Develop Reference

Can't install spams on python 2.7 (Os: Fedora)

I tried to install spams using PiP command but i get this error:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-build-zI4__D/spams/setup.py", line 121, in <module>
with open(os.path.join(this_directory, 'README.md'), encoding='utf-8') as f:
TypeError: 'encoding' is an invalid keyword argument for this function
So, i download the zipped file of spams, and i modified the setup.py file to prevent the encoding keyword problem, and when i install the library i get this error:
warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it with " \
^
/usr/bin/ld: cannot find -lblas
/usr/bin/ld: cannot find -llapack
collect2: error: ld returned 1 exit status
error: Command "g++ -pthread -shared -Wl,-z,relro build/temp.linux-x86_64-2.7/spams_wrap/spams_wrap.o -L/usr/local/lib64 -L/usr/local/lib -L/usr/lib64 -L/usr/lib -L/usr/lib/ -L/usr/lib64 -lstdc++ -lblas -llapack -lpython2.7 -o build/lib.linux-x86_64-2.7/_spams_wrap.so -fopenmp" failed with exit status 1
When i try "pip install spams==2.6.1", i get this error:
error: Command "gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_ FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOUR CE -fPIC -fwrapv -fPIC -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/di ctLearn -I/home/aabdelli/.local/lib/python2.7/site-packages/numpy/core/include - I/usr/include/python2.7 -I/usr/local/include -I/usr/include -I/usr/include/pytho n2.7 -c spams_wrap.cpp -o build/temp.linux-x86_64-2.7/spams_wrap.o -DNDEBUG -DUS E_BLAS_LIB -std=c++11 -fPIC -fopenmp -Wunused-variable -m64" failed with exit st atus 1
----------------------------------------
Command "/usr/bin/python2 -u -c "import setuptools, tokenize;__file__='/tmp/pip- build-8cd3Ds/spams/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file __).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip- OH2Naf-record/install-record.txt --single-version-externally-managed --compile - -user --prefix=" failed with error code 1 in /tmp/pip-build-8cd3Ds/spams/

First upgrade pip:
pip install -U pip setuptools
SPAMS' setup.py imports numpy before installing it so first you have to install numpy:
pip install numpy
SPAMS requires BLAS and LAPACK. You need to install the libraries for Fedora. See https://fedoraproject.org/wiki/PackagingDrafts/BLAS_LAPACK. Try
yum install openblas lapack
Then go with SPAMS:
pip install spams==2.6.1

boost/thread.hpp: No such file or directory

There are many similar posts with the same error what I am facing, but none of the solutions worked for me. Please do not think this as repeated. I am reaching you out after trying with all the solutions suggested.
I am trying to create a python library from c++ file that uses boost library with
#include <boost/thread.hpp>
I have installed Boost in Ubuntu through the commands
./bootstrap.sh --prefix=/usr/local
and then
./b2 install --with-thread
.
Now, when I try to run a file with #include <boost/thread.hpp> it gives me this error saying
src/main.cpp:2:10: fatal error: boost/thread.hpp: No such file or directory
Am I missing on something? Can someone help me how can I solve this.
Error
I will attach a screenshot of the same for viewing.
Also pasting the error description in-case someone does not feel comfortable to view image
Failed building wheel for python-example
Running setup.py clean for python-example
Failed to build python-example
Installing collected packages: python-example
Running setup.py install for python-example ... error
Complete output from command /home/hmi/anaconda3/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-req-build-h4742spy /setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-3l3u7dxm/install-record.txt --single-version-externally- managed --compile:
running install
running build
running build_ext
gcc -pthread -B /home/hmi/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/hmi/anaconda3/include/python3.7m -c /tmp/tmpbv27mdxm.cpp -o tmp/tmpbv27mdxm.o -std=c++17
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/hmi/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/hmi/anaconda3/include/python3.7m -c /tmp/tmps2iqs0qp.cpp -o tmp/tmps2iqs0qp.o -fvisibility=hidden
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
building 'python_example' extension
creating build
creating build/temp.linux-x86_64-3.7
creating build/temp.linux-x86_64-3.7/src
gcc -pthread -B /home/hmi/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/hmi/anaconda3/include -I/home/hmi/anaconda3/include -I/home/hmi/anaconda3/include/python3.7m -c src/main.cpp -o build/temp.linux-x86_64-3.7/src/main.o -DVERSION_INFO="0.0.1" -std=c++17 -fvisibility=hidden
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
src/main.cpp:2:10: fatal error: boost/thread.hpp: No such file or directory
#include <boost/thread.hpp>
^~~~~~~~~~~~~~~~~~
compilation terminated.
error: command 'gcc' failed with exit status 1
I have also tried with this command
g++ -std=c++11 main.cpp -lpthread -lboost_system -lboost_thread -o main
. But similar result.
OS : Ubuntu 18.04
Boost version : 1.55

I have now resolved it with the command mentioned by Botje but with sudo.
sudo apt install libboost-thread-dev
But I did not want to do through root. So I have refrained its usage. But now I did not find any other way. I would be glad to know if any other solution works

Python API: C Extension install error

I'm using Mac, and I am trying to write my own c code to use it from Python. I'm new to this, and trying out a sample example from http://www.tutorialspoint.com/python/python_further_extensions.htm.
But, when I run the setup.py file to install my c file, it gives me an error, and I'm not sure what to do. Below is the resulting error message. Thanks a lot!
$ sudo python3 setup.py install
Password:
running install
running build
running build_ext
building 'sample' extension
clang -Wno-unused-result -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/include -I/usr/local/opt/sqlite/include -DFOO=1 -UBAR -I/some/dir -I/usr/local/Cellar/python3/3.4.2_1/Frameworks/Python.framework/Versions/3.4/include/python3.4m -c pysample.c -o build/temp.macosx-10.10-x86_64-3.4/pysample.o
clang -bundle -undefined dynamic_lookup -L/usr/local/lib -L/usr/local/opt/sqlite/lib build/temp.macosx-10.10-x86_64-3.4/pysample.o -L/usr/local/lib -lsample -o build/lib.macosx-10.10-x86_64-3.4/sample.so
ld: library not found for -lsample
clang: error: linker command failed with exit code 1 (use -v to see invocation)
error: command 'clang' failed with exit status 1

Installing Matplotlib on CentOS 6.5

I'm trying to get matplotlib-1.4.0 installed on CentOS 6.5 with Python 2.7.8. I've tried installing with pip and from source. I initially got an error message stating I needed a newer version of Freetype2, which I then installed (version 2.5.3) to /usr/local/bin, /usr/local/include, and /usr/local/lib. The older version of Freetype2 (2.3.11) is in /usr/bin, /usr/include/freetype2/freetype, and /usr/lib.
Now when I try installing matplotlib (python setup.py build) it looks like the include paths are all pointing to the wrong (old) version of Freetype2, and I can't figure out how to change the appropriate paths to point to the newer version of Freetype2. The actual error message is below, and is pretty messy. I couldn't find much about his error online, but I can see that the wrong Freetype2 path so I'm guessing that's what causing the issue. Any tips?
Found tips on other threads about adding /usr/include/freetype symlink to point to /usr/local/include/freetype2, but that didn't help.
building 'matplotlib.ft2font' extension
gcc -pthread -fno-strict-aliasing -O3 -m64 -mfpmath=sse -msse2 -mtune=generic -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_matplotlib_ft2font_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -I/usr/local/python2/2.7.8/x86_64/gcc46/nonet/lib/python2.7/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/local/include -I/usr/include -I. -Iextern -I/usr/local/python2/2.7.8/x86_64/gcc46/nonet/include/python2.7 -c src/ft2font.cpp -o build/temp.linux-x86_64-2.7/src/ft2font.o
In file included from /usr/local/python2/2.7.8/x86_64/gcc46/nonet/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1761:0,
from /usr/local/python2/2.7.8/x86_64/gcc46/nonet/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from src/file_compat.h:7,
from src/ft2font.cpp:7:
/usr/local/python2/2.7.8/x86_64/gcc46/nonet/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]
In file included from src/ft2font.cpp:7:0:
src/file_compat.h:31:0: warning: "npy_fseek" redefined [enabled by default]
/usr/local/python2/2.7.8/x86_64/gcc46/nonet/lib/python2.7/site-packages/numpy/core/include/numpy/npy_common.h:86:0: note: this is the location of the previous definition
src/file_compat.h:32:0: warning: "npy_ftell" redefined [enabled by default]
/usr/local/python2/2.7.8/x86_64/gcc46/nonet/lib/python2.7/site-packages/numpy/core/include/numpy/npy_common.h:91:0: note: this is the location of the previous definition
src/ft2font.cpp: In member function ‘Py::Object FT2Image::py_write_bitmap(const Py::Tuple&)’:
src/ft2font.cpp:184:15: warning: unused variable ‘offset’ [-Wunused-variable]
gcc -pthread -fno-strict-aliasing -O3 -m64 -mfpmath=sse -msse2 -mtune=generic -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_matplotlib_ft2font_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -I/usr/local/python2/2.7.8/x86_64/gcc46/nonet/lib/python2.7/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/local/include -I/usr/include -I. -Iextern -I/usr/local/python2/2.7.8/x86_64/gcc46/nonet/include/python2.7 -c src/mplutils.cpp -o build/temp.linux-x86_64-2.7/src/mplutils.o
In file included from /usr/local/python2/2.7.8/x86_64/gcc46/nonet/include/python2.7/Python.h:8:0,
from src/mplutils.h:18,
from src/mplutils.cpp:6:
/usr/local/python2/2.7.8/x86_64/gcc46/nonet/include/python2.7/pyconfig.h:1182:0: warning: "_POSIX_C_SOURCE" redefined [enabled by default]
/usr/include/features.h:162:0: note: this is the location of the previous definition
/usr/local/python2/2.7.8/x86_64/gcc46/nonet/include/python2.7/pyconfig.h:1204:0: warning: "_XOPEN_SOURCE" redefined [enabled by default]
/usr/include/features.h:164:0: note: this is the location of the previous definition
gcc -pthread -fno-strict-aliasing -O3 -m64 -mfpmath=sse -msse2 -mtune=generic -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_matplotlib_ft2font_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -I/usr/local/python2/2.7.8/x86_64/gcc46/nonet/lib/python2.7/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/local/include -I/usr/include -I. -Iextern -I/usr/local/python2/2.7.8/x86_64/gcc46/nonet/include/python2.7 -c extern/CXX/cxxsupport.cxx -o build/temp.linux-x86_64-2.7/extern/CXX/cxxsupport.o
gcc -pthread -fno-strict-aliasing -O3 -m64 -mfpmath=sse -msse2 -mtune=generic -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_matplotlib_ft2font_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -I/usr/local/python2/2.7.8/x86_64/gcc46/nonet/lib/python2.7/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/local/include -I/usr/include -I. -Iextern -I/usr/local/python2/2.7.8/x86_64/gcc46/nonet/include/python2.7 -c extern/CXX/cxx_extensions.cxx -o build/temp.linux-x86_64-2.7/extern/CXX/cxx_extensions.o
gcc -pthread -fno-strict-aliasing -O3 -m64 -mfpmath=sse -msse2 -mtune=generic -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_matplotlib_ft2font_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -I/usr/local/python2/2.7.8/x86_64/gcc46/nonet/lib/python2.7/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/local/include -I/usr/include -I. -Iextern -I/usr/local/python2/2.7.8/x86_64/gcc46/nonet/include/python2.7 -c extern/CXX/IndirectPythonInterface.cxx -o build/temp.linux-x86_64-2.7/extern/CXX/IndirectPythonInterface.o
gcc -pthread -fno-strict-aliasing -O3 -m64 -mfpmath=sse -msse2 -mtune=generic -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_matplotlib_ft2font_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -I/usr/local/python2/2.7.8/x86_64/gcc46/nonet/lib/python2.7/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/local/include -I/usr/include -I. -Iextern -I/usr/local/python2/2.7.8/x86_64/gcc46/nonet/include/python2.7 -c extern/CXX/cxxextensions.c -o build/temp.linux-x86_64-2.7/extern/CXX/cxxextensions.o
g++ -pthread -shared build/temp.linux-x86_64-2.7/src/ft2font.o build/temp.linux-x86_64-2.7/src/mplutils.o build/temp.linux-x86_64-2.7/extern/CXX/cxxsupport.o build/temp.linux-x86_64-2.7/extern/CXX/cxx_extensions.o build/temp.linux-x86_64-2.7/extern/CXX/IndirectPythonInterface.o build/temp.linux-x86_64-2.7/extern/CXX/cxxextensions.o -L/usr/local/lib -L/usr/local/lib64 -L/usr/lib -L/usr/lib64 -L/usr/local/python2/2.7.8/x86_64/gcc46/nonet/lib -lfreetype -lstdc++ -lm -lpython2.7 -o build/lib.linux-x86_64-2.7/matplotlib/ft2font.so
/usr/bin/ld: /usr/local/lib/libpython2.7.a(abstract.o): relocation R_X86_64_32S against `_Py_NotImplementedStruct' can not be used when making a shared object; recompile with -fPIC
/usr/local/lib/libpython2.7.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
error: command 'g++' failed with exit status 1

Although I'm using python-2.6 I just bodged a way through the exact same freetype error: essentially you can simply download the matplotlib python archive and edit the requirement for freetype-2.4 to freetype-2.3. This was all done in a virtualenv naturally.
get a copy of the current latest matplotlib
pip install --download . matplotlib==1.4.0
untar the result
tar -xzvf matplotlib-1.4.0.tar.gz
edit the explicit requirement for freetype from 2.4 to 2.3 (line 945)
vi matplotlib-1.4.0/setupext.py
min_version='2.4', version=version)
recreate the archive
tar -czvf matplotlib-1.4.0.tar.gz
install the requirements
pip install numpy
pip install geojson==1.0.6
Install your modified local archive, and watch as it compiles
pip install --verbose matplotlib-1.4.0.tar.gz

I finally had time to return to this and it had nothing to do with Freetype. The issue was the wrong version of libpython2.7 being picked up during the build. Specifically in this line:
g++ -pthread -shared build/temp.linux-x86_64-2.7/src/ft2font.o build/temp.linux-x86_64-2.7/src/mplutils.o build/temp.linux-x86_64-2.7/extern/CXX/cxxsupport.o build/temp.linux-x86_64-2.7/extern/CXX/cxx_extensions.o build/temp.linux-x86_64-2.7/extern/CXX/IndirectPythonInterface.o build/temp.linux-x86_64-2.7/extern/CXX/cxxextensions.o -L/usr/local/lib -L/usr/local/lib64 -L/usr/lib -L/usr/lib64 -L/usr/local/python2/2.7.8/x86_64/gcc46/nonet/lib -lfreetype -lstdc++ -lm -lpython2.7 -o build/lib.linux-x86_64-2.7/matplotlib/ft2font.so
The first -L directory is /usr/local/lib which contained a different version of the python library (libpython2.7.a) than the one I should have been compiling against. I moved this file temporarily and the build was then successful (it found the correct version in /usr/local/python2/2.7.8/x86_64/gcc46/nonet/lib).
I'm not exactly sure where the python lib in /usr/local/lib originated from. If it's the system version then this could be considered a bug in the matplotlib build script.

I also have this problem when compiling the matplotlib-1.4.3 from source code. After this error, I simply export LDFLAGS="/home/ubuntu/softwares/python-2.7.11/lib", then python setup.py install. The error is gone and I can install the matplotlib successfully.

In case you want to install the most recent version of matplotlib compatible with Python 2.6 on CentOS 6 (currently 6.9 when I wrote this), here's how I did.
Logged as root, type:
sudo yum install -y epel-release
sudo yum install -y python-pip
sudo yum install -y gcc gcc-c++ python-argparse python-devel freetype-devel libpng-devel
pip install --upgrade pip
pip install numpy==1.11.3 # latest version working with Python 2.6
pip install --upgrade distribute # required by matplotlib 1.4
pip install -I setuptools # "distribute" installation will remove setuptools, so we need to reinstall it
pip install matplotlib==1.4.3 # latest version working with Python 2.6

Python docx installation isn't working due to unknown error on linux

I'm trying to install pip install python-docx but get the following error. Why doesn't it work?
building 'lxml.etree' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/src
creating build/temp.linux-x86_64-2.7/src/lxml
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/usr/include/libxml2 -I/tmp/pip_build_plakshma/lxml/src/lxml/includes -I/opt/python2.7/include/python2.7 -c src/lxml/lxml.etree.c -o build/temp.linux-x86_64-2.7/src/lxml/lxml.etree.o -w
gcc -pthread -shared build/temp.linux-x86_64-2.7/src/lxml/lxml.etree.o -L/usr/lib64 -L. -lxslt -lexslt -lxml2 -lz -lm -lpython2.7 -o build/lib.linux-x86_64-2.7/lxml/etree.so
/usr/bin/ld: /usr/local/lib/libpython2.7.a(abstract.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC
/usr/local/lib/libpython2.7.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
error: command 'gcc' failed with exit status 1

Type this in your terminal/cmd.
pip install python-docx.
For me when I made typed it in the apple terminal it was an error but type in the Pycharm terminal and it should work.