rtree: rtree version 0.9 install error: OSError: libspatialindex_c.so: cannot open shared object file

Hi, running pip install "rtree>=0.8,<1" fails with this error:

Collecting rtree<1,>=0.8
  Downloading https://files.pythonhosted.org/packages/5e/64/a01a6675c39ddfba2467cc6b432ce9af2e71a3a67e9e8ace106ccda10df8/Rtree-0.9.0.tar.gz (52kB)
    100% |████████████████████████████████| 61kB 2.7MB/s
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-build-r2lpov2a/rtree/setup.py", line 3, in <module>
        import rtree
      File "/tmp/pip-build-r2lpov2a/rtree/rtree/__init__.py", line 1, in <module>
        from .index import Rtree
      File "/tmp/pip-build-r2lpov2a/rtree/rtree/index.py", line 6, in <module>
        from . import core
      File "/tmp/pip-build-r2lpov2a/rtree/rtree/core.py", line 104, in <module>
        rt = ctypes.CDLL(lib_name)
      File "/usr/local/lib/python3.6/ctypes/__init__.py", line 348, in __init__
        self._handle = _dlopen(self._name, mode)
    OSError: libspatialindex_c.so: cannot open shared object file: No such file or directory

    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-r2lpov2a/rtree/

I installed libspatialindex_c.so manually by running the following, but the above error still happens even though /usr/local/lib/libspatialindex_c.so exists now :

LIBSPATIALINDEX_VERSION=spatialindex-src-1.8.5
curl -sLO "http://download.osgeo.org/libspatialindex/$LIBSPATIALINDEX_VERSION.tar.gz" && \
    tar xzf "$LIBSPATIALINDEX_VERSION.tar.gz" && \
    rm -rf "$LIBSPATIALINDEX_VERSION.tar.gz" && \
    cd "$LIBSPATIALINDEX_VERSION" && \
    ./configure && \
    make -j $( getconf _NPROCESSORS_ONLN 2>/dev/null || echo 1 ) && \
    make install

About this issue

Original URL
State: closed
Created 5 years ago
Comments: 17 (10 by maintainers)

Commits related to this issue

use ctypes.utils.find_libary for posix library location #120 — committed to Toblerity/rtree by hobu 5 years ago

Most upvoted comments

worth mentioning that pip install "rtree>=0.8,<0.9"works. this only happens on version 0.9

+24

lior-k on Nov 25, 2019

The package that must be installed on trusty is libspatialindex-c3 and libspatialindex-c4v5 on 16.04 and 18.04

hobu on Dec 10, 2019

Seeing the same issue as of this morning on our CI server.

The system (running Scientific Linux 7) has libspatialindex v1.8.5 installed:

$ yum list installed | grep "spatialindex"
spatialindex.x86_64                   1.8.5-1.el7                 @epel

However, I have no shared library named libspatialindex_c.so, but instead libspatialindex_c.so.4:

$ locate spatialindex_c
/usr/lib64/libspatialindex_c.so.4
/usr/lib64/libspatialindex_c.so.4.1.0

The changes in this diff resulted in rtree being hardcoded to import spatialindex_c.so, rather than calling ctypes.util.find_library("spatialindex_c"), which was previously returning the correct name:

>>> import ctypes.util
>>> ctypes.util.find_library("spatialindex_c")
'libspatialindex_c.so.4'

DanielFEvans on Nov 25, 2019

@hobu - latest master installs without error, unlike 0.9.0. Thanks!

DanielFEvans on Nov 25, 2019

Appears that there was a change in Python 3.6 to cause find_library to search LD_LIBRARY_PATH: https://hg.python.org/cpython/rev/385181e809bc

I wonder if you could make more people happy with a fallback if find_library doesn’t get a result:

lib_name = find_library('spatialindex_c')
if not lib_name:
    if 'linux' in sys.platform:
        lib_name = 'libspatialindex_c.so'
    elif 'darwin' in sys.platform:
        lib_name = 'libspatialindex_c.dylib'
    else:
        lib_name = 'libspatialindex_c'

Of course, that still doesn’t work if you’ve got a libspatialindex_c.so.4 in a non-standard location (luckily, I don’t!).

DanielFEvans on Nov 25, 2019