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Hello,<BR>
<BR>
I am getting install errors with several phenix installations after upgrading to CentOS 6.<BR>
<BR>
<B>I started with the nightly-build</B><BR>
<TT>==========================================================================</TT><BR>
<TT> PHENIX Installation</TT><BR>
<BR>
<TT> version: dev</TT><BR>
<TT> release tag: 1807</TT><BR>
<TT> machine type: intel-linux-2.6-x86_64</TT><BR>
<TT> OS version: 2.6.32-431.29.2.el6.x86_64</TT><BR>
<TT> user shell: /bin/tcsh</TT><BR>
<TT> destination: /usr/local</TT><BR>
<TT> =========================================================================</TT><BR>
<TT> </TT><BR>
<TT>Warning: /usr/local/phenix-dev-1807 already exists, will be overwritten</TT><BR>
<TT>removing existing temporary directory... ok</TT><BR>
<TT>finding existing installations...</TT><BR>
<TT>Removing out-of-date lib directory... ok</TT><BR>
<TT>Removing out-of-date base software directory... ok</TT><BR>
<TT>Installing new binary package... ok</TT><BR>
<TT>Configuring PHENIX components... </TT><BR>
<TT>********************************************************************************</TT><BR>
<TT>configuration step incomplete! See the log file for detailed error messages.</TT><BR>
<TT>********************************************************************************</TT><BR>
<BR>
The log contains only a list of files ending with (./docutils/._MANIFEST.in) and no error messages.<BR>
<BR>
<BR>
<BR>
<B>Then I went back to the latest stable version</B>, which was installed on my server when it ran CentOS 5. Both my server and WS now produce the same error (CentOS 6).<BR>
<BR>
<TT>==========================================================================</TT><BR>
<TT> PHENIX Installation</TT><BR>
<BR>
<TT> version: 1.9</TT><BR>
<TT> release tag: 1692</TT><BR>
<TT> machine type: intel-linux-2.6-x86_64</TT><BR>
<TT> source machine type: intel-linux-2.6-x86_64</TT><BR>
<TT> OS version: redhat-e6.5</TT><BR>
<TT> user shell: /bin/tcsh</TT><BR>
<TT> destination: /usr/local</TT><BR>
<TT>=========================================================================</TT><BR>
<BR>
<TT>==========================================================================</TT><BR>
<TT> Installing from binary bundle</TT><BR>
<TT>==========================================================================</TT><BR>
<BR>
<TT>bundle file:</TT><BR>
<TT> bundle-1.9-1692-intel-linux-2.6-x86_64.tar.gz</TT><BR>
<TT>PHENIX installation source directory set to: </TT><BR>
<TT> /home/white/downloads/phenix-installer-1.9-1692</TT><BR>
<TT>PHENIX installation target directory <PHENIX_LOC > set to: </TT><BR>
<TT> /usr/local/phenix-1.9-1692</TT><BR>
<TT>PHENIX installation build directory set to: </TT><BR>
<TT> <PHENIX_LOC > /build/intel-linux-2.6-x86_64</TT><BR>
<TT>PHENIX temporary build directory set to: </TT><BR>
<TT> build-binary/intel-linux-2.6-x86_64/marvin/tmp</TT><BR>
<TT>PHENIX installation log directory set to: </TT><BR>
<TT> build-binary/intel-linux-2.6-x86_64/marvin/log</TT><BR>
<BR>
<TT>==== warning: "/usr/local/phenix-1.9-1692" already exists ====</TT><BR>
<TT>==== warning: cannot determine installation time-stamp, proceeding ====</TT><BR>
<BR>
<BR>
<TT>installing binary components</TT><BR>
<BR>
<TT>removing existing files in build-binary/intel-linux-2.6-x86_64/marvin/tmp/binary</TT><BR>
<TT>finding installed versions</TT><BR>
<TT>finding binary versions</TT><BR>
<TT>binary components up-to-date</TT><BR>
<TT>the binary package will not be installed</TT><BR>
<BR>
<TT>setting environment</TT><BR>
<BR>
<TT>configuring PHENIX components</TT><BR>
<BR>
<TT>/home/white/downloads/phenix-installer-1.9-1692/bin/install-from-binary: line 361: 19688 Segmentation fault $PHENIX_BUILD/base/bin/python $PHENIX_LOC/cctbx_project/libtbx/configure.py --current_working_directory="$PHENIX_BUILD" $PHENIX_COMPONENTS $CONFIG_OPTS >> $PHENIX_LOG/binary.log 2>&1</TT><BR>
<TT>Error configuring: see /home/white/downloads/phenix-installer-1.9-1692/build-binary/intel-linux-2.6-x86_64/marvin/log/binary.log for details</TT><BR>
<BR>
The log contains only a list of files ending with (./docutils/._MANIFEST.in) and no error messages.<BR>
<BR>
<BR>
<BR>
<B>Then I tried installing phenix-dev-1810 from source:</B><BR>
<BR>
<TT>Installing cairo...</TT><BR>
<TT> log file is /home/white/downloads/phenix-installer-dev-1810/install_tmp/intel-linux-2.6-x86_64/marvin/cairo_install_log</TT><BR>
<TT> getting package cairo-1.8.10.tar.gz...</TT><BR>
<TT> using /home/white/downloads/phenix-installer-dev-1810/gui/cairo-1.8.10.tar.gz</TT><BR>
<TT>Traceback (most recent call last):</TT><BR>
<TT> File "./bin/install.py", line 815, in <module></TT><BR>
<TT> run(sys.argv[1:])</TT><BR>
<TT> File "./bin/install.py", line 72, in __init__</TT><BR>
<TT> self.install_from_source()</TT><BR>
<TT> File "./bin/install.py", line 292, in install_from_source</TT><BR>
<TT> log=out)</TT><BR>
<TT> File "/home/white/downloads/phenix-installer-dev-1810/lib/libtbx/auto_build/install_base_packages.py", line 113, in __init__</TT><BR>
<TT> self.build_cctbx_dependencies()</TT><BR>
<TT> File "/home/white/downloads/phenix-installer-dev-1810/lib/libtbx/auto_build/install_base_packages.py", line 168, in build_cctbx_dependencies</TT><BR>
<TT> self.build_wxpython_dependencies()</TT><BR>
<TT> File "/home/white/downloads/phenix-installer-dev-1810/lib/libtbx/auto_build/install_base_packages.py", line 425, in build_wxpython_dependencies</TT><BR>
<TT> self.build_wxpython_dependencies_linux()</TT><BR>
<TT> File "/home/white/downloads/phenix-installer-dev-1810/lib/libtbx/auto_build/install_base_packages.py", line 504, in build_wxpython_dependencies_linux</TT><BR>
<TT> self.build_compiled_package_simple(pkg_name=pkg, pkg_name_label=name)</TT><BR>
<TT> File "/home/white/downloads/phenix-installer-dev-1810/lib/libtbx/auto_build/install_base_packages.py", line 377, in build_compiled_package_simple</TT><BR>
<TT> log=pkg_log)</TT><BR>
<TT> File "/home/white/downloads/phenix-installer-dev-1810/lib/libtbx/auto_build/install_base_packages.py", line 196, in configure_and_build</TT><BR>
<TT> self.call("make -j %d %s" % (self.nproc, " ".join(list(make_args))), log=log)</TT><BR>
<TT> File "/home/white/downloads/phenix-installer-dev-1810/lib/libtbx/auto_build/install_base_packages.py", line 192, in call</TT><BR>
<TT> return call(args, log=log)</TT><BR>
<TT> File "/home/white/downloads/phenix-installer-dev-1810/lib/libtbx/auto_build/installer_utils.py", line 53, in call</TT><BR>
<TT> raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc))</TT><BR>
<TT>RuntimeError: Call to 'make -j 8 ' failed with exit code 2</TT><BR>
<BR>
<BR>
I would like to install the latest developmental version. Any idea what could be going wrong? I have the latest updates installed.<BR>
<BLOCKQUOTE>
<BR>
</BLOCKQUOTE>
<BR>
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-- <BR>
Yours sincerely, <BR>
<BR>
Mark A. White, Ph.D. <BR>
Associate Professor of Biochemistry and Molecular Biology, <BR>
Manager, Sealy Center for Structural Biology and Molecular Biophysics <BR>
Macromolecular X-ray Laboratory, <BR>
Basic Science Building, Room 6.630 <BR>
University of Texas Medical Branch <BR>
Galveston, TX 77555-0647 <BR>
Tel. (409) 747-4747 <BR>
Fax. (409) 747-1404 <BR>
mailto://mawhite@utmb.edu <BR>
http://xray.utmb.edu <BR>
<BR>
QQ: "Life is no brief candle to me. It is a sort of splendid torch which I have got a hold of for the moment, and I want to make it burn as brightly as possible before handing it on to future generations. " <BR>
- George Bernard Shaw
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