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Re: [Pytom-mail] compilation error in OSX10.10.3
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From: Sara W. <sj...@gm...> - 2015-06-26 19:01:52
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Hi Thomas, Thanks for your email. If I set nosh, nompi4py and nonfft to True, I do successfully compile (going by the suggested tests in the installation guide). Then I did make clean and changed the settings back to False and compiled again. It is still successful, but maintains the errors in the those three libraries. I suppose I'll try running some things and troubleshoot from there. I'll also see if I can get one of my coworkers to install it on a linux computer. Thanks! Best, Sara On Fri, Jun 26, 2015 at 10:19 AM Thomas Hrabe <th...@gm...> wrote: > Hi Sara, > > I would suggest the same procedure as for Cannon before (point 2 in the > email yesterday), disable the additional packages and focus on the core > first. > Once they compiled and tested successfully, I would try to compile the > whole package. > > It’s hard to keep track of Mac settings because all XCode and the included > compiler & environment updates require you to re-adjust all Macport > libraries many times. > I believe that installing it on Mac is the most difficult of all setups => > if you have a linux box that you can use and log in through your desktop > would be easier. > > Let me know how it goes. > > Cheers, > Thomas > > > > > On Jun 26, 2015, at 9:42 AM, Sara Weaver <sj...@gm...> wrote: > > 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 eg... [truncated message content] |
