Re: [ccp4bb] Phaser compile errors

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CCP4bb <-- 2008 <-- May 2008 <-- 16 May 2008

Previous message:
Subject: Re: UV light source for protein xtal detection
From: Robert Sweet sweet {- at -} BNL {- dot -} GOV
Date: 2008-05-16

Next message:
Subject: Re: poll: cutoff for "high resolution"
From: James Holton JMHolton {- at -} LBL {- dot -} GOV
Date: 2008-05-16

Subject: Re: Phaser compile errors
From: "Meyer, Peter" pameyer {- at -} MCW {- dot -} EDU
Date: 2008-05-16

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: CCP4BB@JISCMAIL.AC.UK
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 set to:
/usr/local/ccp4-6.0.2/src/phaser/phaser-1.3.2
PHASER installation build directory set to:
/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::::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::::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 set to:
/usr/local/ccp4-6.0.2/src/phaser/phaser-1.3.2
PHASER installation build directory set to:
/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::::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::::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
nathan.nicely@duke.edu
(919) 681-3917

CCP4bb navigation

CCP4bb <-- 2008 <-- May 2008 <-- 16 May 2008

Previous message:
Subject: Re: UV light source for protein xtal detection
From: Robert Sweet sweet {- at -} BNL {- dot -} GOV
Date: 2008-05-16

Next message:
Subject: Re: poll: cutoff for "high resolution"
From: James Holton JMHolton {- at -} LBL {- dot -} GOV
Date: 2008-05-16