[Pytom-mail] compilation error in OSX10.10.3

[Sara W. <sj...@gm...>]

Hello,

I'm a grad student at Caltech.  I'm trying to compile pytom.  I have been
unable to solve the problem related to transform.hpp or .cpp.  Any ideas?
Please let me know if you need more information.

Thanks!
Sara Weaver

*Here are my package versions: *
OSX10.10.3
gcc43 4.3.6_11
fftw-3 3.3.4_1
fftw-3-single 3.3.4_1
libxml2 2.9.2_2
libxslt 1.1.28_1
python27 2.7.10_2
swig-python 3.0.5
swig 3.0.5
py27-lxml 3.4.1
openmpi 1.7.5_5
boost 1.58.0_3
py27-pil 1.1.7_7
py27-ipython 3.1.0_1
py27-matplotlib 1.4.3
py27-scipy 0.15.1
py27-epydoc 3.0.1_3


*Here is the compile.py output:*

Saras-MacBook-Pro:pytomc saraweaver$ sudo ./compile.py --libDir
/opt/local/lib /opt/local/libexec/openmpi-mp/ /opt/local/lib/openmpi-mp/
/usr/lib/ /usr/local/lib --includeDir /opt/local/include
/opt/local/include/openmpi/ /opt/local/include/boost/
/opt/local/Library/Frameworks/Python.framework/Versions/current/include/python2.7/
/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/numpy/core/include/numpy
--pythonVersion 2.7 --target all

Warning: Your system does not have LD_LIBRARY_PATH set.

PyTom assumes this to be the standard environment variable to store system
paths!


Searching :  mpicc   Found :  True

Searching :  mpic++   Found :  True

Searching :  openmpic++   Found :  False

Searching :  mpicxx-openmpi-gcc45   Found :  True

Searching :  libmpi.dylib   Found :  True

Searching :  mpi.h   Found :  True

Searching :  Python.h   Found :  True

Searching :  libpython2.7.dylib   Found :  True

Searching :  fftw3.h   Found :  True

Searching :  libfftw3.dylib   Found :  True

Searching :  type_traits.hpp   Found :  True

Searching :  ndarrayobject.h   Found :  True

Check compiling prerequisites:



Python     - lib_python: /opt/local/lib

Python     - include_python:
/opt/local/Library/Frameworks/Python.framework/Versions/current/include/python2.7/

FFTW3      - lib_fftw: /opt/local/lib

FFTW3      - include_fftw: /opt/local/include

OpenMPI    - mpic++: mpicxx-openmpi-gcc45

OpenMPI    - libmpi: /opt/local/lib/openmpi-mp/

OpenMPI    - include_mpi: /opt/local/include/openmpi-mp/

Numpy      - include_numpy:
/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/numpy/core/include/numpy

Boost     - include_boost: /opt/local/include/


Flags determined:

export PYTOMC_DIR='/opt/src/pytom/pytomc' && export
LDFLAGS_ADDITIONAL='-D_GLIBCXX_DEBUG' && export
INCLUDE_FFTW='-I/opt/local/include' && export
LDFLAGS_FFTW='-L/opt/local/lib -lfftw3 -lfftw3f' && export
INCLUDE_PYTHON='-I/opt/local/Library/Frameworks/Python.framework/Versions/current/include/python2.7/'
&& export
INCLUDE_NUMPY='-I/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/numpy/core/include/numpy'
&& export LDFLAGS_PYTHON='-L/opt/local/lib -lpython2.7' && export
INCLUDE_MPI='-I/opt/local/include/openmpi-mp/' && export
LDFLAGS_MPI='-L/opt/local/lib/openmpi-mp/ -lmpi' && export
INCLUDE_BOOST=-I'/opt/local/include/' && export OSX=" "


make -C ./libs/libtomc shared

/opt/local/bin/g++-mp-4.3 -Wall -fPIC -Wno-long-long -pedantic -ansi
--std=c++98 -fpermissive -DFPU_SENDS_SIGFPE=1 -D_GLIBCXX_DEBUG -O1
-fthread-jumps -falign-functions  -falign-jumps  -falign-loops
-falign-labels -fcaller-saves -fcrossjumping  -fcse-follow-jumps
-fcse-skip-blocks -fdelete-null-pointer-checks  -fexpensive-optimizations
-fgcse  -fgcse-lm  -foptimize-sibling-calls  -fpeephole2  -fregmove
-freorder-blocks  -freorder-functions  -frerun-cse-after-loop
-fsched-interblock  -fsched-spec  -fschedule-insns2  -fstrict-aliasing
-fstrict-overflow  -ftree-pre  -ftree-vrp  -funswitch-loops
-fgcse-after-reload -ftree-vectorize -fearly-inlining -DTHREAD_SAFE=0
-DHOSTNAME=Saras-MacBook-Pro.local -c -o
/opt/src/pytom/pytomc/libs/libtomc/libs/tom__FreqWeight.o
src/tom/FreqWeight.cpp -I./include -I/opt/local/include
-I/opt/local/include/

/opt/local/bin/g++-mp-4.3 -Wall -fPIC -Wno-long-long -pedantic -ansi
--std=c++98 -fpermissive -DFPU_SENDS_SIGFPE=1 -D_GLIBCXX_DEBUG -O1
-fthread-jumps -falign-functions  -falign-jumps  -falign-loops
-falign-labels -fcaller-saves -fcrossjumping  -fcse-follow-jumps
-fcse-skip-blocks -fdelete-null-pointer-checks  -fexpensive-optimizations
-fgcse  -fgcse-lm  -foptimize-sibling-calls  -fpeephole2  -fregmove
-freorder-blocks  -freorder-functions  -frerun-cse-after-loop
-fsched-interblock  -fsched-spec  -fschedule-insns2  -fstrict-aliasing
-fstrict-overflow  -ftree-pre  -ftree-vrp  -funswitch-loops
-fgcse-after-reload -ftree-vectorize -fearly-inlining -DTHREAD_SAFE=0
-DHOSTNAME=Saras-MacBook-Pro.local -c -o
/opt/src/pytom/pytomc/libs/libtomc/libs/tom__volume.o src/tom/volume.cpp
-I./include -I/opt/local/include -I/opt/local/include/

/opt/local/bin/g++-mp-4.3 -Wall -fPIC -Wno-long-long -pedantic -ansi
--std=c++98 -fpermissive -DFPU_SENDS_SIGFPE=1 -D_GLIBCXX_DEBUG -O1
-fthread-jumps -falign-functions  -falign-jumps  -falign-loops
-falign-labels -fcaller-saves -fcrossjumping  -fcse-follow-jumps
-fcse-skip-blocks -fdelete-null-pointer-checks  -fexpensive-optimizations
-fgcse  -fgcse-lm  -foptimize-sibling-calls  -fpeephole2  -fregmove
-freorder-blocks  -freorder-functions  -frerun-cse-after-loop
-fsched-interblock  -fsched-spec  -fschedule-insns2  -fstrict-aliasing
-fstrict-overflow  -ftree-pre  -ftree-vrp  -funswitch-loops
-fgcse-after-reload -ftree-vectorize -fearly-inlining -DTHREAD_SAFE=0
-DHOSTNAME=Saras-MacBook-Pro.local -c -o
/opt/src/pytom/pytomc/libs/libtomc/libs/tom__volume_fcn.o
src/tom/volume_fcn.cpp -I./include -I/opt/local/include
-I/opt/local/include/

/opt/local/bin/g++-mp-4.3 -Wall -fPIC -Wno-long-long -pedantic -ansi
--std=c++98 -fpermissive -DFPU_SENDS_SIGFPE=1 -D_GLIBCXX_DEBUG -O1
-fthread-jumps -falign-functions  -falign-jumps  -falign-loops
-falign-labels -fcaller-saves -fcrossjumping  -fcse-follow-jumps
-fcse-skip-blocks -fdelete-null-pointer-checks  -fexpensive-optimizations
-fgcse  -fgcse-lm  -foptimize-sibling-calls  -fpeephole2  -fregmove
-freorder-blocks  -freorder-functions  -frerun-cse-after-loop
-fsched-interblock  -fsched-spec  -fschedule-insns2  -fstrict-aliasing
-fstrict-overflow  -ftree-pre  -ftree-vrp  -funswitch-loops
-fgcse-after-reload -ftree-vectorize -fearly-inlining -DTHREAD_SAFE=0
-DHOSTNAME=Saras-MacBook-Pro.local -c -o
/opt/src/pytom/pytomc/libs/libtomc/libs/tom__fftw__fftw_plan.o
src/tom/fftw/fftw_plan.cpp -I./include -I/opt/local/include
-I/opt/local/include/

/opt/local/bin/g++-mp-4.3 -Wall -fPIC -Wno-long-long -pedantic -ansi
--std=c++98 -fpermissive -DFPU_SENDS_SIGFPE=1 -D_GLIBCXX_DEBUG -O1
-fthread-jumps -falign-functions  -falign-jumps  -falign-loops
-falign-labels -fcaller-saves -fcrossjumping  -fcse-follow-jumps
-fcse-skip-blocks -fdelete-null-pointer-checks  -fexpensive-optimizations
-fgcse  -fgcse-lm  -foptimize-sibling-calls  -fpeephole2  -fregmove
-freorder-blocks  -freorder-functions  -frerun-cse-after-loop
-fsched-interblock  -fsched-spec  -fschedule-insns2  -fstrict-aliasing
-fstrict-overflow  -ftree-pre  -ftree-vrp  -funswitch-loops
-fgcse-after-reload -ftree-vectorize -fearly-inlining -DTHREAD_SAFE=0
-DHOSTNAME=Saras-MacBook-Pro.local -c -o
/opt/src/pytom/pytomc/libs/libtomc/libs/tom__io__io.o src/tom/io/io.c
-I./include -I/opt/local/include -I/opt/local/include/

/opt/local/bin/g++-mp-4.3 -Wall -fPIC -Wno-long-long -pedantic -ansi
--std=c++98 -fpermissive -DFPU_SENDS_SIGFPE=1 -D_GLIBCXX_DEBUG -O1
-fthread-jumps -falign-functions  -falign-jumps  -falign-loops
-falign-labels -fcaller-saves -fcrossjumping  -fcse-follow-jumps
-fcse-skip-blocks -fdelete-null-pointer-checks  -fexpensive-optimizations
-fgcse  -fgcse-lm  -foptimize-sibling-calls  -fpeephole2  -fregmove
-freorder-blocks  -freorder-functions  -frerun-cse-after-loop
-fsched-interblock  -fsched-spec  -fschedule-insns2  -fstrict-aliasing
-fstrict-overflow  -ftree-pre  -ftree-vrp  -funswitch-loops
-fgcse-after-reload -ftree-vectorize -fearly-inlining -DTHREAD_SAFE=0
-DHOSTNAME=Saras-MacBook-Pro.local -c -o
/opt/src/pytom/pytomc/libs/libtomc/libs/tom__io__io_cpp.o src/tom/io/io.cpp
-I./include -I/opt/local/include -I/opt/local/include/

/opt/local/bin/g++-mp-4.3 -Wall -fPIC -Wno-long-long -pedantic -ansi
--std=c++98 -fpermissive -DFPU_SENDS_SIGFPE=1 -D_GLIBCXX_DEBUG -O1
-fthread-jumps -falign-functions  -falign-jumps  -falign-loops
-falign-labels -fcaller-saves -fcrossjumping  -fcse-follow-jumps
-fcse-skip-blocks -fdelete-null-pointer-checks  -fexpensive-optimizations
-fgcse  -fgcse-lm  -foptimize-sibling-calls  -fpeephole2  -fregmove
-freorder-blocks  -freorder-functions  -frerun-cse-after-loop
-fsched-interblock  -fsched-spec  -fschedule-insns2  -fstrict-aliasing
-fstrict-overflow  -ftree-pre  -ftree-vrp  -funswitch-loops
-fgcse-after-reload -ftree-vectorize -fearly-inlining -DTHREAD_SAFE=0
-DHOSTNAME=Saras-MacBook-Pro.local -c -o
/opt/src/pytom/pytomc/libs/libtomc/libs/tom__tools__Log.o
src/tom/tools/Log.cpp -I./include -I/opt/local/include -I/opt/local/include/

/opt/local/bin/g++-mp-4.3 -Wall -fPIC -Wno-long-long -pedantic -ansi
--std=c++98 -fpermissive -DFPU_SENDS_SIGFPE=1 -D_GLIBCXX_DEBUG -O1
-fthread-jumps -falign-functions  -falign-jumps  -falign-loops
-falign-labels -fcaller-saves -fcrossjumping  -fcse-follow-jumps
-fcse-skip-blocks -fdelete-null-pointer-checks  -fexpensive-optimizations
-fgcse  -fgcse-lm  -foptimize-sibling-calls  -fpeephole2  -fregmove
-freorder-blocks  -freorder-functions  -frerun-cse-after-loop
-fsched-interblock  -fsched-spec  -fschedule-insns2  -fstrict-aliasing
-fstrict-overflow  -ftree-pre  -ftree-vrp  -funswitch-loops
-fgcse-after-reload -ftree-vectorize -fearly-inlining -DTHREAD_SAFE=0
-DHOSTNAME=Saras-MacBook-Pro.local -c -o
/opt/src/pytom/pytomc/libs/libtomc/libs/tom__tools__ParameterSet.o
src/tom/tools/ParameterSet.cpp -I./include -I/opt/local/include
-I/opt/local/include/

/opt/local/bin/g++-mp-4.3 -Wall -fPIC -Wno-long-long -pedantic -ansi
--std=c++98 -fpermissive -DFPU_SENDS_SIGFPE=1 -D_GLIBCXX_DEBUG -O1
-fthread-jumps -falign-functions  -falign-jumps  -falign-loops
-falign-labels -fcaller-saves -fcrossjumping  -fcse-follow-jumps
-fcse-skip-blocks -fdelete-null-pointer-checks  -fexpensive-optimizations
-fgcse  -fgcse-lm  -foptimize-sibling-calls  -fpeephole2  -fregmove
-freorder-blocks  -freorder-functions  -frerun-cse-after-loop
-fsched-interblock  -fsched-spec  -fschedule-insns2  -fstrict-aliasing
-fstrict-overflow  -ftree-pre  -ftree-vrp  -funswitch-loops
-fgcse-after-reload -ftree-vectorize -fearly-inlining -DTHREAD_SAFE=0
-DHOSTNAME=Saras-MacBook-Pro.local -c -o
/opt/src/pytom/pytomc/libs/libtomc/libs/tom__tools__snippets.o
src/tom/tools/snippets.cpp -I./include -I/opt/local/include
-I/opt/local/include/

/opt/local/bin/g++-mp-4.3 -Wall -fPIC -Wno-long-long -pedantic -ansi
--std=c++98 -fpermissive -DFPU_SENDS_SIGFPE=1 -D_GLIBCXX_DEBUG -O1
-fthread-jumps -falign-functions  -falign-jumps  -falign-loops
-falign-labels -fcaller-saves -fcrossjumping  -fcse-follow-jumps
-fcse-skip-blocks -fdelete-null-pointer-checks  -fexpensive-optimizations
-fgcse  -fgcse-lm  -foptimize-sibling-calls  -fpeephole2  -fregmove
-freorder-blocks  -freorder-functions  -frerun-cse-after-loop
-fsched-interblock  -fsched-spec  -fschedule-insns2  -fstrict-aliasing
-fstrict-overflow  -ftree-pre  -ftree-vrp  -funswitch-loops
-fgcse-after-reload -ftree-vectorize -fearly-inlining -DTHREAD_SAFE=0
-DHOSTNAME=Saras-MacBook-Pro.local -c -o
/opt/src/pytom/pytomc/libs/libtomc/libs/tom__transf__transform_cpp.o
src/tom/transf/transform.cpp -I./include -I/opt/local/include
-I/opt/local/include/

src/tom/transf/transform.cpp:88: error: redefinition of 'void
tom::transf::InterpolTriLinear<T>::setvolume(const tom::Volume<T>&)'

./include/tom/transf/transform.hpp:125: error: 'void
tom::transf::InterpolTriLinear<T>::setvolume(const tom::Volume<T>&)'
previously declared here

src/tom/transf/transform.cpp:111: error: redefinition of 'void
tom::transf::InterpolTriLinear<T>::setvolume(const T*, size_t, size_t,
size_t, size_t, size_t)'

./include/tom/transf/transform.hpp:148: error: 'void
tom::transf::InterpolTriLinear<T>::setvolume(const T*, size_t, size_t,
size_t, size_t, size_t)' previously declared here

src/tom/transf/transform.cpp:129: error: redefinition of 'void
tom::transf::InterpolTriCubic<T>::setvolume(const tom::Volume<T>&)'

./include/tom/transf/transform.hpp:166: error: 'void
tom::transf::InterpolTriCubic<T>::setvolume(const tom::Volume<T>&)'
previously declared here

src/tom/transf/transform.cpp:149: error: redefinition of 'void
tom::transf::InterpolTriCubic<T>::setvolume(const T*, size_t, size_t,
size_t, size_t, size_t)'

./include/tom/transf/transform.hpp:186: error: 'void
tom::transf::InterpolTriCubic<T>::setvolume(const T*, size_t, size_t,
size_t, size_t, size_t)' previously declared here

make[1]: ***
[/opt/src/pytom/pytomc/libs/libtomc/libs/tom__transf__transform_cpp.o]
Error 1

make: *** [libtomc] Error 2