Develop Reference

cvxpy stlibc++ Installation error on MacOS Mojave

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

Error compiling pyglpk for installation (Ubuntu 14.04)

I believe this may be a general python/gcc problem not specific to pyglpk.
I'm trying install to pyglpk on a fresh install of Ubuntu 14.04. As I'm using a fresh install of Ubuntu both Python 2.7 and 3 are installed.
I believe I've properly installed the listed required dependencies (GLPK and GMP) and I've installed the additional dependencies which another post suggested I might be missing:
apt-get install python-dev libxml2-dev libxslt-dev
Here is the error i get when trying to compile pyglpk:
sudo make
python setup.py build
running build
running build_ext
building 'glpk' extension
x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/local/include -Isrc -I/usr/include/python2.7 -c src/glpk.c -o build/temp.linux-x86_64-2.7/src/glpk.o -m32
In file included from /usr/include/python2.7/Python.h:8:0,
from src/glpk.c:20:
/usr/include/python2.7/pyconfig.h:7:49: fatal error: i386-linux-gnu/python2.7/pyconfig.h: No such file or directory
# include <i386-linux-gnu/python2.7/pyconfig.h>
^
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
make: *** [all] Error 1
It looks to me like the actual file it's looking for (pyconfig.h) is here:
/usr/include/x86_64-linux-gnu/python2.7/pyconfig.h
while make/gcc seems to be looking for the equivalent file for 32 bit python:
/usr/include/i386-linux-gnu/python2.7/pyconfig.h
I'm going to try installing 32 bit Ubuntu instead, even though I should be able to use 32 bit programs on a 64 bit system. I'll report back here.
Thanks!

I have finally gotten PyGLPK working!
I was able to "solve"fatal error: i386-linux-gnu/python2.7/pyconfig.h: No such file or directory by installing 32 bit Ubuntu instead of 64 bit.
I would not recommend trying to install the 32 bit version of python on 64 bit Ubuntu as that opens up another huge plethora of issues.
If you know how to fix this error on 64 bit Ubuntu please speak up!
Once I got past that error I experienced a new error:
ImportError: libglpk.so.0: cannot open shared object file: No such file or directory
I discovered that part of this error is the due to PyGLPK being quite old. The newest version of PyGLPK (v. 0.3) is not compatible with the newest version of GLPK (v 4.58). This post suggested GLPK v 4.47 was the last working version compatible with PyGLPK, which seems to be working fine.
After installing GLPK v 4.47 the error still appears to occur. I've found that installing python-glpk using the command sudo apt-get install python-glpk fixes the error. I believe this is because installing python-glpk also installs some dependency which is also necessary for PyGLPK, because even after uninstalling python-glpk PyGLPK continues to work.
I can confirm that following this step while using GLPK v. 4.58 does not work. An older version of GLPK and whatever dependency python-glpk installs are both required.

I had the exact same error/situation (64 bit linux mint, I'm sorry if its somehow different, total noob here). GLPK 4.55. This version works out the box:
https://github.com/bradfordboyle/pyglpk
Hope this helps.

Python pip library search paths

I'm trying to install the python package cvxopt via pip into a virtual environment on a Centos 6 system.
Since lapack is a prerequisite, and since I don't have superuser access to the system, I've installed lapack locally using the following:
$ cmake -DCMAKE_INSTALL_PREFIX=/home/tom .
$ make install
I notice that after this step liblapack.a is located in my local lib directory, /home/tom/lib, as expected.
However, when I activate my virtual environment and run pip install cvxopt I get the following error:
<snip>
gcc -pthread -shared
build/temp.linux-x86_64-2.7/src/C/base.o
build/temp.linux-x86_64-2.7/src/C/dense.o
build/temp.linux-x86_64-2.7/src/C/sparse.o
-L/usr/lib -L/public/apps/python/2.7.4/lib
-lm -llapack -lblas -lpython2.7 -o build/lib.linux-x86_64-2.7/cvxopt/base.so
/usr/bin/ld: cannot find -llapack
collect2: ld returned 1 exit status
error: command 'gcc' failed with exit status 1
I've tried adding /home/tom/lib to both LD_LIBRARY_PATH and LD_RUN_PATH but neither of these seem to affect the gcc command line options that pip is using to build the module.
Can anyone tell me how to give library search paths to pip? Is there a better way?

After some experimentation, I was able to solve the problem. The first thing I had to do was enable the shared libraries for LAPACK:
~/src/lapack-3.5.0 $ cmake -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX=/home/tom .
~/src/lapack-3.5.0 $ make install
Then I exported LD_FLAGS to include the proper library search path:
export LD_FLAGS="-L/home/tom/lib"
Then I re-attempted the install of cvxopt from source into the virtual environment:
~/src/cvxopt-1.1.6 $ . venv/bin/activate
~/src/cvxopt-1.1.6 (venv)$ python setup.py build install
I didn't experiment with LD_LIBRARY_PATH or LD_RUN_PATH to determine whether they were still required with LD_FLAGS. However, I did determine that a shared LAPACK library was definitely required; cvxopt wouldn't link against the static library.

Error compiling PyGraphviz 1.2 on OSX Mavericks with Xcode 5

G'day everyone,
I am trying to install PyGraphviz 1.2 on OSX Mavericks. I have just upgraded from Mountain Lion and now have Xcode 5.0.1 installed with Command Line Tools. I have downloaded the PyGraphviz source package, unpacked it and ran sudo python setup.py install.
I am getting the following error message (there is some output prior to this, including several warnings):
cc -bundle -undefined dynamic_lookup -arch x86_64 -arch i386 -Wl,-F. build/temp.macosx-10.9-intel-2.7/pygraphviz/graphviz_wrap.o -L/usr/local/lib/graphviz -L/usr/local/lib/graphviz -lcgraph -lcdt -o build/lib.macosx-10.9-intel-2.7/pygraphviz/_graphviz.so
ld: library not found for -lcgraph
clang: error: linker command failed with exit code 1 (use -v to see invocation)
error: command 'cc' failed with exit status 1
Also, the first two lines of output are:
library_path=/usr/local/lib/graphviz
include_path=/usr/local/include/graphviz
which leads me to believe that compiler knows where to look for libraries.
What could be the problem? Just to make things clear: for technical reasons I have to use Apple's version of Python 2.7 and everything works fine on my other machine with OSX Lion and Xcode 4... (not sure what the exact version is).

I had a same error and resolved it by installing command line tools for XCode. Assuming you upgraded your XCode to 5.0.1, you can install command line tools by typing "xcode-select --install" to terminal and it will prompt you to install command line tools.

Installing Ephem package in Python 3

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.