Changing Biopython include path for compilation during pip installation

Question

I'm trying to install Biopython (a python package) using PIP on my work machine (OpenSuse x86_64).

It all goes fine until it tries to do some compilation using numpy headers

gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -fPIC -I/usr/lib64/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c Bio/Cluster/clustermodule.c -o build/temp.linux-x86_64-2.7/Bio/Cluster/clustermodule.o

At which point it fails

Bio/Cluster/clustermodule.c:2:31: fatal error: numpy/arrayobject.h: No such file or directory

This is because numpy/arrayobject.h is in

/usr/local/lib64/python2.7/site-packages/numpy/core/include/

and not

/usr/lib64/python2.7/site-packages/numpy/core/include 

Is there a way to update whatever variable is setting the include path (to the /local version), either globally or explicitly for this installation?

UPDATE

Over a year later, I was faced with a similar problem, except this time the .h files simply didn't exist on my system. By just copying the .h from another machine into the

/usr/lib64/python2.7/site-packages/numpy/core/include/numpy

directory installation went fine.

Answer 1

Thanks to @Bort, I discovered this is, apparently a known error (local/user space installation wasn't working anyway).

By editing the Biopython setup.py file in the following places

Original

#Add extensions that requires NumPy to build
if is_Numpy_installed():
   import numpy
   numpy_include_dir = numpy.get_include()
   EXTENSIONS.append(
      Extension('Bio.Cluster.cluster',
              ['Bio/Cluster/clustermodule.c',
               'Bio/Cluster/cluster.c'],
              include_dirs=[numpy_include_dir],
              ))
   EXTENSIONS.append(
      Extension('Bio.KDTree._CKDTree',
              ["Bio/KDTree/KDTree.c",
               "Bio/KDTree/KDTreemodule.c"],
              include_dirs=[numpy_include_dir],
              ))
   EXTENSIONS.append(
      Extension('Bio.Motif._pwm',
              ["Bio/Motif/_pwm.c"],
              include_dirs=[numpy_include_dir],
              ))

Updated

#Add extensions that requires NumPy to build
if is_Numpy_installed():
   import numpy
   numpy_include_dir = numpy.get_include()
   EXTENSIONS.append(
      Extension('Bio.Cluster.cluster',
              ['Bio/Cluster/clustermodule.c',
               'Bio/Cluster/cluster.c'],
              include_dirs=[numpy_include_dir, '/usr/local/lib64/python2.7/site-packages/numpy/core/include/'],
              ))
   EXTENSIONS.append(
      Extension('Bio.KDTree._CKDTree',
              ["Bio/KDTree/KDTree.c",
               "Bio/KDTree/KDTreemodule.c"],
              include_dirs=[numpy_include_dir, '/usr/local/lib64/python2.7/site-packages/numpy/core/include/'],
              ))
   EXTENSIONS.append(
      Extension('Bio.Motif._pwm',
              ["Bio/Motif/_pwm.c"],
              include_dirs=[numpy_include_dir, '/usr/local/lib64/python2.7/site-packages/numpy/core/include/'],
              ))

Then using pip to install from source (I re-compressed the folder with the updated setup.py file in it then ran)

pip install recompressed.tar.gz

and it's installed and good to go.

Update I actually had a very similar problem with this on another openSUSE machine, but this time had no include files anywhere... To get around this I copied them across from the numpy source and fed them in using the include_dirs update above.