<div dir="ltr"><div>hi Nathaniel,<br></div><div><br>2-<br></div><div>i just need to modify a file in :<br>cctbx_project/cctbx/eltbx/neutron.cpp<br>can you be more explicit on what i need to do to recompile from the binary package to take change into account please?<br></div><div><br></div><div>"<br></div><div><div>cd "`libtbx.show_build_path`"</div><div>libtbx.scons -j NUMBER_OF_PROCESSORS</div>"<br></div><div>thanks in advance,<br></div><div>cheerios,<br></div><div><br><br>-------<br></div>1- i tried the no-gui option and it gave the following error:<br><div><div><br>----------<br>Dependencies finished building.<br><br>******************************<br>* BASE INSTALLATION COMPLETE *<br>******************************<br><br>--------------------------------------------------------------------------------<br><br>Building core Phenix components<br> unwrapping cctbx_bundle.tar.gz...<br> unwrapping phenix.tar.gz...<br> unwrapping solve_resolve.tar.gz...<br> unwrapping elbow.tar.gz...<br> unwrapping reel.tar.gz...<br> unwrapping labelit.tar.gz...<br> unwrapping annlib.tar.gz...<br> unwrapping annlib_adaptbx.tar.gz...<br> unwrapping Plex.tar.gz...<br> unwrapping PyQuante.tar.gz...<br> unwrapping pulchra.tar.gz...<br> unwrapping ksdssp.tar.gz...<br> unwrapping muscle.tar.gz...<br> unwrapping Durandal.tar.gz...<br> unwrapping phaser.tar.gz...<br> unwrapping reduce.tar.gz...<br> unwrapping probe.tar.gz...<br> unwrapping king.tar.gz...<br> unwrapping suitename.tar.gz...<br>configuring PHENIX components with optimization...<br>Traceback (most recent call last):<br> File "./bin/install.py", line 815, in <module><br> run(sys.argv[1:])<br> File "./bin/install.py", line 72, in __init__<br> self.install_from_source()<br> File "./bin/install.py", line 352, in install_from_source<br> call([python_bin, config_path] + config_args, log=log)<br> File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/installer_utils.py", line 53, in call<br> raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc))<br>RuntimeError: Call to '/usr/local/phenix-dev-1839/build/intel-linux-2.6-x86_64/base/bin/python /usr/local/phenix-dev-1839/cctbx_project/libtbx/configure.py --build=release --scan_boost --command_version_suffix=dev-1839 --current_working_directory="/usr/local/phenix-dev-1839/build/intel-linux-2.6-x86_64" phenix phaser solve_resolve labelit xfel dxtbx' failed with exit code 2<br>max@A7K:/pgmax/phenix-installer-dev-1839$ <br><br></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">2014-12-09 0:07 GMT+01:00 Nathaniel Echols <span dir="ltr"><<a href="mailto:nechols@lbl.gov" target="_blank">nechols@lbl.gov</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">I'm pretty sure I encountered something similar in the past; unfortunately I can't remember what the explanation was, except that it involved some poorly explained dependencies.<div><br></div><div>However, I think in this case it may be overkill, for two reasons:</div><div><br></div><div>1) If you don't plan on using the Phenix GUI, add "--no-gui" to the install arguments to skip this whole mess entirely.</div><div><br></div><div>2) Since the source code is distributed along with the binaries, you can probably just rebuild starting from the binary installation - all you need to do is this (I think):</div><div><br></div><div>cd "`libtbx.show_build_path`"</div><div>libtbx.scons -j NUMBER_OF_PROCESSORS</div><div><br></div><div>and it will compile only the part that changed. If this works I definitely recommend avoiding the source installer.</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div class="h5">On Mon, Dec 8, 2014 at 2:57 PM, <span dir="ltr"><<a href="mailto:irees@lbl.gov" target="_blank">irees@lbl.gov</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">
<span>Hmm, this one is trickier. I will have to look at it closely. What distribution are you running?<div><br></div>
<div>Thanks,</div>
<div>Ian</div></span><div>
<br>—<br>Sent from <a href="https://www.dropbox.com/mailbox" target="_blank">Mailbox</a>
</div>
<br><br><div class="gmail_quote"><p>On Mon, Dec 8, 2014 at 5:50 PM, Maxime Cuypers <span dir="ltr"><<a href="mailto:maximecuypers@gmail.com" target="_blank">maximecuypers@gmail.com</a>></span> wrote:<br></p><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div>Hi Ian,<br><br>thanks for your suggestion, i installed the x11 headers and it passed the problem. however, now it gets stuck on gtk+<br><br></div>the logfile claims that libxrender can not be found. strange since this library is now installed on my system.<br><div>
<div>"checking for XRenderQueryExtension... no<br>configure: error: *** libXrender not found. Check 'config.log' for more details."<br><br></div>
<div>config.log enclosed from dir .../gtk+-2.10.11/<br></div>
<div><br></div>
<div>any idea?<br>thanks<br></div>
<div>
<br><br>Installing gtk+...<br> log file is /pgmax/phenix-installer-dev-1839/install_tmp/intel-linux-2.6-x86_64/A7K/gtk+_install_log<br> getting package gtk+-2.10.11.tar.gz...<br> using /pgmax/phenix-installer-dev-1839/gui/gtk+-2.10.11.tar.gz<span><br>Traceback (most recent call last):<br> File "./bin/install.py", line 815, in <module><br> run(sys.argv[1:])<br> File "./bin/install.py", line 72, in __init__<br> self.install_from_source()<br> File "./bin/install.py", line 292, in install_from_source<br> log=out)<br> File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 115, in __init__<br> self.build_cctbx_dependencies()<br> File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 170, in build_cctbx_dependencies<br> self.build_wxpython_dependencies()<br> File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 440, in build_wxpython_dependencies<br> self.build_wxpython_dependencies_linux()<br></span> File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 541, in build_wxpython_dependencies_linux<br> self.call("./configure %s" % " ".join(gtk_config_args), log=gtk_log)<span><br> File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 200, in call<br> return call(args, log=log)<br> File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/installer_utils.py", line 53, in call<br> raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc))<br></span>RuntimeError: Call to './configure --prefix="/usr/local/phenix-dev-1839/build/intel-linux-2.6-x86_64/base" --disable-cups --without-libjpeg' failed with exit code 1<br><br></div>
</div>
<div class="gmail_extra">
<br><div class="gmail_quote">2014-12-08 22:32 GMT+01:00 <span dir="ltr"><<a href="mailto:irees@lbl.gov" target="_blank">irees@lbl.gov</a>></span>:<div><div><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<span>Xrender can fail for many reasons, but generally missing X11 libraries or headers on your system. Can you send the log file:<div><br></div>
<div>/pgmax/phenix-installer-dev-1839/install_tmp/intel-linux-2.6-x86_64/A7K/Xrender_install_log</div>
<div><br></div>
<div>Thanks,</div>
<div>Ian</div></span><div>
<br>—<br>Sent from <a href="https://www.dropbox.com/mailbox" target="_blank">Mailbox</a>
</div>
<div><div>
<br><br><div class="gmail_quote">
<p>On Mon, Dec 8, 2014 at 4:30 PM, Maxime Cuypers <span dir="ltr"><<a href="mailto:maximecuypers@gmail.com" target="_blank">maximecuypers@gmail.com</a>></span> wrote:<br></p>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">
<div>
<div>hi all, <br>am getting the following error installing phenix from source dev-1839. (tried with source from 1.9-1692 with same error) am on latest kubuntu.<br><br></div>any idea on how to debug? -see below report...<br></div>
<br>PS: am compiling from source because i need a minor modification of the neutron scattering table which requires compilation.<br><div>
<div><br></div>
<div>cheerios,<br></div>
<div><div>
<br><br>....<br>Installing Xrender...<br> log file is /pgmax/phenix-installer-dev-1839/install_tmp/intel-linux-2.6-x86_64/A7K/Xrender_install_log<br> getting package xrender-0.8.3.tar.gz...<br> using /pgmax/phenix-installer-dev-1839/gui/xrender-0.8.3.tar.gz<br>Traceback (most recent call last):<br> File "./bin/install.py", line 815, in <module><br> run(sys.argv[1:])<br> File "./bin/install.py", line 72, in __init__<br> self.install_from_source()<br> File "./bin/install.py", line 292, in install_from_source<br> log=out)<br> File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 115, in __init__<br> self.build_cctbx_dependencies()<br> File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 170, in build_cctbx_dependencies<br> self.build_wxpython_dependencies()<br> File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 440, in build_wxpython_dependencies<br> self.build_wxpython_dependencies_linux()<br> File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 507, in build_wxpython_dependencies_linux<br> self.build_compiled_package_simple(pkg_name=pkg, pkg_name_label=name)<br> File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 385, in build_compiled_package_simple<br> log=pkg_log)<br> File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 203, in configure_and_build<br> self.call("./configure %s" % " ".join(list(config_args)), log=log)<br> File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 200, in call<br> return call(args, log=log)<br> File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/installer_utils.py", line 53, in call<br> raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc))<br>RuntimeError: Call to './configure --prefix="/usr/local/phenix-dev-1839/build/intel-linux-2.6-x86_64/base"' failed with exit code 1<br><br>max@A7K:/pgmax/phenix-installer-dev-1839$ uname -a<br>Linux A7K 3.13.0-40-generic #69-Ubuntu SMP Thu Nov 13 17:53:56 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux<br><br clear="all"><br>-- <br><div><div dir="ltr"><div><div>
<div>Dr. Maxime Cuypers<br></div>
<br></div></div></div></div>
</div></div>
</div>
</div></blockquote>
</div>
<br></div></div>
</blockquote>
</div></div></div>
<br><br clear="all"><span><font color="#888888"><br>-- <br><div><div dir="ltr"><div><div>
<div>Dr. Maxime Cuypers<br></div>
<br></div></div></div></div>
</font></span></div><span><font color="#888888">
</font></span></div><span><font color="#888888">
<u></u><config.log><u></u></font></span></blockquote></div><br><br></div></div>_______________________________________________<br>
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</blockquote></div><br><br clear="all"><br>-- <br><div class="gmail_signature"><div dir="ltr"><div><div><div>Dr. Maxime Cuypers<br></div>1, avenue des fauvettes<br></div>1341 Ceroux-Mousty<br></div>Belgique<br><div><div><div><br><div>fixed tel:<br>+32 10 61 36 69<br></div><div>Mobile phones: <br>Belgique: +32 499 23 09 42<br></div><div>USA: +1 208-589-6914<br></div></div></div></div></div></div>
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