I am trying to compile a Python PCL module which builds some C++ source. I am getting this error:
$ python setup.py install
running install
running build
running build_py
running build_ext
skipping 'pcl/_pcl.cpp' Cython extension (up-to-date)
building 'pcl._pcl' extension
/usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Library/Python/2.7/site-packages/numpy/core/include -I/usr/local/Cellar/pcl/HEAD/include/pcl-1.8 -I/usr/local/Cellar/eigen/3.2.3/include/eigen3 -I/usr/local/Cellar/pcl/HEAD/include/pcl-1.8 -I/usr/local/Cellar/flann/1.8.4/include -I/usr/local/Cellar/pcl/HEAD/include/pcl-1.8 -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c pcl/_pcl.cpp -o build/temp.macosx-10.6-intel-2.7/pcl/_pcl.o
pcl/_pcl.cpp:244:10: fatal error: 'boost/smart_ptr/shared_ptr.hpp' file not
found
#include "boost/smart_ptr/shared_ptr.hpp"
^
1 error generated.
error: command '/usr/bin/clang'
For whatever reason clang isn't looking in /usr/local/include where it most definitely would find the boost headers. As you can see it is linking all the other dependencies fine. What can I add that so clang will find boost?
On OSX 10.10, nothing fancy happening anywhere. Boost was probably installed by homebrew, but the files are all in /usr/local/include/boost as I'd expect.
Check the output of /usr/bin/clang++ -v some_test_file.cpp but chances are /usr/local/include isn't in the standard search path of the compiler.
You'll need to add -I/usr/local/include to CXXFLAGS or CPPFLAGS or whatever appropriate place in your build script or environment. It seems the python build script is failing to properly detect Boost.
If the above is not true (and /usr/local/include does show up in the output), make sure /usr/local/include/boost/smart_ptr/shared_ptr.hpp exists.
Related
I'm using Cygwin to make the makefile of kore.io on Windows 10 and get the following error:
gcc -Wall -Werror -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wshadow -Wpointer-arith -Wcast-qual -Wsign-compare -Iincludes -std=c99 -pedantic -DPREFIX='"/usr/local"' -O2 -c src/kore.c -o obj/kore.o
src/kore.c:20:24: fatal error: sys/socket.h: No such file or directory
compilation terminated.
make: *** [obj/kore.o] Fout 1
I've looked around, but none of the solutions I found worked for me.
I checked the Cygwin /usr/include/sys folder and did find socket.h.
I read through the makefile and don't see anything wrong with the lib references.
I've been trying to get this work for over an hour now.
Thanks in advance.
To find which package you need to install, use cygcheck to find the package containing sys/socket.h
$ cygcheck -p usr/include/sys/socket.h
Found 5 matches for usr/include/sys/socket.h
cygwin-devel-2.6.1-1 - cygwin-devel: Core development files (installed binaries and support files)
cygwin-devel-2.7.0-1 - cygwin-devel: Core development files
cygwin-devel-2.8.0-1 - cygwin-devel: Core development files
cygwin32-2.5.2-1 - cygwin32: Cygwin 32bit toolchain (installed binaries and support files)
cygwin32-2.6.0-1 - cygwin32: Cygwin 32bit toolchain (installed binaries and support files)
So you need to install cygwin-devel that contains the cygwin standard headers.
I've downloaded from github and built gcc. After that I've tried to compile a code with OpenMP:
../GCC/build/gcc/xgcc -B./../GCC/build/gcc/ -I./../GCC/build/x86_64-unknown-linux-gnu/libgomp -Wno-write-strings -O3 -Wall -fopenmp -lpng -o mandelbrot-omp mandelbrot-omp.cpp
Then I got the following error message:
xgcc: error: libgomp.spec: No such file or directory
I've checked and found out that libgomp directory contains the libgomp.spec file. The directory is included with -I option. What's wrong?
I am trying to install a python module (SPArse Modeling Software) but the install script doesn't seem to be able to find the system's default Python.framework. This is an almost new (no migration assistant) Mac OS 10.9.5 system with both the default system python and Anaconda installed. I briefly installed Enthought Canopy but removed it when I decided to go with Anaconda. /System/Library/Frameworks/Python.framework exists and seems to have all the files you would expect.
In terminal, this is what happens:
bash-3.2$ which python
//anaconda/bin/python
bash-3.2$ cd spams-python
bash-3.2$ python setup.py build
running build
running build_py
running build_ext
building '_spams_wrap' extension
gcc -fno-strict-aliasing -I//anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dictLearn -I//anaconda/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7/ -I//anaconda/include/python2.7 -c spams_wrap.cpp -o build/temp.macosx-10.5-x86_64-2.7/spams_wrap.o -DNDEBUG -DUSE_BLAS_LIB -fPIC -fopenmp -m32
clang: warning: argument unused during compilation: '-fopenmp'
#Omitting some irrelevant (I think) warnings#
4 warnings generated.
gcc -bundle -undefined dynamic_lookup -L//anaconda/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.5-x86_64-2.7/spams_wrap.o -L//anaconda/lib -lstdc++ -lblas -llapack -o build/lib.macosx-10.5-x86_64-2.7/_spams_wrap.so -m32 -framework Python
ld: framework not found Python
clang: error: linker command failed with exit code 1 (use -v to see invocation)
error: command 'gcc' failed with exit status 1
So, my question is, is my diagnosis of the problem correct? How can I tell GCC where Python.framework is? Is there some environment variable that isn't set correctly?
The Anaconda Python is not a Framework build of Python. If the module expects that it's not going to work. Commenting out commenting out "'-framework', 'Python'" in setup.py sounds like a good start, and if it works, then it probably is the right solution.
Compile it with gcc-5, and I successed.
Running the build script from ELLCC results in this error
gcc -DHAVE_CONFIG_H -I. -I../../../src/binutils/binutils -I. -I../../../src/binutils/binutils -I../bfd -I../../../src/binutils/binutils/../bfd -I../../../src/binutils/binutils/../include -I./../intl -DLOCALEDIR="\"/Library/Caches/Homebrew/ellcc--svn-HEAD/lib/share/locale\"" -Dbin_dummy_emulation=bin_vanilla_emulation -W -Wall -Wstrict-prototypes -Wmissing-prototypes -Wshadow -Werror -Wno-unused-value -Wno-shadow -MT nm.o -MD -MP -MF .deps/nm.Tpo -c -o nm.o ../../../src/binutils/binutils/nm.c
../../../src/binutils/binutils/nm.c:1690:28: error: 'sbrk' is deprecated
[-Werror,-Wdeprecated-declarations]
char *lim = (char *) sbrk (0);
^
/usr/include/unistd.h:582:7: note: 'sbrk' declared here
void *sbrk(int);
^
The following compilers have been used with the same result:
gcc 4.8
llvm-gcc 2.8
llvm 3.3
I had the same issue compiling binutils-2.24 on Mac OSX Mavericks 13.2.0 with clang. Thanks to Richard Pennington's suggestion, I was able to get binutils to compile by specifying a few other -Wno-error arguments to gcc by setting CFLAGS before running configure. Namely, these are the commands I ran to build and install binutils:
CFLAGS="-Wno-error=deprecated-declarations -Wno-error=unused-variable -Wno-error=unused-function" ./configure --prefix=/usr/local/toolchain-arm-linux-elf --target=arm-linux-elf
make
make install
EDIT: I just noticed that the binutils configure script accepts an --disable-werror argument, which disables gcc turning warnings into errors, and removes the need for the settings CFLAGS. With this argument, building could be done as follows:
./configure --prefix=/usr/local/toolchain-arm-linux-elf --target=arm-linux-elf --disable-werror
make
make install
This error is occurring because sbrk() is deprecated on OSX, -Werror is enabled for the binutils build, and the compiler (in this case "gcc" is an alias for clang) rightly complains about the use of sbrk(). I'll be looking into eliminating this error this weekend when I won't have to be at my day job. ;-)
I looked into it a bit more. This happened because the latest version of OS X (Mavericks) uses clang as its compiler and /usr/include/unistd.h has a deprecated declaration of sbrk().
The solution was to add a -Wno-error=deprecated-declarations option to the CFLAGS for binutils. I also had to make a few other changes to complete the Max OS build. You can find the latest stuff in the ELLCC subversion tree.
I'm trying to install PyGSL on my computer (64 bit Windows 7), with Python 2.7 and GSL 1.15 installed. I'm pretty much stuck and I would love for some extra help. GSL installed fine, but its the wrapper that's the problem. For some reason I can't build pygsl. Apparently gcc is the problem (got the same problem on another windows machine). Or it could be that pygsl appears to be using a file named AMD64 while my computer is x86. I would love to use the windows binary for pygsl, but it only exists for python 2.5, and my project needs 2.6 or higher. I've used both the windows binary for GSL and built it from source, but I get the same problem either way. I tried copying dlls from GSL into pygsl but that didn't work. Some forums mentioned a file called gsl.dll but I can't seem to find it. I've also tried to use Cygwin and to compile with minGW32 to no avail.
cmds I ran:
python setup.py install
python setup.py build
python setup.py build_ext -i
python setup.py build --compiler=mingw32
Any ideas?? Thanks.
Cheers,
Bereket
Got the same message in Cygwin as in the windows cmd prompt. Error message:
$ /cygdrive/c/Python27/python.exe setup.py build_ext -i
numpy
Forcing DISTUTILS_USE_SDK=1
Building testing ufuncs!
running build_ext
building 'errno' extension
C compiler: gcc -g -DDEBUG -DMS_WIN64 -mno-cygwin -O0 -Wall -Wstrict-prototypes
compile options: '-DSWIG_COBJECT_TYPES=1 -DGSL_RANGE_CHECK=1 -DDEBUG=1 -DNUMERIC=0 -DPYGSL_GSL_MAJOR_VERSION=1 -DPYGSL_GSL_MINOR_VERSION=15 -UNDEBUG -IC:\Users\Bereket\gsl-1.15\include -IInclude -I. -IC:\Python27\lib\site-packages\numpy\core\include -IC:\Python27\include -IC:\Python27\PC -c'
gcc -g -DDEBUG -DMS_WIN64 -mno-cygwin -O0 -Wall -Wstrict-prototypes -DSWIG_COBJECT_TYPES=1 -DGSL_RANGE_CHECK=1 -DDEBUG=1 -DNUMERIC=0 -DPYGSL_GSL_MAJOR_VERSION=1 -DPYGSL_GSL_MINOR_VERSION=15 -UNDEBUG -IC:\Users\Bereket\gsl-1.15\include -IInclude -I. -IC:\Python27\lib\site-packages\numpy\core\include -IC:\Python27\include -IC:\Python27\PC -c src/init/errorno.c -o build\temp.win-amd64-2.7\Release\src\init\errorno.o
Found executable C:\cygwin\bin\gcc.exe
gcc -g -mno-cygwin -shared build\temp.win-amd64-2.7\Release\src\init\errorno.o -LC:\Users\Bereket\gsl-1.15\lib -LC:\Python27\libs -LC:\Python27\PCbuild\amd64 -lgsl -lgslcblas -lm -lpython27 -lmsvcr90 -o C:\Python27\Lib\pygsl-0.9.5\pygsl\errno.pyd
build\temp.win-amd64-2.7\Release\src\init\errorno.o: In function `add_errno':
/cygdrive/c/Python27/Lib/pygsl-0.9.5/src/init/errorno.c:14: undefined reference to `__imp__PyInt_FromLong'
/cygdrive/c/Python27/Lib/pygsl-0.9.5/src/init/errorno.c:20: undefined reference to `__imp__PyDict_SetItemString'
build\temp.win-amd64-2.7\Release\src\init\errorno.o: In function `initerrno':
/cygdrive/c/Python27/Lib/pygsl-0.9.5/src/init/errorno.c:37: undefined reference to `__imp__Py_InitModule4_64'
/cygdrive/c/Python27/Lib/pygsl-0.9.5/src/init/errorno.c:40: undefined reference to `__imp__PyModule_GetDict'
collect2: ld returned 1 exit status
error: Command "gcc -g -mno-cygwin -shared build\temp.win-amd64-2.7\Release\src\init\errorno.o -LC:\Users\Bereket\gsl-1.15\lib -LC:\Python27\libs -LC:\Python27\PCbuild\amd64 -lgsl -lgslcblas -lm -lpython27 -lmsvcr90 -o C:\Python27\Lib\pygsl-0.9.5\pygsl\errno.pyd" failed with exit status 1
I'm pretty sure now that my GSL install with Cygwin failed / had unresolved dependencies. I'm now trying to install it with visual studio 2010. Here are some good sites for doing that:
Instructions
Alt Method
Installing the Python 2.7 compiler for Windows is a good place to start
http://www.microsoft.com/en-gb/download/details.aspx?id=44266
Running python setup.py build_ext --inplace does the trick for me.
If this doesn't work let me know. You might need to add an environment variable.
Is your Python 32 or 64? To check open Python and do
import sys
sys.versions