I try to install pygraphviz on Anaconda. I have done everything I found:
- install graphviz.
- install mingw.
- change values in the setup.py for pygraphviz as below:
include_dirs = 'C:/Program Files (x86)/Graphviz2.38/include/graphviz'
library_dirs = 'C:/Program Files (x86)/Graphviz2.38/lib'
- run python setup.py build -c mingw32 install.
After step 4, I got the following error:
running install
running build
running build_py
running build_ext
building 'pygraphviz._graphviz' extension
C:\MinGW\bin\gcc.exe -mdll -O -Wall -DGVDLL "-IC:/Program Files (x86)/Graphviz2.38/include/graphviz" -IC:\Users\garre_000\Anaconda3\
include -IC:\Users\garre_000\Anaconda3\include -c pygraphviz/graphviz_wrap.c -o build\temp.win-amd64-3.4\Release\pygraphviz\graphviz
_wrap.o
pygraphviz/graphviz_wrap.c:2954:29: fatal error: graphviz/cgraph.h: No such file or directory
#include "graphviz/cgraph.h"
^
compilation terminated.
error: command 'C:\\MinGW\\bin\\gcc.exe' failed with exit status 1
Can anyone give me some advice ?
I just faced the same problem. The include path is incorrect. Use
include_dirs = 'C:/Program Files (x86)/Graphviz2.38/include'
instead. Otherwise you get
'C:/Program Files (x86)/Graphviz2.38/include/graphviz/graphviz/cgraph.h'
Related
I am trying to install the python package biopython from source on my Macbook pro OSX 10.9.4,
I run python setup.py build in the terminal and receive this
running build
running build_py
running build_ext
building 'Bio.cpairwise2' extension
Compiling with an SDK that doesn't seem to exist: /Developer/SDKs/MacOSX10.6.sdk
Please check your Xcode installation
gcc -DNDEBUG -g -O3 -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.6.sdk -Qunused-arguments -Qunused-arguments -I/Applications/Canopy.app/appdata/canopy-1.4.1.1975.macosx-x86_64/Canopy.app/Contents/include/python2.7 -c Bio/cpairwise2module.c -o build/temp.macosx-10.6-x86_64-2.7/Bio/cpairwise2module.o
clang: warning: no such sysroot directory: '/Developer/SDKs/MacOSX10.6.sdk'
In file included from Bio/cpairwise2module.c:12:
/Applications/Canopy.app/appdata/canopy-1.4.1.1975.macosx- x86_64/Canopy.app/Contents/include/python2.7/Python.h:33:10: fatal error:
'stdio.h' file not found
#include <stdio.h>
^
1 error generated.
error: command 'gcc' failed with exit status 1
I checked that Xcode should be properly installed and working
You should be using pip. Try:
pip install biopython
Uninstalled Canopy and everything worked like a charm...
Try installing the Biopython version available from the Canopy "Package Manager" > "Available Packages" > "Canopy Packages".
This way, I seem to have solved a similar problem while installing Pyensembl, that also installs Biopython.
I'm trying to install a python wrapper over constraint programming library Gecode called python-gecode
https://pypi.python.org/pypi/gecode-python/
No matter how I install it I get same error "No such file or directory". Here is setup script output:
running install
running build
running build_py
running build_ext
building 'gecode._gecode' extension
C:\MinGW32-xy\bin\gcc.exe -mno-cygwin -mdll -O -Wall -DDISJUNCTOR "-IC:\Program Files\Gecode\include" -IC:\Python27\include -IC:\Python27\PC -c _gecode.cc -o build\temp.win32-2.7\Release\_gecode.o
_gecode.cc:5:24: fatal error: 4.2.1: No such file or directory
compilation terminated.
error: command 'gcc' failed with exit status 1"
But the _gecode.cc is there in the folder. I don't really understand what's the problem. I tried installing with pip, easy_install, manual install and everytime I get this error.
Any ideas what's causing it?
Thanks!
Gecode-Python supports only up to version 4.0.0 of Gecode, so use that version instead of 4.2.1.
I'm trying to install the M2Crypto on Python26 in Windows, but I am getting the below error.
error: command 'swig.exe' failed: No such file or directory
This error occurs both using the "Easy Install" or "PIP Install" command. Follows the Log:
running build
running build_py
running build_ext
building 'M2Crypto.__m2crypto' extension
swigging SWIG/_m2crypto.i to SWIG/_m2crypto_wrap.c
swig.exe -python -IC:\Python26\include -IC:\Python26\PC
-Ic:\pkg\include -includeall -o SWIG/_m2crypto_wrap.c SWIG/_m2crypto.i
error: command 'swig.exe' failed: No such file or directory
Any Help?
This worked for me: (using winpython2.7)
pip install M2CryptoWin32
reference:
https://github.com/dsoprea/M2CryptoWin32
Putting this in answer format:
You could try to install a binary build from http://chandlerproject.org/Projects/MeTooCrypto
from mata's comment that resolved OP's issue
Hi guys i'm new to rrdtool , i want to use rrdtool for one of my python projects, i'm trying to install rrdtool by typing this script in my command prompt
"python setup.py install build --compiler=mingw32 "
this is the output that i get :
running install
running build
running build_ext
running build_configure
building 'rrdtoolmodule' extension
C:\MinGW\bin\gcc.exe -mno-cygwin -mdll -O -Wall -Irrdtool-1.4.7/src -IC:\Python2
7\include -IC:\Python27\PC -c rrdtool-1.4.7/bindings/python/rrdtoolmodule.c -o b
uild\temp.win32-2.7\Release\rrdtool-1.4.7\bindings\python\rrdtoolmodule.o
rrdtool-1.4.7/bindings/python/rrdtoolmodule.c:41:30: fatal error: ../../rrd_config.h: No such file or directory
compilation terminated.
error: command 'gcc' failed with exit status 1
i have searched for a solution but had no success.
pls can anyone help !!
I tried to install PyCUDA using these instructions: http://wiki.tiker.net/PyCuda/Installation/Linux
and at the point 3 I was compiling with:
su -c "make install"
have this output from console:
running install
running bdist_egg
running egg_info
writing requirements to pycuda.egg-info/requires.txt
writing pycuda.egg-info/PKG-INFO
writing top-level names to pycuda.egg-info/top_level.txt
writing dependency_links to pycuda.egg-info/dependency_links.txt
reading manifest file 'pycuda.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'pycuda.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
running build_ext
building '_driver' extension
gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -fwrapv -Wall -g -fPIC -DPYGPU_PACKAGE=pycuda -DHAVE_CURAND=1 -DBOOST_PYTHON_SOURCE=1 -DPYGPU_PYCUDA=1 -DBOOST_MULTI_INDEX_DISABLE_SERIALIZATION=1 -Dboost=pycudaboost -Isrc/cpp -Ibpl-subset/bpl_subset -I/usr/local/cuda/include -I/usr/lib/python3.2/site-packages/numpy/core/include -I/usr/lib/python3.2/site-packages/numpy/core/include -I/usr/include/python3.2mu -c src/cpp/cuda.cpp -o build/temp.linux-x86_64-3.2/src/cpp/cuda.o
Inf ile included from src/cpp/cuda.cpp:1:0:
src/cpp/cuda.hpp:12:18: fatal error: cuda.h: No such file or directory
compilation terminated.
error: command 'gcc' failed with exit status 1
What should I do?
EDIT: My OS is: Arch Linux 3.3.2.1. GPU: Nvidia GF 9600M GS
Instead of su -c "make install" try sudo su - (to become root), and then, as root: make install (after navigating to the right directory)
This one full command worked for me:
sudo pip3 install --global-option=build_ext --global-option="-I/usr/local/cuda/include" --global-option="-L/usr/local/cuda/lib64" pycuda