10

I am limited on what I can share as this is part of a huge stack of code that I am porting from Ubuntu 14.04 to 16.04.

It should be trivial, but somehow I am struggling with this. It doesn't find numpy/arrayobject.h that I am referencing in my source file with #include <numpy/arrayobject.h>

I will try to share as much as I can, see if someone can guide me through a resolution.

Ubuntu

$ lsb_release -a 
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 16.04.2 LTS
Release:    16.04
Codename:   xenial

make

$ make --version
GNU Make 4.1
Built for x86_64-pc-linux-gnu

g++

$ g++ --version
g++ (Ubuntu 5.4.0-6ubuntu1~16.04.4) 5.4.0 20160609

upgraded to

# g++ --version
g++ (Ubuntu 5.4.1-2ubuntu1~16.04) 5.4.1 20160904
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

python

$ python --version
Python 2.7.12

Some environment variables

PYTHON       /usr/bin/python2.7
ARCH         x86_64
OS           Linux
VERSION      4.4.071generic
PLATFORM     linux2
HOSTNAME     deploy
USER         myUser
WUSS_BUILD   NO
CCVER        gcc
PYLIBDIR     build.x86_64-linux2
LIBDIR       build.x86_64-linux2
BINDIR       build.x86_64-linux2
ODIR         build.x86_64-linux2-gcc
STATICLIBDIR build-static.x86_64-linux2

Error

The make command leads to

+++ Compile mycore/boost_numpy.cc to build.x86_64-linux2-gcc
anycore/boost_numpy.cc:2:31: fatal error: numpy/arrayobject.h: No such file or directory

My source file

user@deploy:~/my-linux$ vim mycore/boost_numpy.cc

#include "anycore/boost_python_headers.h"
#include <numpy/arrayobject.h>           <====== DECLARATION
#include <numpy/ufuncobject.h>        
#include "mycore/boost_numpy.h"
#include "mycore/numerical.h"
#include "mycore/vec3.h"

using namespace boost::python;

PyObject *
read_numeric_file_ficii(FILE *fp, int ncols, char arrtype, int headlines, int taillines)
{
  if (!(arrtype=='d' || arrtype=='f' || arrtype=='i')) {
    PyErr_SetString(PyExc_ValueError, "Unknown array type for read_numeric_file");
    return NULL;
  }
...FILTERED...

Declaration file numpy/arrayobject.h on disk

root@deploy:/home#  find / -name arrayobject.h
/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h

Please let me know how I can improve the question. Directions or pointers are most welcome

UPDATE

$ ls -l /usr/include/numpy
ls: cannot access '/usr/include/numpy': No such file or directory

RESOLVED WITH

sudo ln -s  /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy /usr/include/numpy
zabumba
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  • Related: https://stackoverflow.com/questions/2379898/make-distutils-look-for-numpy-header-files-in-the-correct-place – Bernhard May 18 '23 at 09:40

2 Answers2

20

I have experienced the same behavior on a partly broken Debian installation.

I fixed the error by reestablishing a symbolic link

sudo ln -s /usr/lib/python2.7/dist-packages/numpy/core/include/numpy /usr/include/numpy

Jens Munk
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10

How did you install numpy?

If you install python-numpy correctly, e.g. by sudo apt-get install python-numpy, you will have /usr/include/numpy linked to the correct path:

$ ls -l /usr/include/numpy
lrwxrwxrwx 1 root root 55 Sep 17  2014 /usr/include/numpy -> ../lib/python2.7/dist-packages/numpy/core/include/numpy

It looks like you may build your numpy manually, then you can manually create a soft link accordingly.

Mine
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