Re: [phenixbb] compiling phenix from source error

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. However, I think in this case it may be overkill, for two reasons: 1) If you don't plan on using the Phenix GUI, add "--no-gui" to the install arguments to skip this whole mess entirely. 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): cd "`libtbx.show_build_path`" libtbx.scons -j NUMBER_OF_PROCESSORS and it will compile only the part that changed. If this works I definitely recommend avoiding the source installer. On Mon, Dec 8, 2014 at 2:57 PM, wrote:

Hmm, this one is trickier. I will have to look at it closely. What distribution are you running?

Thanks, Ian

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On Mon, Dec 8, 2014 at 5:50 PM, Maxime Cuypers wrote:

...

Hi Ian,

thanks for your suggestion, i installed the x11 headers and it passed the problem. however, now it gets stuck on gtk+

the logfile claims that libxrender can not be found. strange since this library is now installed on my system. "checking for XRenderQueryExtension... no configure: error: *** libXrender not found. Check 'config.log' for more details."

config.log enclosed from dir .../gtk+-2.10.11/

any idea? thanks

Installing gtk+... log file is /pgmax/phenix-installer-dev-1839/install_tmp/intel-linux-2.6-x86_64/A7K/gtk+_install_log getting package gtk+-2.10.11.tar.gz... using /pgmax/phenix-installer-dev-1839/gui/gtk+-2.10.11.tar.gz Traceback (most recent call last): File "./bin/install.py", line 815, in <module> run(sys.argv[1:]) File "./bin/install.py", line 72, in __init__ self.install_from_source() File "./bin/install.py", line 292, in install_from_source log=out) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 115, in __init__ self.build_cctbx_dependencies() File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 170, in build_cctbx_dependencies self.build_wxpython_dependencies() File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 440, in build_wxpython_dependencies self.build_wxpython_dependencies_linux() File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 541, in build_wxpython_dependencies_linux self.call("./configure %s" % " ".join(gtk_config_args), log=gtk_log) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 200, in call return call(args, log=log) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/installer_utils.py", line 53, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) 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

2014-12-08 22:32 GMT+01:00 :

Xrender can fail for many reasons, but generally missing X11 libraries or

...

headers on your system. Can you send the log file:

/pgmax/phenix-installer-dev-1839/install_tmp/intel-linux-2.6-x86_64/A7K/Xrender_install_log

Thanks, Ian

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On Mon, Dec 8, 2014 at 4:30 PM, Maxime Cuypers wrote:

...

hi all, 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.

any idea on how to debug? -see below report...

PS: am compiling from source because i need a minor modification of the neutron scattering table which requires compilation.

cheerios,

.... Installing Xrender... log file is /pgmax/phenix-installer-dev-1839/install_tmp/intel-linux-2.6-x86_64/A7K/Xrender_install_log getting package xrender-0.8.3.tar.gz... using /pgmax/phenix-installer-dev-1839/gui/xrender-0.8.3.tar.gz Traceback (most recent call last): File "./bin/install.py", line 815, in <module> run(sys.argv[1:]) File "./bin/install.py", line 72, in __init__ self.install_from_source() File "./bin/install.py", line 292, in install_from_source log=out) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 115, in __init__ self.build_cctbx_dependencies() File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 170, in build_cctbx_dependencies self.build_wxpython_dependencies() File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 440, in build_wxpython_dependencies self.build_wxpython_dependencies_linux() File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 507, in build_wxpython_dependencies_linux self.build_compiled_package_simple(pkg_name=pkg, pkg_name_label=name) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 385, in build_compiled_package_simple log=pkg_log) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 203, in configure_and_build self.call("./configure %s" % " ".join(list(config_args)), log=log) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/install_base_packages.py", line 200, in call return call(args, log=log) File "/pgmax/phenix-installer-dev-1839/lib/libtbx/auto_build/installer_utils.py", line 53, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to './configure --prefix="/usr/local/phenix-dev-1839/build/intel-linux-2.6-x86_64/base"' failed with exit code 1

max@A7K:/pgmax/phenix-installer-dev-1839$ uname -a 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

-- Dr. Maxime Cuypers

-- Dr. Maxime Cuypers

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