Hello, I did what you recommended, and Phaser did compile. I got a slew of other errors output, though; errors in EditString.C, hardcopy_ctrl.c, xloggraph.c, log_file.c, and some others, all concerning graphical elements, I think. Hopefully they are innocuous. What I see is ccp4i starting and running fine, so that makes me happy.
Thanks, Nate ----- Nathan Nicely, Ph.D. Research Scientist Duke Human Vaccine Institute 106 Research Drive MSRB II, Room 3016-1 DUMC Box 103020 Durham, NC 27710 [EMAIL PROTECTED] (919) 681-3917 "Meyer, Peter" <[EMAIL PROTECTED]> 05/16/2008 11:56 AM To "Nathan I Nicely" <[EMAIL PROTECTED]>, <[email protected]> cc Subject RE: [ccp4bb] Phaser compile errors It looks like you need to install python2.4 (and python2.4-dev if using the package manager) and use that as the default during the build (remove /usr/bin/python and symlink it to python2.4 instead of /usr/bin/python2.5 ; after compiling phaser you can change it back). Pete -----Original Message----- From: CCP4 bulletin board on behalf of Nathan I Nicely Sent: Fri 5/16/2008 7:54 AM To: [email protected] Subject: [ccp4bb] Phaser compile errors I'm installing CCP4 and Phaser/CCTBX on a 64 bit machine (4 intel xeon cpus) running Ubuntu 8.04 with the 2.6.24-16-generic kernel (this linux was downloaded and installed just last week). I followed the instructions (untar ccp4*.tgz, untar phaser*.tgz, edit ccp4.setup, source ccp4.setup, configure, make, make install), and CCP4 seems to have installed just fine but for Phaser. I don't know enough about the compiler errors I'm seeing to make a guess as to which parts matter the most, so I'll past the whole Phaser part of it below. Thanks, Nate Nicely if test -n "src/phaser"; then cd /usr/local/ccp4-6.0.2/src/phaser; \ ./ccp4_build ""; else true; fi Building static phaser executable ========================================================================== PHASER Installation version: 1.3.2 machine type: intel-linux OS version: linux compiler: native destination: /usr/local/ccp4-6.0.2/src/phaser ========================================================================== ========================================================================== Installing from source files ========================================================================== source root directory: /usr/local/ccp4-6.0.2/src/phaser PHASER installation source directory set to: /usr/local/ccp4-6.0.2/src/phaser PHASER installation target directory <PHASER_LOC> set to: /usr/local/ccp4-6.0.2/src/phaser/phaser-1.3.2 PHASER installation build directory set to: <PHASER_LOC>/build/intel-linux PHASER temporary build directory set to: build-source/intel-linux/dhvixtal1/tmp PHASER installation log directory set to: build-source/intel-linux/dhvixtal1/log checking cctbx sources checking phaser sources checking for compiled PHASER components configuring components with optimization Python: 2.5.2 "/usr/bin/python" Compiler: default Build mode: release Static libraries: True Static exe: False Scan Boost headers: False command_version_suffix: 6.0 Top-down list of all modules involved: mmtbx /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/mmtbx iotbx /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/iotbx PyCifRW /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/PyCifRW phaser /usr/local/ccp4-6.0.2/src/phaser/source/phaser cctbx /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/cctbx scitbx /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/scitbx boost+adaptbx /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/boost /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/boost_adaptbx chiltbx /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/chiltbx ccp4io+adaptbx /usr/local/ccp4-6.0.2 /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/ccp4io_adaptbx libtbx /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/libtbx Creating files in build directory: "/usr/local/ccp4-6.0.2/src/phaser/phaser-1.3.2/build/intel-linux" setpaths.sh setpaths.csh setpaths_all.sh setpaths_all.csh setpaths_debug.sh unsetpaths.sh setpaths_debug.csh unsetpaths.csh SConstruct run_tests.csh Processing: "/usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/libtbx/libtbx/command_line" Processing: "/usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/boost_adaptbx/boost/command_line" Processing: "/usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/cctbx/cctbx/command_line" Processing: "/usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/PyCifRW/command_line" Processing: "/usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/iotbx/iotbx/command_line" Processing: "/usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/mmtbx/mmtbx/command_line" Processing: "/usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/scitbx/libtbx_refresh.py" Generating C++ header files in: "/usr/local/ccp4-6.0.2/src/phaser/phaser-1.3.2/build/intel-linux/include/scitbx/array_family" Processing: "/usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/cctbx/libtbx_refresh.py" Generating C++ files in: "/usr/local/ccp4-6.0.2/src/phaser/phaser-1.3.2/build/intel-linux/cctbx/eltbx" setting up environment compiling PHASER components - this might take an hour scons: Reading SConscript files ... libtbx.scons: implicit dependency scan disabled for directory /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/boost Compiling distributed version of phaser scons: done reading SConscript files. scons: Building targets ... g++ -o boost/libs/python/src/object_protocol.o -c -fPIC -ftemplate-depth-120 -w -DBOOST_DISABLE_THREADS -DNDEBUG -O3 -ffast-math -DBOOST_PYTHON_MAX_BASES=2 -DBOOST_PYTHON_SOURCE -I/usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/boost -I/usr/include/python2.5 /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/boost/libs/python/src/object_protocol.cpp /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/boost/libs/python/src/object_protocol.cpp: In function 'PyObject* boost::python::api::<unnamed>::apply_slice(PyObject*, PyObject*, PyObject*)': /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/boost/libs/python/src/object_protocol.cpp:110: error: cannot convert 'int*' to 'Py_ssize_t*' for argument '2' to 'int _PyEval_SliceIndex(PyObject*, Py_ssize_t*)' /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/boost/libs/python/src/object_protocol.cpp:112: error: cannot convert 'int*' to 'Py_ssize_t*' for argument '2' to 'int _PyEval_SliceIndex(PyObject*, Py_ssize_t*)' /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/boost/libs/python/src/object_protocol.cpp: In function 'int boost::python::api::<unnamed>::assign_slice(PyObject*, PyObject*, PyObject*, PyObject*)': /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/boost/libs/python/src/object_protocol.cpp:137: error: cannot convert 'int*' to 'Py_ssize_t*' for argument '2' to 'int _PyEval_SliceIndex(PyObject*, Py_ssize_t*)' /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/boost/libs/python/src/object_protocol.cpp:139: error: cannot convert 'int*' to 'Py_ssize_t*' for argument '2' to 'int _PyEval_SliceIndex(PyObject*, Py_ssize_t*)' scons: *** [boost/libs/python/src/object_protocol.o] Error 1 scons: building terminated because of errors. usr+sys time: 0.56 seconds wall clock time: 1.30 seconds compilation of PHASER components failed ========================================================================== Phaser executable installed in /usr/local/ccp4-6.0.2/bin cctbx library installed in /usr/local/ccp4-6.0.2/lib cctbx include files installed in /usr/local/ccp4-6.0.2/include ========================================================================== Building phaser Python bindings ========================================================================== PHASER Installation version: 1.3.2 machine type: intel-linux OS version: linux compiler: native destination: /usr/local/ccp4-6.0.2/src/phaser ========================================================================== ========================================================================== Installing from source files ========================================================================== source root directory: /usr/local/ccp4-6.0.2/src/phaser PHASER installation source directory set to: /usr/local/ccp4-6.0.2/src/phaser PHASER installation target directory <PHASER_LOC> set to: /usr/local/ccp4-6.0.2/src/phaser/phaser-1.3.2 PHASER installation build directory set to: <PHASER_LOC>/build/intel-linux PHASER temporary build directory set to: build-source/intel-linux/dhvixtal1/tmp PHASER installation log directory set to: build-source/intel-linux/dhvixtal1/log checking cctbx sources checking phaser sources checking for compiled PHASER components configuring components with optimization Python: 2.5.2 "/usr/bin/python" Compiler: default Build mode: release Static libraries: False Static exe: False Scan Boost headers: False command_version_suffix: 6.0 Top-down list of all modules involved: mmtbx /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/mmtbx iotbx /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/iotbx PyCifRW /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/PyCifRW phaser /usr/local/ccp4-6.0.2/src/phaser/source/phaser cctbx /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/cctbx scitbx /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/scitbx boost+adaptbx /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/boost /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/boost_adaptbx chiltbx /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/chiltbx ccp4io+adaptbx /usr/local/ccp4-6.0.2 /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/ccp4io_adaptbx libtbx /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/libtbx Creating files in build directory: "/usr/local/ccp4-6.0.2/src/phaser/phaser-1.3.2/build/intel-linux" setpaths.sh setpaths.csh setpaths_all.sh setpaths_all.csh setpaths_debug.sh unsetpaths.sh setpaths_debug.csh unsetpaths.csh SConstruct run_tests.csh Processing: "/usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/libtbx/libtbx/command_line" Processing: "/usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/boost_adaptbx/boost/command_line" Processing: "/usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/cctbx/cctbx/command_line" Processing: "/usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/PyCifRW/command_line" Processing: "/usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/iotbx/iotbx/command_line" Processing: "/usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/mmtbx/mmtbx/command_line" Processing: "/usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/scitbx/libtbx_refresh.py" Generating C++ header files in: "/usr/local/ccp4-6.0.2/src/phaser/phaser-1.3.2/build/intel-linux/include/scitbx/array_family" Processing: "/usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/cctbx/libtbx_refresh.py" Generating C++ files in: "/usr/local/ccp4-6.0.2/src/phaser/phaser-1.3.2/build/intel-linux/cctbx/eltbx" setting up environment compiling PHASER components - this might take an hour scons: Reading SConscript files ... libtbx.scons: implicit dependency scan disabled for directory /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/boost Compiling distributed version of phaser scons: done reading SConscript files. scons: Building targets ... g++ -o boost/libs/python/src/object_protocol.o -c -fPIC -ftemplate-depth-120 -w -DBOOST_DISABLE_THREADS -DNDEBUG -O3 -ffast-math -DBOOST_PYTHON_MAX_BASES=2 -DBOOST_PYTHON_SOURCE -I/usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/boost -I/usr/include/python2.5 /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/boost/libs/python/src/object_protocol.cpp /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/boost/libs/python/src/object_protocol.cpp: In function 'PyObject* boost::python::api::<unnamed>::apply_slice(PyObject*, PyObject*, PyObject*)': /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/boost/libs/python/src/object_protocol.cpp:110: error: cannot convert 'int*' to 'Py_ssize_t*' for argument '2' to 'int _PyEval_SliceIndex(PyObject*, Py_ssize_t*)' /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/boost/libs/python/src/object_protocol.cpp:112: error: cannot convert 'int*' to 'Py_ssize_t*' for argument '2' to 'int _PyEval_SliceIndex(PyObject*, Py_ssize_t*)' /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/boost/libs/python/src/object_protocol.cpp: In function 'int boost::python::api::<unnamed>::assign_slice(PyObject*, PyObject*, PyObject*, PyObject*)': /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/boost/libs/python/src/object_protocol.cpp:137: error: cannot convert 'int*' to 'Py_ssize_t*' for argument '2' to 'int _PyEval_SliceIndex(PyObject*, Py_ssize_t*)' /usr/local/ccp4-6.0.2/lib/cctbx/cctbx_sources/boost/libs/python/src/object_protocol.cpp:139: error: cannot convert 'int*' to 'Py_ssize_t*' for argument '2' to 'int _PyEval_SliceIndex(PyObject*, Py_ssize_t*)' scons: *** [boost/libs/python/src/object_protocol.o] Error 1 scons: building terminated because of errors. usr+sys time: 0.56 seconds wall clock time: 1.31 seconds compilation of PHASER components failed ========================================================================== To get the full phaser/cctbx environment source the file /usr/local/ccp4-6.0.2/src/phaser/phaser-1.3.2/build/intel-linux/setpaths.sh or /usr/local/ccp4-6.0.2/src/phaser/phaser-1.3.2/build/intel-linux/setpaths.csh ========================================================================== ----- Nathan Nicely, Ph.D. Research Scientist Duke Human Vaccine Institute 106 Research Drive MSRB II, Room 3016-1 DUMC Box 103020 Durham, NC 27710 [EMAIL PROTECTED] (919) 681-3917
