[phenixbb] compiling phenix from source error
Maxime Cuypers
maximecuypers at gmail.com
Mon Dec 8 15:39:44 PST 2014
hi Nathaniel,
2-
i just need to modify a file in :
cctbx_project/cctbx/eltbx/neutron.cpp
can you be more explicit on what i need to do to recompile from the binary
package to take change into account please?
"
cd "`libtbx.show_build_path`"
libtbx.scons -j NUMBER_OF_PROCESSORS
"
thanks in advance,
cheerios,
-------
1- i tried the no-gui option and it gave the following error:
----------
Dependencies finished building.
******************************
* BASE INSTALLATION COMPLETE *
******************************
--------------------------------------------------------------------------------
Building core Phenix components
unwrapping cctbx_bundle.tar.gz...
unwrapping phenix.tar.gz...
unwrapping solve_resolve.tar.gz...
unwrapping elbow.tar.gz...
unwrapping reel.tar.gz...
unwrapping labelit.tar.gz...
unwrapping annlib.tar.gz...
unwrapping annlib_adaptbx.tar.gz...
unwrapping Plex.tar.gz...
unwrapping PyQuante.tar.gz...
unwrapping pulchra.tar.gz...
unwrapping ksdssp.tar.gz...
unwrapping muscle.tar.gz...
unwrapping Durandal.tar.gz...
unwrapping phaser.tar.gz...
unwrapping reduce.tar.gz...
unwrapping probe.tar.gz...
unwrapping king.tar.gz...
unwrapping suitename.tar.gz...
configuring PHENIX components with optimization...
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 352, in install_from_source
call([python_bin, config_path] + config_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
'/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
max at A7K:/pgmax/phenix-installer-dev-1839$
2014-12-09 0:07 GMT+01:00 Nathaniel Echols <nechols at lbl.gov>:
> 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>
>>
>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>
>>
>
--
Dr. Maxime Cuypers
1, avenue des fauvettes
1341 Ceroux-Mousty
Belgique
fixed tel:
+32 10 61 36 69
Mobile phones:
Belgique: +32 499 23 09 42
USA: +1 208-589-6914
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