Re: [Pytom-mail] compilation error in OSX10.10.3

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

Hi all,

I used the transform.cpp file Thomas sent and had some success.  My current
compile.py output is below.

There are a few errors/warnings where I am not sure if I should be worried
that are highlighted below.  And I've also included the full output.  Any
ideas?  Please let me know if you need any other information.

Thanks for all the help!
Sara

*Here are my package versions: *
OSX10.10.3

  boost @1.58.0_3+no_single+no_static+python27 (active)

  fftw-3 @3.3.4_1 (active)

  fftw-3-single @3.3.4_1 (active)

  gcc49 @4.9.2_2 (active)

  libxml2 @2.9.2_2 (active)

  libxslt @1.1.28_1 (active)

  mpich @3.1.4_1 (active)

  openmpi @1.7.5_5 (active)

  py27-epydoc @3.0.1_3 (active)

  py27-ipython @3.2.0_0+notebook+parallel+scientific (active)

  py27-lxml @3.4.1_0 (active)

  py27-matplotlib @1.4.3_0+cairo+tkinter (active)

  py27-pil @1.1.7_7 (active)

  py27-scipy @0.15.1_0+gfortran (active)

  python27 @2.7.10_2 (active)

  swig-python @3.0.5_1 (active)

*At the end of SH Alignment:*

ld: symbol(s) not found for architecture x86_64

clang: error: linker command failed with exit code 1 (use -v to see
invocation)

*In mpi4py library compilation:*

ld: library not found for -lotf

clang: error: linker command failed with exit code 1 (use -v to see
invocation)

warning: build_clib: building library "vt" failed


warning: build_clib: command '/opt/local/bin/mpicc' failed with exit status
1

*In NFFT library compilation:*

checking for fftw_execute in -lfftw3... no

configure: error: The fftw3 library could not be found. You can download it
from#

     http://www.fftw.org. If you have installed fftw3, make sure that#

     this configure script can find it. See ./configure --help for#

     more information.

make: *** No targets specified and no makefile found.  Stop.


export
PYTHON_INCLUDE_PATH="/opt/local/Library/Frameworks/Python.framework/Versions/current/include/python2.7/"
&& export
NUMPY_INCLUDE_PATH="/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/numpy/core/include/"
&& export FFTW_INCLUDE_PATH="/opt/local/include" && export
FFTW_LIB_PATH="/opt/local/lib" && export
NFFT_LIB_PATH="/opt/src/pytom/external/lib/" && export
NFFT_INCLUDE_PATH="/opt/src/pytom/external/include/" && cd nufft/ && chmod
+x mkswig.sh && ./mkswig.sh

nufft.c:25:23: fatal error: nfft3util.h: No such file or directory

 #include "nfft3util.h"

                       ^

compilation terminated.

In file included from
/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804:0,

                 from
/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,

                 from
/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,

                 from nufft_wrap.c:2964:

/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2:
warning: #warning "Using deprecated NumPy API, disable it by " "#defining
NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]

 #warning "Using deprecated NumPy API, disable it by " \

  ^

clang: error: no such file or directory: 'nufft.o'



*The full compile.py output:*

Last login: Fri Jun 26 09:26:42 on console

Saras-MacBook-Pro:~ saraweaver$ cd /opt/src/pytom/pytomc/

Saras-MacBook-Pro:pytomc saraweaver$ sudo make clean

Password:

rm -rf ./libs/libtomc/libs/*

rm -rf ./swigCpp/*

rm -rf ./swigLibs/*

rm -rf ./swigModules/*.py*

rm -rf ./swigModules/*so

rm -rf ./test/*pyc

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
/usr/local/include --pythonVersion 2.7 --target all -Wall

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 :  False

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++: mpic++

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

OpenMPI    - include_mpi: /usr/local/include

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/usr/local/include' && 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-4.9  -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-insns  -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/

src/tom/FreqWeight.cpp: In instantiation of
'tom::FreqWeight_EmFile<T>::FreqWeight_EmFile(const string&, size_t,
size_t, size_t, bool, bool) [with T = float; std::string =
std::basic_string<char>; size_t = long unsigned int]':

./include/tom/FreqWeight.hpp:814:115:   required from here

src/tom/FreqWeight.cpp:1335:22: warning: 'resetVolume' was not declared in
this scope, and no declarations were found by argument-dependent lookup at
the point of instantiation [-fpermissive]

         resetVolume(v);

                      ^

src/tom/FreqWeight.cpp:1335:22: note: declarations in dependent base
'tom::FreqWeight_Volume<float>' are not found by unqualified lookup

src/tom/FreqWeight.cpp:1335:22: note: use 'this->resetVolume' instead

src/tom/FreqWeight.cpp: In instantiation of
'tom::FreqWeight_EmFile<T>::FreqWeight_EmFile(const string&, size_t,
size_t, size_t, bool, bool) [with T = double; std::string =
std::basic_string<char>; size_t = long unsigned int]':

./include/tom/FreqWeight.hpp:817:112:   required from here

src/tom/FreqWeight.cpp:1335:22: warning: 'resetVolume' was not declared in
this scope, and no declarations were found by argument-dependent lookup at
the point of instantiation [-fpermissive]

src/tom/FreqWeight.cpp:1335:22: note: declarations in dependent base
'tom::FreqWeight_Volume<double>' are not found by unqualified lookup

src/tom/FreqWeight.cpp:1335:22: note: use 'this->resetVolume' instead

/opt/local/bin/g++-mp-4.9  -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-insns  -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-4.9  -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-insns  -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/

src/tom/volume_fcn.cpp: In instantiation of 'void
tom::back_project(tom::Volume<T>&, tom::Volume<T>&, int, int, int, float,
float, float, int, int, float, float, float, float, float) [with T =
float]':

src/tom/volume_fcn.cpp:1998:60:   required from here

src/tom/volume_fcn.cpp:137:20: warning: variable 'Tr13' set but not used
[-Wunused-but-set-variable]

  float Tr11, Tr12, Tr13;

                    ^

src/tom/volume_fcn.cpp:138:20: warning: variable 'Tr23' set but not used
[-Wunused-but-set-variable]

  float Tr21, Tr22, Tr23;

                    ^

src/tom/volume_fcn.cpp:139:20: warning: variable 'Tr33' set but not used
[-Wunused-but-set-variable]

  float Tr31, Tr32, Tr33;

                    ^

/opt/local/bin/g++-mp-4.9  -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-insns  -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-4.9  -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-insns  -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/

src/tom/io/io.c: In function 'int64_t tom_io_getFileSize(FILE*)':

src/tom/io/io.c:146:10: warning: variable 'success' set but not used
[-Wunused-but-set-variable]

      int success;

          ^

src/tom/io/io.c: In function 'int tom_io_read_vol(FILE*, const uint32_t*,
int, int, const uint32_t*, const uint32_t*, const uint32_t*, void*, int)':

src/tom/io/io.c:1106:9: warning: variable 'fseek_success' set but not used
[-Wunused-but-set-variable]

     int fseek_success;

         ^

/opt/local/bin/g++-mp-4.9  -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-insns  -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-4.9  -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-insns  -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-4.9  -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-insns  -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-4.9  -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-insns  -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-4.9  -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-insns  -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: In function 'void
{anonymous}::tom__rescale_fs(const tom::Volume<std::complex<_Tp> >&,
std::size_t, tom::Volume<std::complex<_Tp> >&, std::size_t, double, double,
double, bool) [with T = float; std::size_t = long unsigned int]':

src/tom/transf/transform.cpp:1265:40: warning:
'op.{anonymous}::for_each__tom__rescale_fs<float>::shift_tmpz_' may be used
uninitialized in this function [-Wmaybe-uninitialized]

         ::for_each__tom__rescale_fs<T> op(vsrc, sizez_src, vdst,
sizez_dst, shiftx, shifty, shiftz, divide_by_numel);

                                        ^

src/tom/transf/transform.cpp:1265:40: warning:
'op.{anonymous}::for_each__tom__rescale_fs<float>::shift_tmpy_' may be used
uninitialized in this function [-Wmaybe-uninitialized]

src/tom/transf/transform.cpp:1265:40: warning:
'op.{anonymous}::for_each__tom__rescale_fs<float>::shift_tmpx_' may be used
uninitialized in this function [-Wmaybe-uninitialized]

src/tom/transf/transform.cpp:1221:21: warning:
'op.{anonymous}::for_each__tom__rescale_fs<float>::shiftz_' may be used
uninitialized in this function [-Wmaybe-uninitialized]

                     shift_tmp_ += shiftz_ * shift_tmpz_;

                     ^

src/tom/transf/transform.cpp:1265:40: note:
'op.{anonymous}::for_each__tom__rescale_fs<float>::shiftz_' was declared
here

         ::for_each__tom__rescale_fs<T> op(vsrc, sizez_src, vdst,
sizez_dst, shiftx, shifty, shiftz, divide_by_numel);

                                        ^

src/tom/transf/transform.cpp:1216:21: warning:
'op.{anonymous}::for_each__tom__rescale_fs<float>::shifty_' may be used
uninitialized in this function [-Wmaybe-uninitialized]

                     shift_tmp_ += shifty_ * shift_tmpy_;

                     ^

src/tom/transf/transform.cpp:1265:40: note:
'op.{anonymous}::for_each__tom__rescale_fs<float>::shifty_' was declared
here

         ::for_each__tom__rescale_fs<T> op(vsrc, sizez_src, vdst,
sizez_dst, shiftx, shifty, shiftz, divide_by_numel);

                                        ^

src/tom/transf/transform.cpp:1211:21: warning:
'op.{anonymous}::for_each__tom__rescale_fs<float>::shiftx_' may be used
uninitialized in this function [-Wmaybe-uninitialized]

                     shift_tmp_ = shiftx_ * shift_tmpx_;

                     ^

src/tom/transf/transform.cpp:1265:40: note:
'op.{anonymous}::for_each__tom__rescale_fs<float>::shiftx_' was declared
here

         ::for_each__tom__rescale_fs<T> op(vsrc, sizez_src, vdst,
sizez_dst, shiftx, shifty, shiftz, divide_by_numel);

                                        ^

src/tom/transf/transform.cpp: In function 'void
{anonymous}::tom__rescale_fs(const tom::Volume<std::complex<_Tp> >&,
std::size_t, tom::Volume<std::complex<_Tp> >&, std::size_t, double, double,
double, bool) [with T = double; std::size_t = long unsigned int]':

src/tom/transf/transform.cpp:1265:40: warning:
'op.{anonymous}::for_each__tom__rescale_fs<double>::shift_tmpz_' may be
used uninitialized in this function [-Wmaybe-uninitialized]

src/tom/transf/transform.cpp:1265:40: warning:
'op.{anonymous}::for_each__tom__rescale_fs<double>::shift_tmpy_' may be
used uninitialized in this function [-Wmaybe-uninitialized]

src/tom/transf/transform.cpp:1265:40: warning:
'op.{anonymous}::for_each__tom__rescale_fs<double>::shift_tmpx_' may be
used uninitialized in this function [-Wmaybe-uninitialized]

src/tom/transf/transform.cpp:1221:21: warning:
'op.{anonymous}::for_each__tom__rescale_fs<double>::shiftz_' may be used
uninitialized in this function [-Wmaybe-uninitialized]

                     shift_tmp_ += shiftz_ * shift_tmpz_;

                     ^

src/tom/transf/transform.cpp:1265:40: note:
'op.{anonymous}::for_each__tom__rescale_fs<double>::shiftz_' was declared
here

         ::for_each__tom__rescale_fs<T> op(vsrc, sizez_src, vdst,
sizez_dst, shiftx, shifty, shiftz, divide_by_numel);

                                        ^

src/tom/transf/transform.cpp:1216:21: warning:
'op.{anonymous}::for_each__tom__rescale_fs<double>::shifty_' may be used
uninitialized in this function [-Wmaybe-uninitialized]

                     shift_tmp_ += shifty_ * shift_tmpy_;

                     ^

src/tom/transf/transform.cpp:1265:40: note:
'op.{anonymous}::for_each__tom__rescale_fs<double>::shifty_' was declared
here

         ::for_each__tom__rescale_fs<T> op(vsrc, sizez_src, vdst,
sizez_dst, shiftx, shifty, shiftz, divide_by_numel);

                                        ^

src/tom/transf/transform.cpp:1211:21: warning:
'op.{anonymous}::for_each__tom__rescale_fs<double>::shiftx_' may be used
uninitialized in this function [-Wmaybe-uninitialized]

                     shift_tmp_ = shiftx_ * shift_tmpx_;

                     ^

src/tom/transf/transform.cpp:1265:40: note:
'op.{anonymous}::for_each__tom__rescale_fs<double>::shiftx_' was declared
here

         ::for_each__tom__rescale_fs<T> op(vsrc, sizez_src, vdst,
sizez_dst, shiftx, shifty, shiftz, divide_by_numel);

                                        ^

/opt/local/bin/g++-mp-4.9  -shared  -o
/opt/src/pytom/pytomc/libs/libtomc/libs/libtomc.so
/opt/src/pytom/pytomc/libs/libtomc/libs/tom__FreqWeight.o
/opt/src/pytom/pytomc/libs/libtomc/libs/tom__volume.o
/opt/src/pytom/pytomc/libs/libtomc/libs/tom__volume_fcn.o
/opt/src/pytom/pytomc/libs/libtomc/libs/tom__fftw__fftw_plan.o
/opt/src/pytom/pytomc/libs/libtomc/libs/tom__io__io.o
/opt/src/pytom/pytomc/libs/libtomc/libs/tom__io__io_cpp.o
/opt/src/pytom/pytomc/libs/libtomc/libs/tom__tools__Log.o
/opt/src/pytom/pytomc/libs/libtomc/libs/tom__tools__ParameterSet.o
/opt/src/pytom/pytomc/libs/libtomc/libs/tom__tools__snippets.o
/opt/src/pytom/pytomc/libs/libtomc/libs/tom__transf__transform_cpp.o
-L/opt/local/lib -lfftw3 -lfftw3f -lm

/opt/local/bin/g++-mp-4.9  -fPIC -c -g3 -Wall -Wno-long-long -pedantic
-ansi --std=c++98 -fpermissive  -D_GLIBCXX_DEBUG -I./libs/libtomc/include
-I./include -I/opt/local/include
-I/opt/local/Library/Frameworks/Python.framework/Versions/current/include/python2.7/
-I/opt/local/include/
-I/opt/local/Library/Frameworks/Python.framework/Versions/current/include/python2.7/
-I/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/numpy/core/include/numpy
src/swigVolume.cpp -o swigLibs/swigVolume.o

swig -Wall -python -c++ -outdir ./swigModules/  -I./libs/libtomc/include
-I./include -I/opt/local/include
-I/opt/local/Library/Frameworks/Python.framework/Versions/current/include/python2.7/
-I/opt/local/include/
-I/opt/local/Library/Frameworks/Python.framework/Versions/current/include/python2.7/
-I/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/numpy/core/include/numpy
-I./src -o swigCpp/pytom_volume_wrap.cpp swigCode/pytom_volume.i

swigCode/pytom_volume.i:74: Warning 321: 'sum' conflicts with a built-in
name in python

swigCode/pytom_volume.i:75: Warning 321: 'sum' conflicts with a built-in
name in python

swigCode/pytom_volume.i:79: Warning 321: 'min' conflicts with a built-in
name in python

swigCode/pytom_volume.i:80: Warning 321: 'max' conflicts with a built-in
name in python

swigCode/pytom_volume.i:82: Warning 321: 'abs' conflicts with a built-in
name in python

swigCode/pytom_volume.i:83: Warning 321: 'abs' conflicts with a built-in
name in python

./include/swigVolume.hpp:1: Warning 401: Nothing known about base class
'tom::Volume< float >'. Ignored.

./include/swigVolume.hpp:1: Warning 401: Maybe you forgot to instantiate
'tom::Volume< float >' using %template.

./include/swigVolume.hpp:1: Warning 401: Nothing known about base class
'tom::Volume< std::complex< float > >'. Ignored.

./include/swigVolume.hpp:1: Warning 401: Maybe you forgot to instantiate
'tom::Volume< std::complex< float > >' using %template.

/opt/local/bin/g++-mp-4.9  -fPIC -c -g3 -Wall -Wno-long-long -pedantic
-ansi --std=c++98 -fpermissive  -D_GLIBCXX_DEBUG -I./libs/libtomc/include
-I./include -I/opt/local/include
-I/opt/local/Library/Frameworks/Python.framework/Versions/current/include/python2.7/
-I/opt/local/include/
-I/opt/local/Library/Frameworks/Python.framework/Versions/current/include/python2.7/
-I/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/numpy/core/include/numpy
swigCpp/pytom_volume_wrap.cpp -o swigLibs/pytom_volume_wrap.o

In file included from swigCpp/pytom_volume_wrap.cpp:3061:0:

swigCpp/../src/swigVolumeFnc.cpp: In instantiation of
'swigTom::swigVolume<T, TSCALE_SHIFT> swigTom::projectSum(const
swigTom::swigVolume<T, TSCALE_SHIFT>&, int) [with T = float; TSCALE_SHIFT =
float]':

swigCpp/pytom_volume_wrap.cpp:9364:131:   required from here

swigCpp/../src/swigVolumeFnc.cpp:419:16: warning: comparison between signed
and unsigned integer expressions [-Wsign-compare]

  for(int i=0; i<x; i++)

                ^

swigCpp/../src/swigVolumeFnc.cpp:420:17: warning: comparison between signed
and unsigned integer expressions [-Wsign-compare]

   for(int j=0; j<y; j++)

                 ^

swigCpp/../src/swigVolumeFnc.cpp:425:21: warning: comparison between signed
and unsigned integer expressions [-Wsign-compare]

     for(int ii=0; ii<sizeX; ii++)

                     ^

swigCpp/../src/swigVolumeFnc.cpp:429:21: warning: comparison between signed
and unsigned integer expressions [-Wsign-compare]

     for(int jj=0; jj<sizeY; jj++)

                     ^

swigCpp/../src/swigVolumeFnc.cpp:433:21: warning: comparison between signed
and unsigned integer expressions [-Wsign-compare]

     for(int kk=0; kk<sizeZ; kk++)

                     ^

swigCpp/../src/swigVolumeFnc.cpp: In instantiation of
'swigTom::swigVolume<T, TSCALE_SHIFT>
swigTom::reducedToFull(swigTom::swigVolume<T, TSCALE_SHIFT>&) [with T =
float; TSCALE_SHIFT = float]':

swigCpp/pytom_volume_wrap.cpp:9710:85:   required from here

swigCpp/../src/swigVolumeFnc.cpp:504:23: warning: comparison between signed
and unsigned integer expressions [-Wsign-compare]

   if((z-y == 1 || z-y == -1) && y == x)

                       ^

swigCpp/../src/swigVolumeFnc.cpp: In instantiation of
'swigTom::swigVolume<T, TSCALE_SHIFT>
swigTom::reducedToFull(swigTom::swigVolume<T, TSCALE_SHIFT>&) [with T =
std::complex<float>; TSCALE_SHIFT = float]':

swigCpp/pytom_volume_wrap.cpp:9741:101:   required from here

swigCpp/../src/swigVolumeFnc.cpp:504:23: warning: comparison between signed
and unsigned integer expressions [-Wsign-compare]

swigCpp/../src/swigVolumeFnc.cpp: In instantiation of 'void
swigTom::writeSubregion(swigTom::swigVolume<T, T>&, std::string,
std::size_t, std::size_t, std::size_t) [with T = float; std::string =
std::basic_string<char>; std::size_t = long unsigned int]':

swigCpp/pytom_volume_wrap.cpp:10471:91:   required from here

swigCpp/../src/swigVolumeFnc.cpp:601:58: warning: narrowing conversion of
'positionX' from 'std::size_t {aka long unsigned int}' to 'uint32_t {aka
unsigned int}' inside { } is ill-formed in C++11 [-Wnarrowing]

  uint32_t first_voxel[3]={positionX, positionY, positionZ};

                                                          ^

swigCpp/../src/swigVolumeFnc.cpp:601:58: warning: narrowing conversion of
'positionY' from 'std::size_t {aka long unsigned int}' to 'uint32_t {aka
unsigned int}' inside { } is ill-formed in C++11 [-Wnarrowing]

swigCpp/../src/swigVolumeFnc.cpp:601:58: warning: narrowing conversion of
'positionZ' from 'std::size_t {aka long unsigned int}' to 'uint32_t {aka
unsigned int}' inside { } is ill-formed in C++11 [-Wnarrowing]

swigCpp/../src/swigVolumeFnc.cpp: In instantiation of 'void
swigTom::updateResFromIdx(swigTom::swigVolume<T, TSCALE_SHIFT>&, const
swigTom::swigVolume<T, TSCALE_SHIFT>&, swigTom::swigVolume<T,
TSCALE_SHIFT>&, std::size_t) [with T = float; TSHIFT_SCALE = float;
std::size_t = long unsigned int]':

swigCpp/pytom_volume_wrap.cpp:10534:140:   required from here

swigCpp/../src/swigVolumeFnc.cpp:625:16: warning: comparison between signed
and unsigned integer expressions [-Wsign-compare]

  for(int i=0; i<sizeX; i++)

                ^

swigCpp/../src/swigVolumeFnc.cpp:626:17: warning: comparison between signed
and unsigned integer expressions [-Wsign-compare]

   for(int j=0; j<sizeY; j++)

                 ^

swigCpp/../src/swigVolumeFnc.cpp:627:18: warning: comparison between signed
and unsigned integer expressions [-Wsign-compare]

    for(int k=0; k<sizeZ; k++)

                  ^

swigCpp/../src/swigVolumeFnc.cpp: In instantiation of 'void
swigTom::updateResFromVol(swigTom::swigVolume<T, TSCALE_SHIFT>&, const
swigTom::swigVolume<T, TSCALE_SHIFT>&, swigTom::swigVolume<T,
TSCALE_SHIFT>&, const swigTom::swigVolume<T, TSCALE_SHIFT>&) [with T =
float; TSHIFT_SCALE = float]':

swigCpp/pytom_volume_wrap.cpp:10600:185:   required from here

swigCpp/../src/swigVolumeFnc.cpp:658:16: warning: comparison between signed
and unsigned integer expressions [-Wsign-compare]

  for(int i=0; i<sizeX; i++)

                ^

swigCpp/../src/swigVolumeFnc.cpp:659:17: warning: comparison between signed
and unsigned integer expressions [-Wsign-compare]

   for(int j=0; j<sizeY; j++)

                 ^

swigCpp/../src/swigVolumeFnc.cpp:660:18: warning: comparison between signed
and unsigned integer expressions [-Wsign-compare]

    for(int k=0; k<sizeZ; k++)

                  ^

swigCpp/../src/swigVolumeFnc.cpp: In instantiation of 'void
swigTom::mirrorVolume(swigTom::swigVolume<T, TSCALE_SHIFT>&,
swigTom::swigVolume<T, TSCALE_SHIFT>&) [with T = float; TSHIFT_SCALE =
float]':

swigCpp/pytom_volume_wrap.cpp:10642:81:   required from here

swigCpp/../src/swigVolumeFnc.cpp:681:16: warning: comparison between signed
and unsigned integer expressions [-Wsign-compare]

  for(int i=0; i<sizeX; i++)

                ^

swigCpp/../src/swigVolumeFnc.cpp:682:17: warning: comparison between signed
and unsigned integer expressions [-Wsign-compare]

   for(int j=0; j<sizeY; j++)

                 ^

swigCpp/../src/swigVolumeFnc.cpp:683:18: warning: comparison between signed
and unsigned integer expressions [-Wsign-compare]

    for(int k=0; k<sizeZ; k++)

                  ^

swigCpp/../src/swigVolumeFnc.cpp: In instantiation of
'swigTom::swigVolume<std::complex<_Tp>, TSCALE_SHIFT>
swigTom::sfFourierShift(const swigTom::swigVolume<std::complex<_Tp>,
TSCALE_SHIFT>&, double, int, int, int, int, double, double, double) [with T
= float; TSCALE_SHIFT = float]':

swigCpp/pytom_volume_wrap.cpp:11661:186:   required from here

swigCpp/../src/swigVolumeFnc.cpp:1021:19: warning: comparison between
signed and unsigned integer expressions [-Wsign-compare]

  if(vol.getSizeX()!=4*b*b || vol.getSizeY()!=1 || vol.getSizeZ()!=1)

                   ^

/opt/local/bin/g++-mp-4.9   swigLibs/pytom_volume_wrap.o -o
swigModules/_pytom_volume.so  -lstdc++ -shared -ltomc -fpermissive
-L/opt/local/lib -lfftw3 -lfftw3f -fpermissive  -L/opt/local/lib
-lpython2.7 -L/opt/local/lib/openmpi-mp/ -lmpi
-L/opt/src/pytom/pytomc/libs/libtomc/libs/

swig -Wall -python -c++ -outdir ./swigModules/  -I./libs/libtomc/include
-I./include -I/opt/local/include
-I/opt/local/Library/Frameworks/Python.framework/Versions/current/include/python2.7/
-I/opt/local/include/
-I/opt/local/Library/Frameworks/Python.framework/Versions/current/include/python2.7/
-I/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/numpy/core/include/numpy
-I./src -o swigCpp/pytom_fftplan_wrap.cpp swigCode/pytom_fftplan.i

/opt/local/bin/g++-mp-4.9  -fPIC -c -g3 -Wall -Wno-long-long -pedantic
-ansi --std=c++98 -fpermissive  -D_GLIBCXX_DEBUG -I./libs/libtomc/include
-I./include -I/opt/local/include
-I/opt/local/Library/Frameworks/Python.framework/Versions/current/include/python2.7/
-I/opt/local/include/
-I/opt/local/Library/Frameworks/Python.framework/Versions/current/include/python2.7/
-I/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/numpy/core/include/numpy
swigCpp/pytom_fftplan_wrap.cpp -o swigLibs/pytom_fftplan_wrap.o

/opt/local/bin/g++-mp-4.9   swigLibs/pytom_fftplan_wrap.o -o
swigModules/_pytom_fftplan.so  -lstdc++ -shared -ltomc -fpermissive
-L/opt/local/lib -lfftw3 -lfftw3f -fpermissive  -L/opt/local/lib
-lpython2.7 -L/opt/local/lib/openmpi-mp/ -lmpi
-L/opt/src/pytom/pytomc/libs/libtomc/libs/

swig -Wall -python -c++ -outdir ./swigModules/  -I./libs/libtomc/include
-I./include -I/opt/local/include
-I/opt/local/Library/Frameworks/Python.framework/Versions/current/include/python2.7/
-I/opt/local/include/
-I/opt/local/Library/Frameworks/Python.framework/Versions/current/include/python2.7/
-I/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/numpy/core/include/numpy
-I./src -o swigCpp/pytom_freqweight_wrap.cpp swigCode/pytom_freqweight.i

./include/swigFreqWeight.hpp:88: Warning 321: 'apply' conflicts with a
built-in name in python

./include/swigFreqWeight.hpp:88: Warning 321: 'apply' conflicts with a
built-in name in python

/opt/local/bin/g++-mp-4.9  -fPIC -c -g3 -Wall -Wno-long-long -pedantic
-ansi --std=c++98 -fpermissive  -D_GLIBCXX_DEBUG -I./libs/libtomc/include
-I./include -I/opt/local/include
-I/opt/local/Library/Frameworks/Python.framework/Versions/current/include/python2.7/
-I/opt/local/include/
-I/opt/local/Library/Frameworks/Python.framework/Versions/current/include/python2.7/
-I/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/numpy/core/include/numpy
swigCpp/pytom_freqweight_wrap.cpp -o swigLibs/pytom_freqweight_wrap.o

/opt/local/bin/g++-mp-4.9   swigLibs/pytom_freqweight_wrap.o -o
swigModules/_pytom_freqweight.so  -lstdc++ -shared -ltomc -fpermissive
-L/opt/local/lib -lfftw3 -lfftw3f -fpermissive  -L/opt/local/lib
-lpython2.7 -L/opt/local/lib/openmpi-mp/ -lmpi
-L/opt/src/pytom/pytomc/libs/libtomc/libs/

mpic++ -fPIC -c -g3 -Wall -Wno-long-long -pedantic -ansi --std=c++98
-fpermissive  -D_GLIBCXX_DEBUG -I./libs/libtomc/include -I./include
-I/opt/local/include
-I/opt/local/Library/Frameworks/Python.framework/Versions/current/include/python2.7/
-I/opt/local/include/
-I/opt/local/Library/Frameworks/Python.framework/Versions/current/include/python2.7/
-I/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/numpy/core/include/numpy
-I/usr/local/include src/swigMPI.cpp -o swigLibs/swigMPI.o

*src/swigMPI.cpp:* In function ‘*std::__cxx11::string receive()*’:

*src/swigMPI.cpp:84:24:* *warning: *logical not is only applied to the left
hand side of comparison [-Wlogical-not-parentheses]

  if(!status.MPI_SOURCE == status2.MPI_SOURCE){

*                        ^*

swig -Wall -python -c++ -outdir ./swigModules/  -I./libs/libtomc/include
-I./include -I/opt/local/include
-I/opt/local/Library/Frameworks/Python.framework/Versions/current/include/python2.7/
-I/opt/local/include/
-I/opt/local/Library/Frameworks/Python.framework/Versions/current/include/python2.7/
-I/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/numpy/core/include/numpy
-I./src -I/usr/local/include -o swigCpp/pytom_mpi_wrap.cpp
swigCode/pytom_mpi.i

mpic++ -fPIC -c -g3 -Wall -Wno-long-long -pedantic -ansi --std=c++98
-fpermissive  -D_GLIBCXX_DEBUG -I./libs/libtomc/include -I./include
-I/opt/local/include
-I/opt/local/Library/Frameworks/Python.framework/Versions/current/include/python2.7/
-I/opt/local/include/
-I/opt/local/Library/Frameworks/Python.framework/Versions/current/include/python2.7/
-I/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/numpy/core/include/numpy
swigCpp/pytom_mpi_wrap.cpp -o swigLibs/pytom_mpi_wrap.o

In file included from *swigCpp/pytom_mpi_wrap.cpp:3051:0*:

*swigCpp/../src/swigMPI.cpp:* In function ‘*std::__cxx11::string receive()*
’:

*swigCpp/../src/swigMPI.cpp:84:24:* *warning: *logical not is only applied
to the left hand side of comparison [-Wlogical-not-parentheses]

  if(!status.MPI_SOURCE == status2.MPI_SOURCE){

*                        ^*

mpic++  swigLibs/pytom_mpi_wrap.o -o swigModules/_pytom_mpi.so  -lstdc++
-shared -ltomc -fpermissive -L/opt/local/lib -lfftw3 -lfftw3f -fpermissive
-L/opt/local/lib -lpython2.7 -L/opt/local/lib/openmpi-mp/ -lmpi
-L/opt/local/lib/openmpi-mp/ -lmpi
-L/opt/src/pytom/pytomc/libs/libtomc/libs/ -I/usr/local/include

swig -Wall -python -c++ -outdir ./swigModules/  -I./libs/libtomc/include
-I./include -I/opt/local/include
-I/opt/local/Library/Frameworks/Python.framework/Versions/current/include/python2.7/
-I/opt/local/include/
-I/opt/local/Library/Frameworks/Python.framework/Versions/current/include/python2.7/
-I/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/numpy/core/include/numpy
-I./src -o swigCpp/pytom_numpy_wrap.cpp swigCode/pytom_numpy.i

./src/swigTomNumpy.cpp:79: Warning 302: Identifier 'volume_to_numpy'
redefined (ignored),

./include/swigTomNumpy.hpp:18: Warning 302: previous definition of
'volume_to_numpy'.

./src/swigTomNumpy.cpp:121: Warning 302: Identifier 'numpy_to_volume'
redefined (ignored),

./include/swigTomNumpy.hpp:21: Warning 302: previous definition of
'numpy_to_volume'.

swigCode/pytom_numpy.i:27: Warning 302: Identifier 'npy2vol' redefined
(ignored) (Renamed from 'numpy_to_volume< std::complex< float >,float >'),

swigCode/pytom_numpy.i:26: Warning 302: previous definition of 'npy2vol'
(Renamed from 'numpy_to_volume< float,float >').

/opt/local/bin/g++-mp-4.9  -fPIC -c -g -Wall -Wno-long-long  -ansi
--std=c++98 -I./libs/libtomc/include -I./include -I/opt/local/include
-I/opt/local/Library/Frameworks/Python.framework/Versions/current/include/python2.7/
-I/opt/local/include/
-I/opt/local/Library/Frameworks/Python.framework/Versions/current/include/python2.7/
-I/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/numpy/core/include/numpy
swigCpp/pytom_numpy_wrap.cpp -o swigLibs/pytom_numpy_wrap.o #-I

In file included from
/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804:0,

                 from
/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,

                 from ./include/swigTomNumpy.hpp:13,

                 from swigCpp/pytom_numpy_wrap.cpp:3049:

/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2:
warning: #warning "Using deprecated NumPy API, disable it by " "#defining
NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]

 #warning "Using deprecated NumPy API, disable it by " \

  ^

/opt/local/bin/g++-mp-4.9   swigLibs/pytom_numpy_wrap.o -o
swigModules/_pytom_numpy.so  -lstdc++ -shared -ltomc -fpermissive
-L/opt/local/lib -lfftw3 -lfftw3f -fpermissive  -L/opt/local/lib
-lpython2.7 -L/opt/local/lib/openmpi-mp/ -lmpi
-L/opt/src/pytom/pytomc/libs/libtomc/libs/


############ Start to compile the SH Alignment Library ############


Search include files ...

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

Search dynamic library files ...

Compile ...

export
PYTHON_INCLUDE_PATH="/opt/local/Library/Frameworks/Python.framework/Versions/current/include/python2.7/"
&& export
NUMPY_INCLUDE_PATH="/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/numpy/core/include/"
&& export FFTW_INCLUDE_PATH="/opt/local/include" && export
FFTW_LIB_PATH="/opt/local/lib" && cd sh_alignment/SpharmonicKit27 && make
all

make \

legendre \

sphere \

shared

make \

test_naive \

test_stability_naive \

test_semi \

test_flt_classic \

test_flt_dhmid \

test_flt_hybrid

make[2]: `test_naive' is up to date.

make[2]: `test_stability_naive' is up to date.

make[2]: `test_semi' is up to date.

make[2]: `test_flt_classic' is up to date.

make[2]: `test_flt_dhmid' is up to date.

make[2]: `test_flt_hybrid' is up to date.

make \

FST_precomp2disk \

test_FST_semi_memo \

test_FST_semi_disk \

test_FST_semi_fly \

CONV_SEMI_DISK \

CONV_SEMI_MEMO \

CONV_SEMI_FLY \

test_FST_hybrid_disk \

test_FST_hybrid_memo \

test_FST_hybrid_memoX \

CONV_HYBRID_DISK \

CONV_HYBRID_MEMO

make[2]: `FST_precomp2disk' is up to date.

make[2]: `test_FST_semi_memo' is up to date.

make[2]: `test_FST_semi_disk' is up to date.

make[2]: `test_FST_semi_fly' is up to date.

make[2]: `CONV_SEMI_DISK' is up to date.

make[2]: `CONV_SEMI_MEMO' is up to date.

make[2]: `CONV_SEMI_FLY' is up to date.

make[2]: `test_FST_hybrid_disk' is up to date.

make[2]: `test_FST_hybrid_memo' is up to date.

make[2]: `test_FST_hybrid_memoX' is up to date.

make[2]: `CONV_HYBRID_DISK' is up to date.

make[2]: `CONV_HYBRID_MEMO' is up to date.

cc -shared OURperms.o OURmods.o newFCT.o weights.o cospmls.o seminaive.o
oddweights.o csecond.o primitive.o FST_semi_memo.o naive_synthesis.o
primitive_FST.o permroots.o indextables.o FFTcode.o fft_grids.o -o
libsphkit.so

export
PYTHON_INCLUDE_PATH="/opt/local/Library/Frameworks/Python.framework/Versions/current/include/python2.7/"
&& export
NUMPY_INCLUDE_PATH="/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/numpy/core/include/"
&& export FFTW_INCLUDE_PATH="/opt/local/include" && export
FFTW_LIB_PATH="/opt/local/lib" && cd sh_alignment/frm/src/ && make lib

make: Nothing to be done for `lib'.

export
PYTHON_INCLUDE_PATH="/opt/local/Library/Frameworks/Python.framework/Versions/current/include/python2.7/"
&& export
NUMPY_INCLUDE_PATH="/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/numpy/core/include/"
&& export FFTW_INCLUDE_PATH="/opt/local/include" && export
FFTW_LIB_PATH="/opt/local/lib" && cd sh_alignment/frm/swig/ && chmod +x
mkswig.sh && ./mkswig.sh

In file included from
/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804:0,

                 from
/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,

                 from
/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,

                 from frm_wrap.c:2961:

/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2:
warning: #warning "Using deprecated NumPy API, disable it by " "#defining
NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]

 #warning "Using deprecated NumPy API, disable it by " \

  ^

ld: warning: directory not found for option '-L-l'

Undefined symbols for architecture x86_64:

  "_PyArg_ParseTuple", referenced from:

      __wrap_get_constraint_vol in frm_wrap.o

      __wrap_enlarge2 in frm_wrap.o

      __wrap_find_topn_angles in frm_wrap.o

      __wrap_frm_fourier_corr in frm_wrap.o

      __wrap_frm_corr in frm_wrap.o

      __wrap_frm in frm_wrap.o

  "_PyArg_UnpackTuple", referenced from:

      _SwigPyObject_own in frm_wrap.o

  "_PyBool_FromLong", referenced from:

      _SwigPyObject_own in frm_wrap.o

      _SwigPyObject_richcompare in frm_wrap.o

  "_PyCObject_AsVoidPtr", referenced from:

      _init_swig_frm in frm_wrap.o

  "_PyCObject_Type", referenced from:

      _init_swig_frm in frm_wrap.o

  "_PyCallable_Check", referenced from:

      _pytype_string in frm_wrap.o

  "_PyCapsule_GetPointer", referenced from:

      _SWIG_Python_DestroyModule in frm_wrap.o

  "_PyCapsule_Import", referenced from:

      _init_swig_frm in frm_wrap.o

  "_PyCapsule_New", referenced from:

      _init_swig_frm in frm_wrap.o

  "_PyDict_New", referenced from:

      _init_swig_frm in frm_wrap.o

  "_PyDict_SetItem", referenced from:

      _init_swig_frm in frm_wrap.o

  "_PyDict_SetItemString", referenced from:

      _init_swig_frm in frm_wrap.o

  "_PyErr_Clear", referenced from:

      __wrap_get_constraint_vol in frm_wrap.o

      __wrap_enlarge2 in frm_wrap.o

      __wrap_find_topn_angles in frm_wrap.o

      _init_swig_frm in frm_wrap.o

  "_PyErr_Format", referenced from:

      _obj_to_array_no_conversion in frm_wrap.o

      _require_dimensions in frm_wrap.o

      _require_dimensions_n in frm_wrap.o

      _require_size in frm_wrap.o

      __wrap_enlarge2 in frm_wrap.o

      __wrap_find_topn_angles in frm_wrap.o

      __wrap_frm_fourier_corr in frm_wrap.o

      ...

  "_PyErr_Occurred", referenced from:

      __wrap_get_constraint_vol in frm_wrap.o

      __wrap_enlarge2 in frm_wrap.o

      __wrap_find_topn_angles in frm_wrap.o

      _init_swig_frm in frm_wrap.o

  "_PyErr_Print", referenced from:

      _init_swig_frm in frm_wrap.o

  "_PyErr_SetString", referenced from:

      __wrap_get_constraint_vol in frm_wrap.o

      _require_contiguous in frm_wrap.o

      __wrap_enlarge2 in frm_wrap.o

      __wrap_find_topn_angles in frm_wrap.o

      _init_swig_frm in frm_wrap.o

      _require_contiguous.part.16 in frm_wrap.o

  "_PyExc_AttributeError", referenced from:

      _init_swig_frm in frm_wrap.o

  "_PyExc_ImportError", referenced from:

      _init_swig_frm in frm_wrap.o

  "_PyExc_OverflowError", referenced from:

      __wrap_get_constraint_vol in frm_wrap.o

      __wrap_enlarge2 in frm_wrap.o

      __wrap_find_topn_angles in frm_wrap.o

  "_PyExc_RuntimeError", referenced from:

      _init_swig_frm in frm_wrap.o

  "_PyExc_TypeError", referenced from:

      _obj_to_array_no_conversion in frm_wrap.o

      __wrap_get_constraint_vol in frm_wrap.o

      _require_contiguous in frm_wrap.o

      _require_dimensions in frm_wrap.o

      _require_dimensions_n in frm_wrap.o

      _require_size in frm_wrap.o

      __wrap_enlarge2 in frm_wrap.o

      ...

  "_PyFile_Type", referenced from:

      _pytype_string in frm_wrap.o

  "_PyFloat_AsDouble", referenced from:

      __wrap_get_constraint_vol in frm_wrap.o

      __wrap_find_topn_angles in frm_wrap.o

  "_PyFloat_Type", referenced from:

      _pytype_string in frm_wrap.o

      __wrap_get_constraint_vol in frm_wrap.o

      __wrap_find_topn_angles in frm_wrap.o

  "_PyImport_ImportModule", referenced from:

      _init_swig_frm in frm_wrap.o

  "_PyInstance_NewRaw", referenced from:

      _init_swig_frm in frm_wrap.o

  "_PyInstance_Type", referenced from:

      _pytype_string in frm_wrap.o

  "_PyInt_AsLong", referenced from:

      __wrap_get_constraint_vol in frm_wrap.o

      __wrap_enlarge2 in frm_wrap.o

      __wrap_find_topn_angles in frm_wrap.o

  "_PyInt_FromLong", referenced from:

      __wrap_get_constraint_vol in frm_wrap.o

      __wrap_enlarge2 in frm_wrap.o

      __wrap_find_topn_angles in frm_wrap.o

      __wrap_frm_fourier_corr in frm_wrap.o

      __wrap_frm_corr in frm_wrap.o

      __wrap_frm in frm_wrap.o

  "_PyLong_AsDouble", referenced from:

      __wrap_get_constraint_vol in frm_wrap.o

      __wrap_find_topn_angles in frm_wrap.o

  "_PyLong_AsLong", referenced from:

      __wrap_get_constraint_vol in frm_wrap.o

      __wrap_enlarge2 in frm_wrap.o

      __wrap_find_topn_angles in frm_wrap.o

  "_PyLong_FromVoidPtr", referenced from:

      _SwigPyObject_long in frm_wrap.o

      _SwigPyObject_oct in frm_wrap.o

      _SwigPyObject_hex in frm_wrap.o

  "_PyModule_AddObject", referenced from:

      _init_swig_frm in frm_wrap.o

  "_PyModule_GetDict", referenced from:

      _init_swig_frm in frm_wrap.o

  "_PyModule_Type", referenced from:

      _pytype_string in frm_wrap.o

  "_PyObject_Call", referenced from:

      _init_swig_frm in frm_wrap.o

  "_PyObject_CallFunctionObjArgs", referenced from:

      _SwigPyObject_dealloc in frm_wrap.o

  "_PyObject_Free", referenced from:

      _SwigPyPacked_dealloc in frm_wrap.o

      _SwigPyObject_dealloc in frm_wrap.o

      _init_swig_frm in frm_wrap.o

  "_PyObject_GenericGetAttr", referenced from:

      _SwigPyPacked_dealloc in frm_wrap.o

      _init_swig_frm in frm_wrap.o

      _tmp.8949 in frm_wrap.o

  "_PyObject_GetAttrString", referenced from:

      _init_swig_frm in frm_wrap.o

  "_PyObject_Init", referenced from:

      _SwigPyObject_dealloc in frm_wrap.o

      _init_swig_frm in frm_wrap.o

  "_PyObject_IsTrue", referenced from:

      _SwigPyObject_own in frm_wrap.o

  "_PyObject_Malloc", referenced from:

      _SwigPyObject_dealloc in frm_wrap.o

      _init_swig_frm in frm_wrap.o

  "_PyString_ConcatAndDel", referenced from:

      _SwigPyObject_repr in frm_wrap.o

  "_PyString_Format", referenced from:

      _SwigPyObject_oct in frm_wrap.o

      _SwigPyObject_hex in frm_wrap.o

  "_PyString_FromFormat", referenced from:

      _SwigPyPacked_str in frm_wrap.o

      _SwigPyPacked_repr in frm_wrap.o

      _SwigPyObject_repr in frm_wrap.o

  "_PyString_FromString", referenced from:

      _SwigPyObject_oct in frm_wrap.o

      _SwigPyPacked_str in frm_wrap.o

      _SWIG_Python_DestroyModule in frm_wrap.o

      _SwigPyObject_hex in frm_wrap.o

      _init_swig_frm in frm_wrap.o

  "_PyTuple_New", referenced from:

      _SwigPyObject_oct in frm_wrap.o

      _SwigPyObject_hex in frm_wrap.o

  "_PyTuple_SetItem", referenced from:

      _SwigPyObject_oct in frm_wrap.o

      _SwigPyObject_hex in frm_wrap.o

  "_PyType_IsSubtype", referenced from:

      _pytype_string in frm_wrap.o

      _obj_to_array_no_conversion in frm_wrap.o

      __wrap_get_constraint_vol in frm_wrap.o

      _obj_to_array_allow_conversion in frm_wrap.o

      _obj_to_array_contiguous_allow_conversion in frm_wrap.o

      __wrap_find_topn_angles in frm_wrap.o

  "_PyType_Ready", referenced from:

      _SwigPyPacked_dealloc in frm_wrap.o

      _SwigPyObject_append in frm_wrap.o

      _SwigPyObject_dealloc in frm_wrap.o

      _init_swig_frm in frm_wrap.o

  "_Py_InitModule4_64", referenced from:

      _init_swig_frm in frm_wrap.o

  "__PyObject_GetDictPtr", referenced from:

      _init_swig_frm in frm_wrap.o

  "__PyObject_New", referenced from:

      _init_swig_frm in frm_wrap.o

  "__Py_NoneStruct", referenced from:

      _SwigPyObject_disown in frm_wrap.o

      _SwigPyObject_acquire in frm_wrap.o

      _SwigPyObject_own in frm_wrap.o

      _SwigPyObject_next in frm_wrap.o

      _SwigPyObject_append in frm_wrap.o

      _init_swig_frm in frm_wrap.o

  "__Py_NotImplementedStruct", referenced from:

      _SwigPyObject_richcompare in frm_wrap.o

ld: symbol(s) not found for architecture x86_64

clang: error: linker command failed with exit code 1 (use -v to see
invocation)


Finished!



############ Start to compile mpi4py Library ############


Searching :  mpicc   Found :  True

running build

running build_src

running build_py

running build_clib

MPI configuration: [mpi] from 'mpi.cfg'

MPI C compiler:    /opt/local/bin/mpicc

checking for library 'vt-mpi' ...

/opt/local/bin/mpicc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -Wstrict-prototypes -c _configtest.c -o _configtest.o

/opt/local/bin/mpicc _configtest.o -lvt-mpi -o _configtest

success!

removing: _configtest.c _configtest.o _configtest

building 'vt' dylib library

/opt/local/bin/mpicc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -Wstrict-prototypes -c src/pmpi-vt.c -o
build/temp.macosx-10.10-x86_64-2.7/src/pmpi-vt.o

/opt/local/bin/mpicc -bundle -undefined dynamic_lookup -L/opt/local/lib
-Wl,-headerpad_max_install_names -L/opt/local/lib/db48
build/temp.macosx-10.10-x86_64-2.7/src/pmpi-vt.o -o
build/lib.macosx-10.10-x86_64-2.7/mpi4py/lib-pmpi/libvt.dylib -lvt-mpi
-lotf -lz -ldl

ld: library not found for -lotf

clang: error: linker command failed with exit code 1 (use -v to see
invocation)

warning: build_clib: building library "vt" failed


warning: build_clib: command '/opt/local/bin/mpicc' failed with exit status
1


running build_ext

MPI configuration: [mpi] from 'mpi.cfg'

MPI C compiler:    /opt/local/bin/mpicc

running build_exe

MPI configuration: [mpi] from 'mpi.cfg'

MPI C compiler:    /opt/local/bin/mpicc

running install

running build

running build_src

running build_py

running build_clib

MPI configuration: [mpi] from 'mpi.cfg'

MPI C compiler:    /opt/local/bin/mpicc

MPI C++ compiler:  /opt/local/bin/mpicxx

MPI F77 compiler:  /opt/local/bin/mpif77

MPI F90 compiler:  /opt/local/bin/mpif90

checking for library 'vt-mpi' ...

/opt/local/bin/mpicc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -Wstrict-prototypes -c _configtest.c -o _configtest.o

/opt/local/bin/mpicc _configtest.o -lvt-mpi -o _configtest

success!

removing: _configtest.c _configtest.o _configtest

building 'vt' dylib library

/opt/local/bin/mpicc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -Wstrict-prototypes -c src/pmpi-vt.c -o
build/temp.macosx-10.10-x86_64-2.7/src/pmpi-vt.o

/opt/local/bin/mpicc -bundle -undefined dynamic_lookup -L/opt/local/lib
-Wl,-headerpad_max_install_names -L/opt/local/lib/db48
build/temp.macosx-10.10-x86_64-2.7/src/pmpi-vt.o -o
build/lib.macosx-10.10-x86_64-2.7/mpi4py/lib-pmpi/libvt.dylib -lvt-mpi
-lotf -lz -ldl

ld: library not found for -lotf

clang: error: linker command failed with exit code 1 (use -v to see
invocation)

warning: build_clib: building library "vt" failed


warning: build_clib: command '/opt/local/bin/mpicc' failed with exit status
1


running build_ext

MPI configuration: [mpi] from 'mpi.cfg'

MPI C compiler:    /opt/local/bin/mpicc

MPI C++ compiler:  /opt/local/bin/mpicxx

MPI F77 compiler:  /opt/local/bin/mpif77

MPI F90 compiler:  /opt/local/bin/mpif90

running build_exe

MPI configuration: [mpi] from 'mpi.cfg'

MPI C compiler:    /opt/local/bin/mpicc

MPI C++ compiler:  /opt/local/bin/mpicxx

MPI F77 compiler:  /opt/local/bin/mpif77

MPI F90 compiler:  /opt/local/bin/mpif90

running install_lib

writing byte-compilation script '/tmp/tmpe6I3vQ.py'

/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
-O /tmp/tmpe6I3vQ.py

removing /tmp/tmpe6I3vQ.py

running install_egg_info

Removing ../..//lib/python2.7/site-packages/mpi4py-1.3.1-py2.7.egg-info

Writing ../..//lib/python2.7/site-packages/mpi4py-1.3.1-py2.7.egg-info



############ Start to compile NFFT Library ############


checking build system type... i386-apple-darwin14.3.0

checking host system type... i386-apple-darwin14.3.0

checking for gcc... gcc

checking for C compiler default output file name... a.out

checking whether the C compiler works... yes

checking whether we are cross compiling... no

checking for suffix of executables...

checking for suffix of object files... o

checking whether we are using the GNU C compiler... yes

checking whether gcc accepts -g... yes

checking for gcc option to accept ISO C89... none needed

checking for a sed that does not truncate output... /opt/local/bin/gsed

checking for grep that handles long lines and -e... /usr/bin/grep

checking for egrep... /usr/bin/grep -E

checking for fgrep... /usr/bin/grep -F

checking for ld used by gcc... /opt/local/bin/ld

checking if the linker (/opt/local/bin/ld) is GNU ld... no

checking for BSD- or MS-compatible name lister (nm)... /opt/local/bin/nm

checking the name lister (/opt/local/bin/nm) interface... BSD nm

checking whether ln -s works... yes

checking the maximum length of command line arguments... 196608

checking whether the shell understands some XSI constructs... yes

checking whether the shell understands "+="... yes

checking for /opt/local/bin/ld option to reload object files... -r

checking for objdump... no

checking how to recognize dependent libraries... pass_all

checking for ar... ar

checking for strip... strip

checking for ranlib... ranlib

checking command to parse /opt/local/bin/nm output from gcc object... ok

checking for dsymutil... dsymutil

checking for nmedit... nmedit

checking for lipo... lipo

checking for otool... otool

checking for otool64... no

checking for -single_module linker flag... yes

checking for -exported_symbols_list linker flag... yes

checking how to run the C preprocessor... gcc -E

checking for ANSI C header files... yes

checking for sys/types.h... yes

checking for sys/stat.h... yes

checking for stdlib.h... yes

checking for string.h... yes

checking for memory.h... yes

checking for strings.h... yes

checking for inttypes.h... yes

checking for stdint.h... yes

checking for unistd.h... yes

checking for dlfcn.h... yes

checking for objdir... .libs

checking if gcc supports -fno-rtti -fno-exceptions... no

checking for gcc option to produce PIC... -fno-common -DPIC

checking if gcc PIC flag -fno-common -DPIC works... yes

checking if gcc static flag -static works... no

checking if gcc supports -c -o file.o... yes

checking if gcc supports -c -o file.o... (cached) yes

checking whether the gcc linker (/opt/local/bin/ld) supports shared
libraries... yes

checking dynamic linker characteristics... darwin14.3.0 dyld

checking how to hardcode library paths into programs... immediate

checking whether stripping libraries is possible... yes

checking if libtool supports shared libraries... yes

checking whether to build shared libraries... yes

checking whether to build static libraries... yes

checking whether make sets $(MAKE)... yes

checking for a BSD-compatible install... /usr/bin/install -c

checking whether build environment is sane... yes

checking for a thread-safe mkdir -p... config/install-sh -c -d

checking for gawk... no

checking for mawk... no

checking for nawk... no

checking for awk... awk

checking for style of include used by make... GNU

checking dependency style of gcc... gcc3

checking whether to enable maintainer-specific portions of Makefiles... no

checking for an ANSI C-conforming const... yes

checking for C/C++ restrict keyword... __restrict

checking for inline... inline

checking if C compiler supports blocks... no

checking for C compiler vendor... apple

checking for a BSD-compatible install... /usr/bin/install -c

checking whether ln -s works... yes

checking for libdispatch... no

checking whether to check for Matlab... no

checking fftw3.h usability... yes

checking fftw3.h presence... yes

checking for fftw3.h... yes

checking for fftw_execute in -lfftw3... no

configure: error: The fftw3 library could not be found. You can download it
from#

     http://www.fftw.org. If you have installed fftw3, make sure that#

     this configure script can find it. See ./configure --help for#

     more information.

make: *** No targets specified and no makefile found.  Stop.


export
PYTHON_INCLUDE_PATH="/opt/local/Library/Frameworks/Python.framework/Versions/current/include/python2.7/"
&& export
NUMPY_INCLUDE_PATH="/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/numpy/core/include/"
&& export FFTW_INCLUDE_PATH="/opt/local/include" && export
FFTW_LIB_PATH="/opt/local/lib" && export
NFFT_LIB_PATH="/opt/src/pytom/external/lib/" && export
NFFT_INCLUDE_PATH="/opt/src/pytom/external/include/" && cd nufft/ && chmod
+x mkswig.sh && ./mkswig.sh

nufft.c:25:23: fatal error: nfft3util...
 
[truncated message content]