Dear all,
I would like to try phenix.rosetta_refine and it is said in the online
tutorial that the phenix should be built from source code in linux. However
I ran into some errors, and I am too far from a linux export to figure it
out. I am using Debian Wheezy with kernel 3.2.0-4-amd64. I download the
source installer (phenix-installer-1.9-1683-source.tar) and run the
installer as:
# ./install --prefix=/usr/local/src --nproc=8 --no-gui (it seems from
README-DEV that there is no --python-shared flag as described in the online
tutorial)
After while, I receive the following error message:
*************************************************************************************************************************
Installing Imaging...
log file is
/workspace/setup/phenix-installer-1.9-1683/build-source/intel-linux-2.6-x86_64/cz-thinkpadw530-debian/tmp/Imaging_install_log
getting package Imaging-1.1.7.tar.gz...
using
/workspace/setup/phenix-installer-1.9-1683/base/Imaging-1.1.7.tar.gz
Traceback (most recent call last):
File
"/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install",
line 9, in <module>
install_cctbx_base.installer(args=sys.argv, log=sys.stdout)
File
"/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py",
line 95, in __init__
self.build_cctbx_dependencies()
File
"/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py",
line 134, in build_cctbx_dependencies
self.build_imaging()
File
"/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py",
line 349, in build_imaging
confirm_import_module="Image")
File
"/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py",
line 325, in build_python_module_simple
log=pkg_log)
File
"/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py",
line 150, in call
return call(args, log=log)
File
"/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/installer_utils.py",
line 51, in call
raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc))
RuntimeError: Call to
'/usr/local/src/phenix-1.9-1683/build/intel-linux-2.6-x86_64/base/bin/python
setup.py build ' failed with exit code 1
FATAL ERROR: aborting installation.
*************************************************************************************************************************
I looked into Imaging_install_log, and at the end, I have the following
errors:
*************************************************************************************************************************
/usr/bin/ld: /usr/local/lib/libpython2.7.a(abstract.o): relocation
R_X86_64_32S against `_Py_NotImplementedStruct' can not be used when making
a shared object; recompile with -fPIC
/usr/local/lib/libpython2.7.a: could not read symbols: Bad value
collect2: error: ld returned 1 exit status
error: command 'gcc' failed with exit status 1
***************************************************************************************************************************
Could anybody help me out?
Thank you so much,
Chen
