<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<meta name="Generator" content="Microsoft Word 14 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri","sans-serif";
mso-fareast-language:EN-US;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="EN-GB" link="blue" vlink="purple">
<div class="WordSection1">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Dear David<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">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:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> import os<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> import platform<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> # Ubuntu & Xrender - libtool is broken - replace with system one if<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> # installed...<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> if 'xrender' in os.path.split(os.getcwd())[-1] and \<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> 'Ubuntu' in platform.platform() and os.path.exists('libtool'):<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> if os.path.exists(os.path.join('/', 'usr', 'bin', 'libtool')):<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> self.log.write('Removing xrender libtool; replace with system\n')<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> os.remove('libtool')<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> os.symlink(os.path.join('/', 'usr', 'bin', 'libtool'), 'libtool')<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> else:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> self.log.write('Cannot removing xrender libtool; not installed\n')<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> return<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Please try doing the same by hand & see if it makes the problem go away.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">You may find an alternative solution is to install the dependencies on the machine through apt-get & install cctbx using the system Python<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Overall this may be less painful…<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">best wishes Graeme<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> cctbxbb-bounces@phenix-online.org [mailto:cctbxbb-bounces@phenix-online.org]
<b>On Behalf Of </b>Dave Lodowski<br>
<b>Sent:</b> 16 March 2015 15:57<br>
<b>To:</b> cctbxbb@phenix-online.org<br>
<b>Subject:</b> [cctbxbb] compilation issues<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal"><span style="font-size:18.0pt">Hi, sorry if this is a repeat, but an email sent to the
<a href="mailto:cctbx@cci.lbl.gov">cctbx@cci.lbl.gov</a> 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<o:p></o:p></span></p>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<div>
<p class="MsoNormal">text from console upon failure:<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"> Installing Xrender...<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> log file is /home/dave/cctbx/build/base_tmp/Xrender_install_log<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> getting package xrender-0.8.3.tar.gz...<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> downloading from <a href="http://cci.lbl.gov/cctbx_dependencies">
http://cci.lbl.gov/cctbx_dependencies</a> : local copy is current<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> using ./xrender-0.8.3.tar.gz (cached)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> installing xrender-0.8.3.tar.gz...<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Traceback (most recent call last):<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> File "../auto_build/install", line 9, in <module><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> install_base_packages.installer(args=sys.argv, log=sys.stdout)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> File "../auto_build/install_base_packages.py", line 161, in __init__<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> self.build_dependencies(packages=packages)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> File "../auto_build/install_base_packages.py", line 505, in build_dependencies<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> getattr(self, 'build_%s'%i)()<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> File "../auto_build/install_base_packages.py", line 781, in build_render<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> self.build_compiled_package_simple(pkg_name=pkg, pkg_name_label=name)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> File "../auto_build/install_base_packages.py", line 407, in build_compiled_package_simple<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> log=pkg_log)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> File "../auto_build/install_base_packages.py", line 392, in configure_and_build<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> self.call("./configure %s" % " ".join(list(config_args)), log=log)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> File "../auto_build/install_base_packages.py", line 243, in call<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> return call(args, log=log, verbose=self.verbose, **kwargs)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> File "../auto_build/installer_utils.py", line 71, in call<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc))<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">RuntimeError: Call to './configure --prefix="/home/dave/cctbx/build/base"' failed with exit code 1<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:18.0pt">Log file indicates everything fine till X is required then :<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal">checking for X... no<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">configure: error: X is required, but it was either disabled or not found.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:18.0pt">any suggestions as to how to proceed would be appreciated<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:18.0pt">thanks,<o:p></o:p></span></p>
</div>
</div>
</div>
</div>
<div>
<p class="MsoNormal">--David Lodowski<o:p></o:p></p>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><o:p> </o:p></p>
</div>
</div>
</div>
</div>
</div>
</div>
<p align="justify"> </p>
<p align="justify">-- </p>
<p align="justify">This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail.<br />Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. <br />Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message.<br />Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom<br /> </p></body>
</html>