[phenixbb] compiling phenix from source error

Nathaniel Echols nechols at lbl.gov
Mon Dec 8 15:07:51 PST 2014 

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, <irees at lbl.gov> wrote:

> Hmm, this one is trickier. I will have to look at it closely. What
> distribution are you running?
>
> Thanks,
> Ian
>
> —
> Sent from Mailbox <https://www.dropbox.com/mailbox>
>
>
> On Mon, Dec 8, 2014 at 5:50 PM, Maxime Cuypers <maximecuypers at gmail.com>
> 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 <irees at lbl.gov>:
>>
>> 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
>>>
>>> —
>>> Sent from Mailbox <https://www.dropbox.com/mailbox>
>>>
>>>
>>> On Mon, Dec 8, 2014 at 4:30 PM, Maxime Cuypers <maximecuypers at gmail.com>
>>> 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 at 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
>>
>>  <config.log>
>
>
>
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