when compiling IMP 2.2.0 (on CentOS 5), `make` exits with the following
errors:
imp-2.2.0 > make
Scanning dependencies of target IMP-containers
[ 0%] Built target IMP-containers
Scanning dependencies of target IMP-version
[ 0%] Computing version number
[ 0%] Built target IMP-version
Scanning dependencies of target IMP.base-version
[ 0%] Building module version info
[ 0%] Built target IMP.base-version
Scanning dependencies of target IMP.base-all-header
[ 0%] Built target IMP.base-all-header
Scanning dependencies of target IMP.base-lib
[ 0%] Building CXX object
modules/base/src/CMakeFiles/IMP.base-lib.dir/__/__/__/src/base/paths.cpp.o
[ 0%] Building CXX object
modules/base/src/CMakeFiles/IMP.base-lib.dir/__/__/__/src/base_all.cpp.o
/g/software/linux/pack/imp-2.2.0/SRC/imp-2.2.0/modules/base/src/statistics.cpp:
In function 'void IMP::base::show_timings(IMP::base::TextOutput)':
/g/software/linux/pack/imp-2.2.0/SRC/imp-2.2.0/modules/base/src/statistics.cpp:31:
error: a function-definition is not allowed here before ':' token
/g/software/linux/pack/imp-2.2.0/SRC/imp-2.2.0/modules/base/src/utility.cpp:36:
error: expected primary-expression at end of input
/g/software/linux/pack/imp-2.2.0/SRC/imp-2.2.0/modules/base/src/utility.cpp:36:
error: expected `;' at end of input
/g/software/linux/pack/imp-2.2.0/SRC/imp-2.2.0/modules/base/src/utility.cpp:36:
error: expected primary-expression at end of input
/g/software/linux/pack/imp-2.2.0/SRC/imp-2.2.0/modules/base/src/utility.cpp:36:
error: expected `)' at end of input
/g/software/linux/pack/imp-2.2.0/SRC/imp-2.2.0/modules/base/src/utility.cpp:36:
error: expected statement at end of input
/g/software/linux/pack/imp-2.2.0/SRC/imp-2.2.0/modules/base/src/utility.cpp:36:
error: expected `}' at end of input
/g/software/linux/pack/imp-2.2.0/SRC/imp-2.2.0/modules/base/src/utility.cpp:
At global scope:
/g/software/linux/pack/imp-2.2.0/SRC/imp-2.2.0/modules/base/src/utility.cpp:36:
error: expected `}' at end of input
/g/software/linux/pack/imp-2.2.0/SRC/imp-2.2.0/modules/base/src/utility.cpp:36:
error: expected `}' at end of input
make[2]: ***
[modules/base/src/CMakeFiles/IMP.base-lib.dir/__/__/__/src/base_all.cpp.o]
Error 1
-- The C compiler identification is GNU 4.1.2
-- The CXX compiler identification is GNU 4.1.2
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Running check_common_problems
-- Running clean_build_dir
-- Running setup_cmake
-- GCC version: 4.1.2
-- GCC version: 4.1.2
Traceback (most recent call last):
File "<string>", line 1, in ?
ImportError: No module named etree.ElementTree
-- Python xml.etree not found, docs disabled.
-- Python version is 2.4
-- Found PythonLibs: /usr/lib64/libpython2.4.so (found suitable exact
version "2.4.3")
-- Running setup
-- Running setup_all
-- Running making containers
-- Running setup_module_alias for compatibility
-- Setting up alias for module base as compatibility
-- Running setup_module_alias for kernel
-- Setting up alias for module kernel as
-- Boost version: 1.46.0
-- Found the following Boost libraries:
-- system
-- filesystem
-- thread
-- program_options
-- Performing Test IMP_COMPILER_HAS_AUTO
-- Performing Test IMP_COMPILER_HAS_AUTO - Failed
-- Performing Test IMP_COMPILER_HAS_DEBUG_VECTOR
-- Performing Test IMP_COMPILER_HAS_DEBUG_VECTOR - Success
GPerfTools not found
Log4CXX not found
TCMalloc_HeapChecker not found
TCMalloc_HeapProfiler not found
-- Running generate paths.cpp
Configuring module base ... yes
-- Running setup_swig_wrappers base
-- Running IMP.base making all header
-- Updating /g/software/linux/pack/imp-2.2.0/SRC/build/include/IMP/base.h
Configuring module benchmark ... yes
-- Running setup_swig_wrappers benchmark
-- Running IMP.benchmark making all header
-- Updating
/g/software/linux/pack/imp-2.2.0/SRC/build/include/IMP/benchmark.h
-- CGAL not found. Set the CGAL_DIR cmake variable or environment
variable to the directory containing CGALConfig.cmake. This is either
the binary directory where CGAL was configured or PREFIX/lib/CGAL for an
installation.
Configuring module cgal ... CGAL not found
Different data/build_info/sorted_modules
-cgal
Module IMP.cgal disabled
Configuring module kmeans ... yes
-- Running setup_swig_wrappers kmeans
-- Running IMP.kmeans making all header
-- Updating /g/software/linux/pack/imp-2.2.0/SRC/build/include/IMP/kmeans.h
Configuring module module_template ... yes
-- Running setup_swig_wrappers module_template
-- Running IMP.module_template making all header
Configuring module misc ... yes
-- Running setup_swig_wrappers misc
-- Running IMP.misc making all header
-- Updating /g/software/linux/pack/imp-2.2.0/SRC/build/include/IMP/misc.h
-- Performing Test RMF_environment
-- Performing Test RMF_environment - Failed
-- Building internal RMF
-- Boost version: 1.46.0
-- Found the following Boost libraries:
-- system
-- filesystem
-- thread
-- program_options
-- iostreams
-- Found HDF5:
/g/software/linux/pack/hdf5-1.8.4/lib/libhdf5.so;/g/software/linux/pack/hdf5-1.8.4/lib/libhdf5.so;/g/software/linux/pack/hdf5-1.8.4/lib/libhdf5.so;/g/software/linux/pack/szlib-2.1/lib/libsz.so;/usr/lib64/libz.so;/usr/lib64/libm.so
-- Deprecated backends (and hdf5) are enabled
-- GCC version: 4.1.2
-- GCC version: 4.1.2
-- Running Making RMF/HDF5.h