Re: [Pcsim-users] problems of installing PCSim (Pecevski Dejan)

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Hi Dejan,
Thanks for your reply. I followed your advice and there are still some
errors. When i run  ---$ sudo python build.py -j 2 wipe, it seems ok.
however when i run  ---sudo python build.py -j 2 install, errors occur
again:
the bash said:

>>>> cd /home/hou/pcsim/pcsim-0.5.4/_build
>>>> cmake -D CMAKE_BUILD_TYPE:STRING=Release -D CMAKE_INSTALL_PREFIX:PATH=/home/hou/pcsim/pcsim-0.5.4 -D PYPCSIM_INSTALL_DIR:PATH=. -D PCSIM_INSTALL_DIR:PATH=. -D EXTRA_INSTALL:STRING=NO /home/hou/pcsim/pcsim-0.5.4
-- The C compiler identification is GNU
-- The CXX compiler identification is GNU
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- 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
   Build type   = Release
   Platform     = linux-i686
   Make tool    = /usr/bin/make
   Make command = /usr/bin/make -i
-- Looking for python executable ...
-- Found PythonInterp: /usr/bin/python
   Python executable : /usr/bin/python version 2.6
-- Looking for python libraries ...
   Python libraries : /usr/lib/python2.6/config
   Python includes : /usr/include/python2.6
-- Looking for doxygen executable ...
   Doxygen executable : /usr/bin/doxygen
-- Looking for GCCXML executable ...
   GCCXML executable : /usr/bin/gccxml
BOOST_LIB_SUFFIX IS gcc-mt
BOOST_LIB_SUFFIX_2 IS gcc41-mt
-- Looking for Boost C++ libraries ... - toolset    = gcc
-- Looking for Boost C++ libraries ... - lib suffixes = gcc-mt gcc41-mt
   Boost C++ library boost_python : /usr/local/lib/libboost_python-gcc41-mt.so
   Boost C++ library boost_thread : /usr/local/lib/libboost_thread-gcc41-mt.so
   Boost C++ library boost_date_time :
/usr/local/lib/libboost_date_time-gcc41-mt.so
   Boost C++ libraries : /usr/local/lib
   Boost C++ include path : /usr/local/include/boost-1_34_1
-- Looking for MPICH2 ...
   MPICH2 library: /usr/local/lib/libmpich.so
   MPICH2 include path : /usr/local/include
-- Looking for GNU Scientific library ...
   GNU Scientific library : /usr/local/lib/libgsl.so
-- Looking for Xerces-C library ...
   Xerces library : /usr/lib/libxerces-c.so
-- Looking for CppUnit ...
   CppUnit : /usr/local/lib/libcppunit.so
   JNI headers : /usr/lib/jvm/java-6-openjdk/include
-- Checking to see if CXX compiler accepts flag -pthread
-- Checking to see if CXX compiler accepts flag -pthread - yes
-- Configuring done
-- Generating done
-- Build files have been written to: /home/hou/pcsim/pcsim-0.5.4/_build
>>>> cd /home/hou/pcsim/pcsim-0.5.4/_build
>>>> /usr/bin/make -j 2 rebuild_cache
Running CMake to regenerate build system...
   Build type   = Release
   Platform     = linux-i686
   Make tool    = /usr/bin/make
   Make command = /usr/bin/make -i
   Python executable : /usr/bin/python version 2.6
   Python libraries : /usr/lib/python2.6/config
   Python includes : /usr/include/python2.6
   Doxygen executable : /usr/bin/doxygen
   GCCXML executable : /usr/bin/gccxml
BOOST_LIB_SUFFIX IS gcc-mt
BOOST_LIB_SUFFIX_2 IS gcc41-mt
   Boost C++ library boost_python : /usr/local/lib/libboost_python-gcc41-mt.so
   Boost C++ library boost_thread : /usr/local/lib/libboost_thread-gcc41-mt.so
   Boost C++ library boost_date_time :
/usr/local/lib/libboost_date_time-gcc41-mt.so
   Boost C++ libraries : /usr/local/lib
   Boost C++ include path : /usr/local/include/boost-1_34_1
   MPICH2 library: /usr/local/lib/libmpich.so
   MPICH2 include path : /usr/local/include
   GNU Scientific library : /usr/local/lib/libgsl.so
   Xerces library : /usr/lib/libxerces-c.so
   CppUnit : /usr/local/lib/libcppunit.so
   JNI headers : /usr/lib/jvm/java-6-openjdk/include
-- Configuring done
-- Generating done
-- Build files have been written to: /home/hou/pcsim/pcsim-0.5.4/_build
*******************************************
*  GENERATING PY++ WRAPPER CPP FILES      *
*******************************************
>>>> cd /home/hou/pcsim/pcsim-0.5.4/_build
>>>> /usr/bin/make -j 2 generate_code
[100%] Generating ../../python/pypcsim.h
[100%] Generating ../../python/pypcsim/pypcsim.indicator.cpp
/usr/local/lib/python2.6/dist-packages/pygccxml/parser/declarations_cache.py:8:
DeprecationWarning: the md5 module is deprecated; use hashlib instead
  import md5

INFO Parsing source file "pypcsim.h" ...

INFO gccxml cmd: /usr/bin/gccxml  --gccxml-cxxflags -pthread
-fpermissive   -I"." -I"/home/hou/pcsim/pcsim-0.5.4/pcsim/simutils"
-I"/home/hou/pcsim/pcsim-0.5.4/pcsim/simcore"
-I"/home/hou/pcsim/pcsim-0.5.4/pcsim/construction"
-I"/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml"
-I"/home/hou/pcsim/pcsim-0.5.4/pcsim/simobjects"
-I"/home/hou/pcsim/pcsim-0.5.4/libxsd"
-I"/usr/local/include/boost-1_34_1"  -D"MPICH_IGNORE_CXX_SEEK"
-D"BOOST_HAS_THREADS" -D"BOOST_PYTHON_MAX_ARITY=30"  "pypcsim.h"
-fxml="/tmp/tmpapqeKv.xml"
/usr/local/lib/python2.6/dist-packages/pygccxml/parser/source_reader.py:152:
DeprecationWarning: os.popen4 is deprecated.  Use the subprocess
module.
  input_, output = os.popen4( command_line )
Traceback (most recent call last):
  File "/home/hou/pcsim/pcsim-0.5.4/scripts/generate_boost_python_wrapper_code.py",
line 143, in <module>
    encoding = 'utf-8'
  File "/usr/local/lib/python2.6/dist-packages/pyplusplus/module_builder/builder.py",
line 90, in __init__
    , indexing_suite_version)
  File "/usr/local/lib/python2.6/dist-packages/pyplusplus/module_builder/builder.py",
line 144, in __parse_declarations
    decls = reader.read_files( files, compilation_mode )
  File "/usr/local/lib/python2.6/dist-packages/pygccxml/parser/project_reader.py",
line 225, in read_files
    return self.__parse_file_by_file(files)
  File "/usr/local/lib/python2.6/dist-packages/pygccxml/parser/project_reader.py",
line 250, in __parse_file_by_file
    decls = reader.read_file( header )
  File "/usr/local/lib/python2.6/dist-packages/pygccxml/parser/source_reader.py",
line 198, in read_file
    return self.read_gccxml_file( source_file )
  File "/usr/local/lib/python2.6/dist-packages/pygccxml/parser/source_reader.py",
line 225, in read_gccxml_file
    raise error
pygccxml.parser.source_reader.gccxml_runtime_error_t: Error occured
while running GCC-XML: In file included from
/home/hou/pcsim/pcsim-0.5.4/libxsd/xsd/cxx/parser/xerces/elements.txx:16,
                 from
/home/hou/pcsim/pcsim-0.5.4/libxsd/xsd/cxx/parser/xerces/elements.hxx:449,
                 from
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/skeleton/NeuroML_Level3_v1.7.1-pskel.hpp:76,
                 from
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/parser/implementation/NeuroML_Level3_v1.7.1-pimpl.hpp:11,
                 from
/home/hou/pcsim/pcsim-0.5.4/pcsim/neuroml/NeuroMLImporter.h:7,
                 from pypcsim.h:148:
/home/hou/pcsim/pcsim-0.5.4/libxsd/xsd/cxx/xml/sax/std-input-source.hxx:
In member function 'virtual xercesc_3_1::BinInputStream*
xsd::cxx::xml::sax::std_input_source::makeStream() const':
/home/hou/pcsim/pcsim-0.5.4/libxsd/xsd/cxx/xml/sax/std-input-source.hxx:156:
error: cannot allocate an object of abstract type
'xsd::cxx::xml::sax::std_input_stream'
/home/hou/pcsim/pcsim-0.5.4/libxsd/xsd/cxx/xml/sax/std-input-source.hxx:25:
note:   because the following virtual functions are pure within
'xsd::cxx::xml::sax::std_input_stream':
/usr/local/include/xercesc/util/BinInputStream.hpp:67: note: 	virtual
const XMLCh* xercesc_3_1::BinInputStream::getContentType() const

make[3]: *** [../python/pypcsim/pypcsim.indicator.cpp] Error 1
make[2]: *** [python/CMakeFiles/generate_python_wrapper_code.dir/all] Error 2
make[1]: *** [CMakeFiles/generate_code.dir/rule] Error 2
make: *** [generate_code] Error 2
BUILD PROCESS FAILED. ERROR = 512
Command: /usr/bin/make -j 2 generate_code

Best Regards
Hou Zhicheng