Homebrew-core: gdal: Symbol not found: _GEOSArea

[rebelliard]

I just started getting this error after reinstalling my local environment with the latest from homebrew:

$ ./manage.py migrate
Traceback (most recent call last):
  File "./manage.py", line 9, in <module>
    execute_from_command_line(sys.argv)
  File "/Users/rafael/.virtualenvs/goodbed/lib/python2.7/site-packages/django/core/management/__init__.py", line 354, in execute_from_command_line
    utility.execute()
  File "/Users/rafael/.virtualenvs/goodbed/lib/python2.7/site-packages/django/core/management/__init__.py", line 328, in execute
    django.setup()
  File "/Users/rafael/.virtualenvs/goodbed/lib/python2.7/site-packages/django/__init__.py", line 18, in setup
    apps.populate(settings.INSTALLED_APPS)
  File "/Users/rafael/.virtualenvs/goodbed/lib/python2.7/site-packages/django/apps/registry.py", line 85, in populate
    app_config = AppConfig.create(entry)
  File "/Users/rafael/.virtualenvs/goodbed/lib/python2.7/site-packages/django/apps/config.py", line 86, in create
    module = import_module(entry)
  File "/usr/local/Cellar/python/2.7.12/Frameworks/Python.framework/Versions/2.7/lib/python2.7/importlib/__init__.py", line 37, in import_module
    __import__(name)
  File "/Users/rafael/workspace/goodbed/beds/sitecomments/__init__.py", line 5, in <module>
    from beds.sitecomments.models import Comment
  File "/Users/rafael/workspace/goodbed/beds/sitecomments/models.py", line 1, in <module>
    from django_comments.models import Comment as DjangoComment
  File "/Users/rafael/.virtualenvs/goodbed/lib/python2.7/site-packages/django_comments/models.py", line 7, in <module>
    from .abstracts import (
  File "/Users/rafael/.virtualenvs/goodbed/lib/python2.7/site-packages/django_comments/abstracts.py", line 18, in <module>
    class BaseCommentAbstractModel(models.Model):
  File "/Users/rafael/.virtualenvs/goodbed/lib/python2.7/site-packages/django/db/models/base.py", line 139, in __new__
    new_class.add_to_class('_meta', Options(meta, **kwargs))
  File "/Users/rafael/.virtualenvs/goodbed/lib/python2.7/site-packages/django/db/models/base.py", line 324, in add_to_class
    value.contribute_to_class(cls, name)
  File "/Users/rafael/.virtualenvs/goodbed/lib/python2.7/site-packages/django/db/models/options.py", line 250, in contribute_to_class
    self.db_table = truncate_name(self.db_table, connection.ops.max_name_length())
  File "/Users/rafael/.virtualenvs/goodbed/lib/python2.7/site-packages/django/db/__init__.py", line 36, in __getattr__
    return getattr(connections[DEFAULT_DB_ALIAS], item)
  File "/Users/rafael/.virtualenvs/goodbed/lib/python2.7/site-packages/django/db/utils.py", line 241, in __getitem__
    backend = load_backend(db['ENGINE'])
  File "/Users/rafael/.virtualenvs/goodbed/lib/python2.7/site-packages/django/db/utils.py", line 112, in load_backend
    return import_module('%s.base' % backend_name)
  File "/usr/local/Cellar/python/2.7.12/Frameworks/Python.framework/Versions/2.7/lib/python2.7/importlib/__init__.py", line 37, in import_module
    __import__(name)
  File "/Users/rafael/.virtualenvs/goodbed/lib/python2.7/site-packages/django/contrib/gis/db/backends/postgis/base.py", line 8, in <module>
    from .features import DatabaseFeatures
  File "/Users/rafael/.virtualenvs/goodbed/lib/python2.7/site-packages/django/contrib/gis/db/backends/postgis/features.py", line 1, in <module>
    from django.contrib.gis.db.backends.base.features import BaseSpatialFeatures
  File "/Users/rafael/.virtualenvs/goodbed/lib/python2.7/site-packages/django/contrib/gis/db/backends/base/features.py", line 3, in <module>
    from django.contrib.gis.db.models import aggregates
  File "/Users/rafael/.virtualenvs/goodbed/lib/python2.7/site-packages/django/contrib/gis/db/models/__init__.py", line 7, in <module>
    from django.contrib.gis.geos import HAS_GEOS
  File "/Users/rafael/.virtualenvs/goodbed/lib/python2.7/site-packages/django/contrib/gis/geos/__init__.py", line 15, in <module>
    from .geometry import GEOSGeometry, wkt_regex, hex_regex
  File "/Users/rafael/.virtualenvs/goodbed/lib/python2.7/site-packages/django/contrib/gis/geos/geometry.py", line 10, in <module>
    from django.contrib.gis.gdal.error import SRSException
  File "/Users/rafael/.virtualenvs/goodbed/lib/python2.7/site-packages/django/contrib/gis/gdal/__init__.py", line 47, in <module>
    from django.contrib.gis.gdal.driver import Driver  # NOQA
  File "/Users/rafael/.virtualenvs/goodbed/lib/python2.7/site-packages/django/contrib/gis/gdal/driver.py", line 5, in <module>
    from django.contrib.gis.gdal.prototypes import ds as vcapi, raster as rcapi
  File "/Users/rafael/.virtualenvs/goodbed/lib/python2.7/site-packages/django/contrib/gis/gdal/prototypes/ds.py", line 9, in <module>
    from django.contrib.gis.gdal.libgdal import lgdal
  File "/Users/rafael/.virtualenvs/goodbed/lib/python2.7/site-packages/django/contrib/gis/gdal/libgdal.py", line 48, in <module>
    lgdal = CDLL(lib_path)
  File "/usr/local/Cellar/python/2.7.12/Frameworks/Python.framework/Versions/2.7/lib/python2.7/ctypes/__init__.py", line 362, in __init__
    self._handle = _dlopen(self._name, mode)
OSError: dlopen(/usr/local/lib/libgdal.dylib, 6): Symbol not found: _GEOSArea
  Referenced from: /usr/local/opt/libspatialite/lib/libspatialite.7.dylib
  Expected in: flat namespace
 in /usr/local/opt/libspatialite/lib/libspatialite.7.dylib

Help?

[detectedstealth]

Have the same issue just did a clean reinstall of macOS and same issue with brew.

[detectedstealth]

My issue has been resolved I was using Postgres.app which had it's own install/configuration of gdal and because I put /Applications/Postgres.app/Contents/Versions/latest/bin in my path.

Running the doctor gave me the following error, removing gdal that I used brew to install fixed the issue.

Warning: "config" scripts exist outside your system or Homebrew directories.
`./configure` scripts often look for *-config scripts to determine if
software packages are installed, and what additional flags to use when
compiling and linking.

Having additional scripts in your path can confuse software installed via
Homebrew if the config script overrides a system or Homebrew provided
script of the same name. We found the following "config" scripts:
    /Applications/Postgres.app/Contents/Versions/latest/bin/gdal-config

[acdha]

@rebelliard did you by any chance record the steps you took to fix this? I just encountered the same problem, durable across a full uninstall / reinstall of the Homebrew GIS-related packages, and it'd save a bit of time.

[acdha]

This is not a fix but there's some sort of load-time ordering dependency as the crash can be avoided by having ctypes import gdal earlier in the startup process:

https://gist.github.com/acdha/ee4e4efee0f47e6953c05b2f060eb4ad#gistcomment-1889163

Possible candidates for the change which triggered this:

proj rebuild-the-GIS-world update: https://github.com/Homebrew/homebrew-core/pull/5289
Python 2.7.12 in https://github.com/Homebrew/homebrew-core/pull/2452 and a bunch of updates in 003c0563c870766d02620d479be12493a23f61e1, 6b08d86854de8668cb873f8fb27acd61296e19a5, b96027bb69386fe5bfaeefd07cb234d6001b3195, c8807b3021b3a4c903a51d17419198e367d3e423, etc.

[ivorbosloper]

I had two versions of libspatialite installed (4.3.0a_3 and 4.3.0a_2) and switched to the older version with brew switch libspatialite 4.3.0a_2. Problem solved for now.

$ brew info libspatialite
libspatialite: stable 4.3.0a (bottled), HEAD
Adds spatial SQL capabilities to SQLite
https://www.gaia-gis.it/fossil/libspatialite/index
/usr/local/Cellar/libspatialite/4.3.0a_2 (30 files, 19.3M)
  Poured from bottle on 2016-03-06 at 23:50:11
/usr/local/Cellar/libspatialite/4.3.0a_3 (31 files, 19.5M) *
  Poured from bottle on 2016-10-21 at 00:16:21
From: https://github.com/Homebrew/homebrew-core/blob/master/Formula/libspatialite.rb

$ brew switch libspatialite 4.3.0a_2

[acdha]

If anyone else runs into this, I just did a rebuild against 682c98237f86945708d24a71cbbc14d50f3d0dd2 to fix this on a few other Macs:

$ brew uninstall libspatialite gdal proj
$ cd /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core
$ git checkout 682c98237f86945708d24a71cbbc14d50f3d0dd2
$ HOMEBREW_NO_AUTO_UPDATE=1 HOMEBREW_BUILD_FROM_SOURCE=1 brew install libspatialite proj gdal

@MikeMcQuaid I left a pointer in #5979 but this issue is also closed. Does it make more sense to open a new issue or to re-open this one?

[MikeMcQuaid]

Does it make more sense to open a new issue or to re-open this one?

@acdha If you can follow the requested steps on the Troubleshooting page and open a new one with that information and reproducible failure instructions that'd be ❤️

[zvanmeter]

@acdha That fix worked great for me, thank you. Two notes for anyone else trying it out:

1. I was getting an error of fatal: reference is not a tree when I tried to checkout 682c982. This was due to me having a shallow clone of homebrew-core. Removing my homebrew-core directory and re-cloning homebrew-core resolved that issue.
2. Building gdal from source was taking quite a while, so I tried the below in place of the last step and had success:

$ HOMEBREW_NO_AUTO_UPDATE=1 HOMEBREW_BUILD_FROM_SOURCE=1 brew install libspatialite proj
$ HOMEBREW_NO_AUTO_UPDATE=1 brew install gdal