I am trying to install couchapp from the terminal on macOs High Sierra.
I have python 2.7.10 installed (by default) and I run $ pip2 install couchapp according to the couchapp documentation.
This is the error I get:
src/watchdog_fsevents.c:22:10: fatal error: 'Python/Python.h' file not found
#include <Python/Python.h>
^~~~~~~~~~~~~~~~~
1 error generated.
error: command 'cc' failed with exit status 1
----------------------------------------
Failed building wheel for watchdog
Here is what I have when I do $ ls in /System/Library/Frameworks/Python.framework/
Examples
Modules
Python
Resources
Versions
module.map
What I have tried so far:
Check that Xcode CL Tools are already installed running $ xcode-select --install
Try to use pip3 instead of pip2 (I have installed python 3.6 with Homebrew), but I get the same error message.
Do you have any idea? I have read other posts but they did not solve my problem.
Thank you
Had a very similar problem on my High Sierra (10.13.5) setup with Xcode CLI tools installed; for me the Python.h was found in /System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7
(Some resources say the location can be found via find /usr/local/Cellar/ -name Python.h, however this seems not work if your python was not installed with brew.)
Add the location to your C include path, or at compile time as a flag by setting -I flag as such: -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7.
The part that tripped me up was the import statement should then look like: #include <Python.h> rather than #include <Python/Python.h> if your Python.h is directly in the python2.7 directory.
Hope that helps,
Related
I'm trying to install python-rocksdb on a windows 10 machine and I'm coming across some issues with the install.
I have successfully installed rocksdb first using the vcpkg method.
When running pip install python-rocksdb I get the following error:
cl : Command line error D8021 : invalid numeric argument '/Wextra'
error: command 'C:\\Program Files\\Microsoft Visual Studio\\2022\\Community\\VC\\Tools\\MSVC\\14.34.31933\\bin\\HostX86\\x64\\cl.exe' failed with exit code 2
Looking around suggested attempting to install with GCC or G++, so I downloaded cygwin and then attempted to install the python package using
pip install --global-option build_ext --global-option --compiler=cygwin python-rocksdb which yielded the following error:
gcc: error: unrecognized command-line option ‘-mcygwin’
error: command 'C:\\cygwin64\\bin\\gcc.exe' failed with exit code 1
This post seems to suggest that you need to use g++ specifically, but it looks like the cygwin command is defaulting to gcc.
Just note that I'm not using the virtual env with python.
Any assistance is greatly appreciated.
While trying to install cvxpy package using pip install on Mac, I get the following error message:
warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
In file included from cvxpy/cvxcore/src/cvxcore.cpp:15:
cvxpy/cvxcore/src/cvxcore.hpp:18:10: fatal error: 'vector' file not found
#include <vector>
^~~~~~~~
1 warning and 1 error generated.
error: command '/usr/bin/clang' failed with exit status 1
Mac is running OS Mojave.
I solved the issue using the following steps,
First I tried changing the flags to instruct the installation to use libc++,
CFLAGS=-stdlib=libc++ pip install cvxpy
Then it complained about having an invalid deployment target for -stdlib=libc++ (requires OS X 10.7 or later).
Then I ran the following command to set the deployment target,
export MACOSX_DEPLOYMENT_TARGET=10.10
Then running the first command(CFLAGS=-stdlib=libc++ pip install cvxpy) again installed cvxpy successfully.
I have been struggling with this all weekend and the most success I have found so far is installing cvxpy in an anaconda environment with these two lines:
conda install -c conda-forge lapack
conda install -c cvxgrp cvxpy
I had a similar error on Mojave. The problem is that the location of the headers installed by XCode command-line tools (which includes clang) have changed. I was able to get it working by adding this to my ~/.bash_profile and opening a new shell:
export CFLAGS="-I/usr/local/include -L/usr/local/lib -I$(brew --prefix openssl)/include -I$(xcrun --show-sdk-path)/usr/include"
This adds flags to CLANG that tell it to run the xcrun command to find the headers. It also adds the homebrew openssl headers to the clang path, which may not be necessary for this case (and assumes you have them installed).
See: https://stackoverflow.com/a/52871908/8344813
Just trying to run a
pip install CrossMap
on OSX 10.11.6 with a brew installed python (version 2.7.12) and pip (version 9.0.1) and running into this error:
htslib/hts_os.c:30:10: fatal error: 'os/rand.c' file not found
#include "os/rand.c"
^
1 error generated.
error: command 'clang' failed with exit status 1
I have looked everywhere for information on this error and it has come up empty. Where does this dependency come from and how do I install it?
Thanks!
CrossMap depends on pysam which is a wrapper for sam tools. You need to install htslib before compiling pysam.
Initial Question
I've installed scipopsuite by following these instructions: http://scip.zib.de/doc/html/MAKE.php#BRIEFINSTALL
Make tests - complete without error.
Then when I try pip install pyscipopt I get the following error.
src/pyscipopt/scip.c:467:10: fatal error: 'scip/scip.h' file not found
#include "scip/scip.h"
^
1 error generated.
error: command 'gcc' failed with exit status 1
Specs: Anaconda Python 2.7, latest OSX
Follow Up
In response to comments(#mattmilten), I've done the following.
(1) Installed the make file - When i tried to run the install it failed because the name of the O.darwin.x86_64.gnu.shared.opt folder was set to 'static' instead of shared. I changed that name and then the install completed but did have these warnings:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: lib/libscipopt-4.0.0.darwin.x86_64.gnu.opt.a(stkchk.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: lib/libscipopt-4.0.0.darwin.x86_64.gnu.opt.a(stkchk.o) has no symbols
When i try:
>>> import pyscipopt
, I now get the following error.
Any suggestions would be appreciated.
ImportError: dlopen(/Users/"local"/anaconda/lib/python2.7/site-packages/pyscipopt/scip.so, 2): Symbol not found: ___gmp_version
Referenced from: /Users/"local"/anaconda/lib/python2.7/site-packages/pyscipopt/scip.so
Expected in: flat namespace in /Users/"local"/anaconda/lib/python2.7/site-packages/pyscipopt/scip.so
I'm guessing these things are linked - thanks.
As explained in the PySCIPOpt INSTALL you need to tell Python where you installed the SCIP Opt Suite: export SCIPOPTDIR=<path_to_install_dir>
The setup.py looks for this environment variable so you need to set it before you run pip install pyscipopt
Edit:
You need to install the SCIP Opt Suite (this basically copies the compiled files to some directory) as also explained in the INSTALL file
I would like to install the ephem package in my Python 3.3.0 version under Windows XP.
I tried first the pip install ephem route from the system command prompt. The process aborted with the error message of Unable to find vcvarsall.bat.
I read prior advice on the net for such a difficulty. Following it I installed mingw32 in my computer, added C:\MinGW\bin to the PATH variable and provided Lib / distutils with a new file called distutils.cfg and the content:
[build]
compiler=mingw32
On running now any of the install commands (pip, *easy_install* and setup.py all work the same) the following error results:
C:\MinGW\bin\gcc.exe -mno-cygwin -mdll -O -Wall -Ilibastro-3.7.5 -IC:\Python33\
include -IC:\Python33\include -c extensions/_libastro.c -o build\temp.win32-3.3\
Release\extensions\_libastro.o
cc1.exe: error: unrecognised command line option '-mno-cygwin'
error: command 'gcc' failed with exit status 1
I have tried to understand and solve the problem, but have been unsuccesful. I have not been able even to find the place in the code where such values are established.
¿Could somebody provide any help? ¿Would ephem be one of the cases alluded by Installing Python modules in the 3.3.0 Documentation with "Not all extensions can be built with MinGW or Cygwin, but many can."?
Thanks in advance
Paco
Here is an extremely useful page of Windows binaries of python packages: http://www.lfd.uci.edu/~gohlke/pythonlibs/.
It includes binaries for pyephem.