpoon at lbl.gov
Tue Feb 2 09:17:29 PST 2016


Hi Dave,

It looks like there is a missing dependency for the CentOS6 build. Do other
programs work in X? And what version are you running? The _XGetRequest
symbol is from xorg-x11. We build on CentOS 6.5, so it probably needs the
version from RedHat 6.5. You can try updating just the xorg-x11 rpms or
updating to RedHat 6.5. If you can't do that, you may need to compile from
source. Let us know if you have issues. Thanks!

--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909
Web: https://phenix-online.org

On Tue, Feb 2, 2016 at 3:13 AM, David Briggs <drdavidcbriggs at gmail.com>
wrote:

> Hi Phenix,
>
> We are trying to upgrade Phenix on our Linux box running RHEL 6.3,
>  kernel 2.6.32-279.14.1.el6.x86_64.
>
> I have attempted to install the Centos 5 build and I get an error message
> during installation:
>
> Configuring Phenix components... Traceback (most recent call last): File
> "./bin/install.py", line 262, in <module> installer(sys.argv[1:]).install()
> File
> "/home/public/packages/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos5/lib/libtbx/auto_build/install_distribution.py",
> line 185, in install self.install_from_binary() File
> "/home/public/packages/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos5/lib/libtbx/auto_build/install_distribution.py",
> line 295, in install_from_binary self.reconfigure(log=log) File
> "/home/public/packages/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos5/lib/libtbx/auto_build/install_distribution.py",
> line 460, in reconfigure call(args=args, log=log,
> verbose=self.options.verbose) File
> "/home/public/packages/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos5/lib/libtbx/auto_build/installer_utils.py",
> line 81, in call raise RuntimeError("Call to '%s' failed with exit code %d"
> % (args, rc)) RuntimeError: Call to
> '/home/public/packages/phenix-1.10.1-2155/base/bin/python
> /home/public/packages/phenix-1.10.1-2155/modules/cctbx_project/libtbx/configure.py
> --current_working_directory /home/public/packages/phenix-1.10.1-2155/build
> --command_version_suffix 1.10.1-2155 phenix phaser solve_resolve labelit'
> failed with exit code -11
>
> When I attempt install the CentOS6 build I can install Phenix, but when I
> try and launch it I get a different error message:
>
> Traceback (most recent call last): File
> "/home/public/packages/phenix-1.10.1-2155/build/../modules/phenix/wxGUI2/command_line/main.py",
> line 23, in <module> run(sys.argv[1:]) File
> "/home/public/packages/phenix-1.10.1-2155/build/../modules/phenix/wxGUI2/command_line/main.py",
> line 16, in run from wxGUI2 import App File
> "/home/public/packages/phenix-1.10.1-2155/modules/phenix/wxGUI2/App.py",
> line 15, in <module> import wx File
> "/home/public/packages/phenix-1.10.1-2155/base/lib/python2.7/site-packages/wx-2.8-gtk2-unicode/wx/__init__.py",
> line 45, in <module> from wx._core import * File
> "/home/public/packages/phenix-1.10.1-2155/base/lib/python2.7/site-packages/wx-2.8-gtk2-unicode/wx/_core.py",
> line 4, in <module> import _core_ ImportError:
> /home/public/packages/phenix-1.10.1-2155/base/bin/../lib/libXrender.so.1:
> undefined symbol: _XGetRequest
>
>
> Should I give up and attempt to compile from the source, or is there a fix
> for these issues?
>
> Kind regards,
>
> Dave
> --
>
> --
>
> David Briggs
> about.me/david_briggs
>
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