[cctbxbb] dials install error

Aaron Brewster asbrewster at lbl.gov
Tue Jan 12 12:00:20 PST 2016


Hello Sid,

We're not sure we can reproduce this error.  Can you try yum upgrade, then
try again?

We are discussing adding some new tests to catch this kind of error.

-Aaron

On Tue, Jan 12, 2016 at 3:47 AM, <markus.gerstel at diamond.ac.uk> wrote:

> Dear Sid,
>
>
>
> Unfortunately I don’t know what the proper solution to your problem is.
>
> We had issues with pango/glibc reported just a few days ago, but I don’t
> know what the outcome to that was.
>
> Dear David, Nick, Billy,
>
> Following up on the discussion in the thread ‘bootstrap.py build on
> Ubuntu’, here is an installer failure on CentOS5 that comes down to
> pango/libfontconfig/libglib missing some libraries, trace attached.
>
>
>
> -Markus
>
>
>
>
>
> *From:* Sidhu, Khushwant (Dr.) [mailto:k.sidhu at leicester.ac.uk]
> *Sent:* 12 January 2016 11:26
> *To:* Gerstel, Markus (DLSLtd,RAL,LSCI)
> *Cc:* Sidhu, Khushwant (Dr.)
> *Subject:* Re: dials install error
>
>
>
> Dear Markus,
>
>
>
> using the --verbose flag, I get the following ….
>
>
>
>  ./install --verbose
>
> (snip)
>
> : Regenerating module files in /usr/local/dials-dev20160112/base
>
> : generating pangorc file at
> /usr/local/dials-dev20160112/base/etc/pango/pangorc
>
> : generating pango.modules file at
> /usr/local/dials-dev20160112/base/etc/pango/pango.modules
>
> : /usr/local/dials-dev20160112/base/bin/pango-querymodules:
> /lib64/libc.so.6: version `GLIBC_2.7' not found (required by
> /usr/local/dials-dev20160112/base/lib/libfontconfig.so.1)
>
> : /usr/local/dials-dev20160112/base/bin/pango-querymodules:
> /lib64/libc.so.6: version `GLIBC_2.7' not found (required by
> /usr/local/dials-dev20160112/base/lib/libglib-2.0.so.0)
>
> : Traceback (most recent call last):
>
> : File
> "/usr/local/dials-dev20160112/modules/cctbx_project/libtbx/configure.py",
> line 22, in <module>
>
> : if not run():
>
> : File
> "/usr/local/dials-dev20160112/modules/cctbx_project/libtbx/configure.py",
> line 17, in run
>
> : libtbx.env_config.cold_start(sys.argv)
>
> : File
> "/usr/local/dials-dev20160112/modules/cctbx_project/libtbx/env_config.py",
> line 2267, in cold_start
>
> : env.refresh()
>
> : File
> "/usr/local/dials-dev20160112/modules/cctbx_project/libtbx/env_config.py",
> line 1544, in refresh
>
> : regenerate_module_files.run(libtbx.env.under_base('.'),
> only_if_needed=True)
>
> : File
> "/usr/local/dials-dev20160112/modules/cctbx_project/libtbx/auto_build/regenerate_module_files.py",
> line 153, in run
>
> : fix_pango(base_dir, out)
>
> : File
> "/usr/local/dials-dev20160112/modules/cctbx_project/libtbx/auto_build/regenerate_module_files.py",
> line 59, in fix_pango
>
> : call(("%s/bin/pango-querymodules > %s") % (base_dir, pangomodules),
> log=out)
>
> : File
> "/usr/local/dials-dev20160112/modules/cctbx_project/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
> '/usr/local/dials-dev20160112/base/bin/pango-querymodules >
> /usr/local/dials-dev20160112/base/etc/pango/pango.modules' failed with exit
> code 1
>
> Traceback (most recent call last):
>
>   File "/usr/local/dials-installer-dev/bin/install.py", line 46, in ?
>
>     installer(sys.argv[1:]).install()
>
>   File
> "/usr/local/dials-installer-dev/lib/libtbx/auto_build/install_distribution.py",
> line 197, in install
>
>     self.install_from_binary()
>
>   File
> "/usr/local/dials-installer-dev/lib/libtbx/auto_build/install_distribution.py",
> line 318, in install_from_binary
>
>     self.reconfigure(log=log)
>
>   File
> "/usr/local/dials-installer-dev/lib/libtbx/auto_build/install_distribution.py",
> line 484, in reconfigure
>
>     call(args=args, log=log, verbose=self.options.verbose)
>
>   File
> "/usr/local/dials-installer-dev/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 '/usr/local/dials-dev20160112/base/bin/python
> /usr/local/dials-dev20160112/modules/cctbx_project/libtbx/configure.py
> --current_working_directory /usr/local/dials-dev20160112/build dials xia2'
> failed with exit code 1
>
>
>
> regards
>
>
>
> Sid
>
>
>
>
>
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