[cctbxbb] dials install error

markus.gerstel at diamond.ac.uk markus.gerstel at diamond.ac.uk
Tue Jan 12 03:47:48 PST 2016

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.


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
: 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 ?
  File "/usr/local/dials-installer-dev/lib/libtbx/auto_build/install_distribution.py", line 197, in install
  File "/usr/local/dials-installer-dev/lib/libtbx/auto_build/install_distribution.py", line 318, in install_from_binary
  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



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