[cctbxbb] dials install error

Tue Jan 12 16:49:38 PST 2016

I suppose this error:
version `GLIBC_2.7' not found (required by
/usr/local/dials-dev20160112/base/lib/libfontconfig.so.1)
means that binaries compiled on a system with glibc 2.7+ are used on a
system with older glibc.

Marcin

On Tue, Jan 12, 2016 at 8:00 PM, Aaron Brewster <asbrewster at lbl.gov> wrote:
> 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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