Troubles installing QPALMA

Question

[changhan1110]

Hi!

This is my first post in this site.

I have troubles with QPALMA installing.

vteddy@hawk:/BiO/Store/Program/BioTools/qpalma-0.9.3$ ./setup_qpalma.sh 
Warning: variable QPALMA_PATH not set; consider running ./setup_qpalma.sh
QPalma setup script (version 1.0)
===================================

QPalma base directory (currently set to "", suggest to set to "/BiO/Store/Program/BioTools/qpalma-0.9.3")
/BiO/Store/Program/BioTools/qpalma-0.9.3
=> Setting QPALMA base directory to "/BiO/Store/Program/BioTools/qpalma-0.9.3"

PALMapper base directory (currently set to "")
/BiO/Store/Program/BioTools$ cd palmapper-0.4-rc3
=> Setting PALMapper base directory to "/BiO/Store/Program/BioTools$ cd palmapper-0.4-rc3"

Which optimizer should be used:
1. Mosek (commercial optimizer with available trial license)
2. CVXOPT (free optimizer)
2

To install CVXOPT, download it from
http://abel.ee.ucla.edu/cvxopt/download/index.html
and follow the instructions.

CVXOPT installation bin directory (currently set to "")
/BiO/Store/Program/BioTools/cvxopt-1.1.5
=> Setting CVXOPT bin directory to "/BiO/Store/Program/BioTools/cvxopt-1.1.5"

Compiling modules:

1. Parameter Parser Module
--------------------------
Building ParaParser module
swig -c++ -python ParaParser.i
make: swig: Command not found
make: *** [all] Error 127

Troubles Installing Qpalma To Run Palmapper ... seems similar but I thiink this error is a different type.

What should I do to install QPALMA?

[marina.v.yurieva]

As I understand in the previous question the problem was with python-config, and you seem to have a problem with swig. Do you have it installed?

[changhan1110]

I just installed it, but I meet another problem.

---

vteddy@hawk:/BiO/Store/Program/BioTools/qpalma-0.9.3$ ./setup_qpalma.sh 
Warning: variable QPALMA_PATH not set; consider running ./setup_qpalma.sh
QPalma setup script (version 1.0)
===================================

QPalma base directory (currently set to "", suggest to set to "/BiO/Store/Program/BioTools/qpalma-0.9.3")
/BiO/Store/Program/BioTools/qpalma-0.9.3
=> Setting QPALMA base directory to "/BiO/Store/Program/BioTools/qpalma-0.9.3"

PALMapper base directory (currently set to "")
/BiO/Store/Program/BioTools/palmapper-0.4-rc3
=> Setting PALMapper base directory to "/BiO/Store/Program/BioTools/palmapper-0.4-rc3"

Which optimizer should be used:
1. Mosek (commercial optimizer with available trial license)
2. CVXOPT (free optimizer)
2

To install CVXOPT, download it from
http://abel.ee.ucla.edu/cvxopt/download/index.html
and follow the instructions.

CVXOPT installation bin directory (currently set to "")
/BiO/Store/Program/BioTools/cvxopt-1.1.5
=> Setting CVXOPT bin directory to "/BiO/Store/Program/BioTools/cvxopt-1.1.5"

Compiling modules:

1. Parameter Parser Module
--------------------------
Building ParaParser module
swig -c++ -python ParaParser.i
g++ -Wall -Wshadow -std=c++98 -O3 -fPIC `python-config --cflags` -c getline.cpp -o getline.o
cc1plus: warning: command line option ??-Wstrict-prototypes?? is valid for C/ObjC but not for C++ [enabled by default]
g++ -Wall -Wshadow -std=c++98 -O3 -fPIC `python-config --cflags` -c ParaParser_wrap.cxx -o ParaParser_wrap.o
cc1plus: warning: command line option ??-Wstrict-prototypes?? is valid for C/ObjC but not for C++ [enabled by default]
ParaParser_wrap.cxx: In function ??PyObject* SWIG_Python_NewShadowInstance(SwigPyClientData*, PyObject*)??:
ParaParser_wrap.cxx:2439:74: warning: declaration of ??swig_this?? shadows a global declaration [-Wshadow]
 SWIG_Python_NewShadowInstance(SwigPyClientData *data, PyObject *swig_this)
                                                                          ^
ParaParser_wrap.cxx:2180:18: warning: shadowed declaration is here [-Wshadow]
 static PyObject *swig_this = NULL;
                  ^
ParaParser_wrap.cxx: In function ??void SWIG_Python_SetSwigThis(PyObject*, PyObject*)??:
ParaParser_wrap.cxx:2514:60: warning: declaration of ??swig_this?? shadows a global declaration [-Wshadow]
 SWIG_Python_SetSwigThis(PyObject *inst, PyObject *swig_this)
                                                            ^
ParaParser_wrap.cxx:2180:18: warning: shadowed declaration is here [-Wshadow]
 static PyObject *swig_this = NULL;
                  ^
g++ -Wall -Wshadow -std=c++98 -O3 -fPIC `python-config --cflags` -shared `python-config --ldflags` ParaParser.o ParaParser_wrap.o getline.o -o _ParaParser.so -dynamiclib
python -c "import ParaParser" && echo "Creation of ParaParser module was successful!"
Creation of ParaParser module was successful!

2. Dynamic Programming Module
-----------------------------
g++ -Wall -std=c++98 -ggdb -O9 -fPIC `python-config --cflags`   -c -o Mathmatics.o Mathmatics.cpp
cc1plus: warning: command line option ??-Wstrict-prototypes?? is valid for C/ObjC but not for C++ [enabled by default]
g++ -Wall -std=c++98 -ggdb -O9 -fPIC `python-config --cflags`   -c -o fill_matrix.o fill_matrix.cpp
cc1plus: warning: command line option ??-Wstrict-prototypes?? is valid for C/ObjC but not for C++ [enabled by default]
In file included from fill_matrix.cpp:43:0:
fill_matrix.h:39:1: warning: ??typedef?? was ignored in this declaration [enabled by default]
 };
 ^
fill_matrix.cpp: In function ??void fill_matrix(int, Pre_score**, int, int, char*, char*, double*, penalty_struct*, double*, penalty_struct*, double*, double*, bool, int, int*, int*)??:
fill_matrix.cpp:430:15: error: ??sleep?? was not declared in this scope
     sleep(5000) ;
               ^
fill_matrix.cpp:462:13: error: ??sleep?? was not declared in this scope
   sleep(5000) ;
             ^
make: *** [fill_matrix.o] Error 1

---

I cannot understand what this means