[cctbxbb] compilation issues

Graeme.Winter at diamond.ac.uk Graeme.Winter at diamond.ac.uk
Mon Mar 16 09:01:32 PDT 2015

Dear David

There is some weirdness to do with how Ubuntu lay out their X-window stuff, but in this case I have a feeling the problem is more to do with it having it’s own libtool – when I was trying to make the bootstrap installer work on Ubuntu 14.4r2 I had to add the following hack:

    import os
    import platform

    # Ubuntu & Xrender - libtool is broken - replace with system one if
    # installed...

    if 'xrender' in os.path.split(os.getcwd())[-1] and \
      'Ubuntu' in platform.platform() and os.path.exists('libtool'):
      if os.path.exists(os.path.join('/', 'usr', 'bin', 'libtool')):
        self.log.write('Removing xrender libtool; replace with system\n')
        os.symlink(os.path.join('/', 'usr', 'bin', 'libtool'), 'libtool')
        self.log.write('Cannot removing xrender libtool; not installed\n')


Please try doing the same by hand & see if it makes the problem go away.

You may find an alternative solution is to install the dependencies on the machine through apt-get & install cctbx using the system Python

Overall this may be less painful…

best wishes Graeme

From: cctbxbb-bounces at phenix-online.org [mailto:cctbxbb-bounces at phenix-online.org] On Behalf Of Dave Lodowski
Sent: 16 March 2015 15:57
To: cctbxbb at phenix-online.org
Subject: [cctbxbb] compilation issues

Hi, sorry if this is a repeat, but an email sent to the cctbx at cci.lbl.gov<mailto:cctbx at cci.lbl.gov> bounced back to me. We are attempting to install the DIALS package and CCTBX is required for compilation. During compilation of CCTBX, Xrender fails to find the X windows server. OS is Ubuntu LTS 12.04.5

text from console upon failure:

 Installing Xrender...
  log file is /home/dave/cctbx/build/base_tmp/Xrender_install_log
  getting package xrender-0.8.3.tar.gz...
    downloading from http://cci.lbl.gov/cctbx_dependencies : local copy is current
    using ./xrender-0.8.3.tar.gz (cached)
  installing xrender-0.8.3.tar.gz...
Traceback (most recent call last):
  File "../auto_build/install", line 9, in <module>
    install_base_packages.installer(args=sys.argv, log=sys.stdout)
  File "../auto_build/install_base_packages.py", line 161, in __init__
  File "../auto_build/install_base_packages.py", line 505, in build_dependencies
    getattr(self, 'build_%s'%i)()
  File "../auto_build/install_base_packages.py", line 781, in build_render
    self.build_compiled_package_simple(pkg_name=pkg, pkg_name_label=name)
  File "../auto_build/install_base_packages.py", line 407, in build_compiled_package_simple
  File "../auto_build/install_base_packages.py", line 392, in configure_and_build
    self.call("./configure %s" % " ".join(list(config_args)), log=log)
  File "../auto_build/install_base_packages.py", line 243, in call
    return call(args, log=log, verbose=self.verbose, **kwargs)
  File "../auto_build/installer_utils.py", line 71, in call
    raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc))
RuntimeError: Call to './configure --prefix="/home/dave/cctbx/build/base"' failed with exit code 1

​Log file indicates everything fine till X is required then :​
checking for X... no
configure: error: X is required, but it was either disabled or not found.

​any suggestions as to how to proceed would be appreciated
--David Lodowski

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