Fiona: fiona-1.7.11.post2 error: Symbol not found: _sqlite3_column_table_name

[miccferr]

I have installed the 1.7.10.post2 version of fiona, installed using pip version 10.0.1 (no anaconda) and running python 3.6.

GDAL 2.2.4 was installed via Homebrew

I'm on OSX 10.11.5

While importing the fiona module, the same error as #294 and #582 appeared.

python -c "import fiona"
Traceback (most recent call last):
 File "<string>", line 1, in <module>
 File "/Users/mferretti/.virtualenvs/ciclabili/lib/python3.6/site-packages/fiona/__init__.py", line 69, in <module>
   from fiona.collection import Collection, BytesCollection, vsi_path
 File "/Users/mferretti/.virtualenvs/ciclabili/lib/python3.6/site-packages/fiona/collection.py", line 9, in <module>
   from fiona.ogrext import Iterator, ItemsIterator, KeysIterator
ImportError: dlopen(/Users/mferretti/.virtualenvs/ciclabili/lib/python3.6/site-packages/fiona/ogrext.cpython-36m-darwin.so, 2): Symbol not found: _sqlite3_column_table_name
 Referenced from: /Users/mferretti/.virtualenvs/ciclabili/lib/python3.6/site-packages/fiona/.dylibs/libgdal.20.dylib
 Expected in: /usr/lib/libsqlite3.dylib
in /Users/mferretti/.virtualenvs/ciclabili/lib/python3.6/site-packages/fiona/.dylibs/libgdal.20.dylib

Downgrading the version from fiona-1.7.11.post2 to fiona-1.7.11.post1 fixes the issue.

[sgillies]

The difference between post1 and post2 is that the latter links libsqlite3.

I'm unable to reproduce the problem. On my macbook (with 10.13), the system libsqlite3 (in /usr/lib) is loaded and Fiona works. See the output in my terminal with DYLD_PRINT_LIBRARIES=YES below (commentary continues after the output).

(sqlite3) MapBox-FC:~ sean$ DYLD_PRINT_LIBRARIES=YES fio info ~/code/Fiona/tests/data/coutwildrnp.shp
dyld: loaded: /Users/sean/envs/sqlite3/bin/python3.6
dyld: loaded: /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
dyld: loaded: /Users/sean/envs/sqlite3/bin/../.Python
dyld: loaded: /usr/lib/libSystem.B.dylib
dyld: loaded: /usr/lib/libDiagnosticMessagesClient.dylib
dyld: loaded: /usr/lib/libicucore.A.dylib
dyld: loaded: /usr/lib/libobjc.A.dylib
dyld: loaded: /usr/lib/libz.1.dylib
dyld: loaded: /usr/lib/system/libcache.dylib
dyld: loaded: /usr/lib/system/libcommonCrypto.dylib
dyld: loaded: /usr/lib/system/libcompiler_rt.dylib
dyld: loaded: /usr/lib/system/libcopyfile.dylib
dyld: loaded: /usr/lib/system/libcorecrypto.dylib
dyld: loaded: /usr/lib/system/libdispatch.dylib
dyld: loaded: /usr/lib/system/libdyld.dylib
dyld: loaded: /usr/lib/system/libkeymgr.dylib
dyld: loaded: /usr/lib/system/liblaunch.dylib
dyld: loaded: /usr/lib/system/libmacho.dylib
dyld: loaded: /usr/lib/system/libquarantine.dylib
dyld: loaded: /usr/lib/system/libremovefile.dylib
dyld: loaded: /usr/lib/system/libsystem_asl.dylib
dyld: loaded: /usr/lib/system/libsystem_blocks.dylib
dyld: loaded: /usr/lib/system/libsystem_c.dylib
dyld: loaded: /usr/lib/system/libsystem_configuration.dylib
dyld: loaded: /usr/lib/system/libsystem_coreservices.dylib
dyld: loaded: /usr/lib/system/libsystem_darwin.dylib
dyld: loaded: /usr/lib/system/libsystem_dnssd.dylib
dyld: loaded: /usr/lib/system/libsystem_info.dylib
dyld: loaded: /usr/lib/system/libsystem_m.dylib
dyld: loaded: /usr/lib/system/libsystem_malloc.dylib
dyld: loaded: /usr/lib/system/libsystem_network.dylib
dyld: loaded: /usr/lib/system/libsystem_networkextension.dylib
dyld: loaded: /usr/lib/system/libsystem_notify.dylib
dyld: loaded: /usr/lib/system/libsystem_sandbox.dylib
dyld: loaded: /usr/lib/system/libsystem_secinit.dylib
dyld: loaded: /usr/lib/system/libsystem_kernel.dylib
dyld: loaded: /usr/lib/system/libsystem_platform.dylib
dyld: loaded: /usr/lib/system/libsystem_pthread.dylib
dyld: loaded: /usr/lib/system/libsystem_symptoms.dylib
dyld: loaded: /usr/lib/system/libsystem_trace.dylib
dyld: loaded: /usr/lib/system/libunwind.dylib
dyld: loaded: /usr/lib/system/libxpc.dylib
dyld: loaded: /usr/lib/closure/libclosured.dylib
dyld: loaded: /usr/lib/libc++abi.dylib
dyld: loaded: /usr/lib/libc++.1.dylib
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/lib-dynload/_heapq.cpython-36m-darwin.so
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/lib-dynload/_struct.cpython-36m-darwin.so
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/site-packages/fiona/ogrext.cpython-36m-darwin.so
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/site-packages/fiona/.dylibs/libgdal.20.dylib
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/site-packages/fiona/.dylibs/libproj.12.dylib
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/site-packages/fiona/.dylibs/libjson-c.2.dylib
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/site-packages/fiona/.dylibs/libwebp.7.dylib
dyld: loaded: /usr/lib/libsqlite3.dylib
dyld: loaded: /usr/lib/libexpat.1.dylib
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/site-packages/fiona/.dylibs/libopenjp2.2.3.0.dylib
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/site-packages/fiona/.dylibs/libnetcdf.11.dylib
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/site-packages/fiona/.dylibs/libhdf5_hl.100.dylib
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/site-packages/fiona/.dylibs/libhdf5.101.dylib
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/site-packages/fiona/.dylibs/libtiff.5.dylib
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/site-packages/fiona/.dylibs/libjpeg.9.dylib
dyld: loaded: /usr/lib/libpcre.0.dylib
dyld: loaded: /usr/lib/libcurl.4.dylib
dyld: loaded: /usr/lib/libiconv.2.dylib
dyld: loaded: /usr/lib/libxml2.2.dylib
dyld: loaded: /usr/lib/libcrypto.35.dylib
dyld: loaded: /usr/lib/libssl.35.dylib
dyld: loaded: /System/Library/Frameworks/LDAP.framework/Versions/A/LDAP
dyld: loaded: /System/Library/Frameworks/Kerberos.framework/Versions/A/Kerberos
dyld: loaded: /usr/lib/libapple_nghttp2.dylib
dyld: loaded: /System/Library/PrivateFrameworks/TrustEvaluationAgent.framework/Versions/A/TrustEvaluationAgent
dyld: loaded: /usr/lib/libsasl2.2.dylib
dyld: loaded: /System/Library/Frameworks/Security.framework/Versions/A/Security
dyld: loaded: /System/Library/PrivateFrameworks/CoreDaemon.framework/Versions/B/CoreDaemon
dyld: loaded: /usr/lib/libresolv.9.dylib
dyld: loaded: /System/Library/Frameworks/SystemConfiguration.framework/Versions/A/SystemConfiguration
dyld: loaded: /System/Library/Frameworks/IOKit.framework/Versions/A/IOKit
dyld: loaded: /System/Library/Frameworks/Foundation.framework/Versions/C/Foundation
dyld: loaded: /usr/lib/libOpenScriptingUtil.dylib
dyld: loaded: /usr/lib/libauto.dylib
dyld: loaded: /usr/lib/libbsm.0.dylib
dyld: loaded: /usr/lib/libcoretls.dylib
dyld: loaded: /usr/lib/libcoretls_cfhelpers.dylib
dyld: loaded: /usr/lib/libpam.2.dylib
dyld: loaded: /usr/lib/libxar.1.dylib
dyld: loaded: /System/Library/Frameworks/DiskArbitration.framework/Versions/A/DiskArbitration
dyld: loaded: /usr/lib/libarchive.2.dylib
dyld: loaded: /System/Library/Frameworks/CFNetwork.framework/Versions/A/CFNetwork
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices
dyld: loaded: /usr/lib/liblangid.dylib
dyld: loaded: /usr/lib/libCRFSuite.dylib
dyld: loaded: /usr/lib/libenergytrace.dylib
dyld: loaded: /usr/lib/system/libkxld.dylib
dyld: loaded: /usr/lib/libbz2.1.0.dylib
dyld: loaded: /usr/lib/liblzma.5.dylib
dyld: loaded: /usr/lib/libnetwork.dylib
dyld: loaded: /usr/lib/libpcap.A.dylib
dyld: loaded: /usr/lib/libboringssl.dylib
dyld: loaded: /usr/lib/libusrtcp.dylib
dyld: loaded: /usr/lib/libapple_crypto.dylib
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/FSEvents.framework/Versions/A/FSEvents
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CarbonCore.framework/Versions/A/CarbonCore
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/Metadata.framework/Versions/A/Metadata
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/OSServices.framework/Versions/A/OSServices
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/SearchKit.framework/Versions/A/SearchKit
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/AE.framework/Versions/A/AE
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/LaunchServices
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/DictionaryServices.framework/Versions/A/DictionaryServices
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/SharedFileList.framework/Versions/A/SharedFileList
dyld: loaded: /System/Library/Frameworks/NetFS.framework/Versions/A/NetFS
dyld: loaded: /System/Library/PrivateFrameworks/NetAuth.framework/Versions/A/NetAuth
dyld: loaded: /System/Library/PrivateFrameworks/login.framework/Versions/A/Frameworks/loginsupport.framework/Versions/A/loginsupport
dyld: loaded: /System/Library/PrivateFrameworks/TCC.framework/Versions/A/TCC
dyld: loaded: /usr/lib/libmecabra.dylib
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices
dyld: loaded: /System/Library/Frameworks/CoreGraphics.framework/Versions/A/CoreGraphics
dyld: loaded: /System/Library/Frameworks/CoreText.framework/Versions/A/CoreText
dyld: loaded: /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO
dyld: loaded: /System/Library/Frameworks/ColorSync.framework/Versions/A/ColorSync
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/ATS
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ColorSyncLegacy.framework/Versions/A/ColorSyncLegacy
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/HIServices.framework/Versions/A/HIServices
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/LangAnalysis.framework/Versions/A/LangAnalysis
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/PrintCore.framework/Versions/A/PrintCore
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/QD.framework/Versions/A/QD
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/SpeechSynthesis.framework/Versions/A/SpeechSynthesis
dyld: loaded: /System/Library/PrivateFrameworks/SkyLight.framework/Versions/A/SkyLight
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
dyld: loaded: /System/Library/Frameworks/CoreDisplay.framework/Versions/A/CoreDisplay
dyld: loaded: /System/Library/Frameworks/IOSurface.framework/Versions/A/IOSurface
dyld: loaded: /System/Library/Frameworks/Metal.framework/Versions/A/Metal
dyld: loaded: /System/Library/PrivateFrameworks/MultitouchSupport.framework/Versions/A/MultitouchSupport
dyld: loaded: /System/Library/Frameworks/QuartzCore.framework/Versions/A/QuartzCore
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/vecLib
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvDSP.dylib
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBNNS.dylib
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libQuadrature.dylib
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvMisc.dylib
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLinearAlgebra.dylib
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libSparse.dylib
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libSparseBLAS.dylib
dyld: loaded: /System/Library/PrivateFrameworks/GPUWrangler.framework/Versions/A/GPUWrangler
dyld: loaded: /System/Library/PrivateFrameworks/IOAccelerator.framework/Versions/A/IOAccelerator
dyld: loaded: /System/Library/PrivateFrameworks/IOPresentment.framework/Versions/A/IOPresentment
dyld: loaded: /System/Library/PrivateFrameworks/DSExternalDisplay.framework/Versions/A/DSExternalDisplay
dyld: loaded: /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreFSCache.dylib
dyld: loaded: /System/Library/Frameworks/CoreImage.framework/Versions/A/CoreImage
dyld: loaded: /System/Library/Frameworks/CoreVideo.framework/Versions/A/CoreVideo
dyld: loaded: /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL
dyld: loaded: /System/Library/PrivateFrameworks/GraphVisualizer.framework/Versions/A/GraphVisualizer
dyld: loaded: /System/Library/Frameworks/MetalPerformanceShaders.framework/Versions/A/MetalPerformanceShaders
dyld: loaded: /usr/lib/libFosl_dynamic.dylib
dyld: loaded: /System/Library/PrivateFrameworks/FaceCore.framework/Versions/A/FaceCore
dyld: loaded: /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL
dyld: loaded: /usr/lib/libcompression.dylib
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontParser.dylib
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontRegistry.dylib
dyld: loaded: /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJPEG.dylib
dyld: loaded: /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libTIFF.dylib
dyld: loaded: /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libPng.dylib
dyld: loaded: /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libGIF.dylib
dyld: loaded: /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJP2.dylib
dyld: loaded: /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libRadiance.dylib
dyld: loaded: /System/Library/PrivateFrameworks/AppleJPEG.framework/Versions/A/AppleJPEG
dyld: loaded: /System/Library/Frameworks/MetalPerformanceShaders.framework/Frameworks/MPSCore.framework/Versions/A/MPSCore
dyld: loaded: /System/Library/Frameworks/MetalPerformanceShaders.framework/Frameworks/MPSImage.framework/Versions/A/MPSImage
dyld: loaded: /System/Library/Frameworks/MetalPerformanceShaders.framework/Frameworks/MPSNeuralNetwork.framework/Versions/A/MPSNeuralNetwork
dyld: loaded: /System/Library/Frameworks/MetalPerformanceShaders.framework/Frameworks/MPSMatrix.framework/Versions/A/MPSMatrix
dyld: loaded: /System/Library/PrivateFrameworks/MetalTools.framework/Versions/A/MetalTools
dyld: loaded: /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib
dyld: loaded: /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib
dyld: loaded: /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib
dyld: loaded: /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib
dyld: loaded: /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.dylib
dyld: loaded: /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib
dyld: loaded: /usr/lib/libcups.2.dylib
dyld: loaded: /System/Library/Frameworks/GSS.framework/Versions/A/GSS
dyld: loaded: /System/Library/PrivateFrameworks/Heimdal.framework/Versions/A/Heimdal
dyld: loaded: /usr/lib/libheimdal-asn1.dylib
dyld: loaded: /System/Library/Frameworks/OpenDirectory.framework/Versions/A/OpenDirectory
dyld: loaded: /System/Library/PrivateFrameworks/CommonAuth.framework/Versions/A/CommonAuth
dyld: loaded: /System/Library/Frameworks/OpenDirectory.framework/Versions/A/Frameworks/CFOpenDirectory.framework/Versions/A/CFOpenDirectory
dyld: loaded: /System/Library/Frameworks/SecurityFoundation.framework/Versions/A/SecurityFoundation
dyld: loaded: /System/Library/PrivateFrameworks/APFS.framework/Versions/A/APFS
dyld: loaded: /usr/lib/libutil.dylib
dyld: loaded: /System/Library/Frameworks/CoreAudio.framework/Versions/A/CoreAudio
dyld: loaded: /System/Library/Frameworks/AudioToolbox.framework/Versions/A/AudioToolbox
dyld: loaded: /System/Library/PrivateFrameworks/AppleSauce.framework/Versions/A/AppleSauce
dyld: loaded: /System/Library/PrivateFrameworks/LinguisticData.framework/Versions/A/LinguisticData
dyld: loaded: /usr/lib/libmarisa.dylib
dyld: loaded: /System/Library/PrivateFrameworks/Lexicon.framework/Versions/A/Lexicon
dyld: loaded: /usr/lib/libChineseTokenizer.dylib
dyld: loaded: /usr/lib/libcmph.dylib
dyld: loaded: /System/Library/PrivateFrameworks/LanguageModeling.framework/Versions/A/LanguageModeling
dyld: loaded: /System/Library/Frameworks/CoreData.framework/Versions/A/CoreData
dyld: loaded: /System/Library/PrivateFrameworks/CoreEmoji.framework/Versions/A/CoreEmoji
dyld: loaded: /System/Library/Frameworks/ServiceManagement.framework/Versions/A/ServiceManagement
dyld: loaded: /System/Library/PrivateFrameworks/BackgroundTaskManagement.framework/Versions/A/BackgroundTaskManagement
dyld: loaded: /usr/lib/libxslt.1.dylib
dyld: loaded: /System/Library/PrivateFrameworks/AppleSRP.framework/Versions/A/AppleSRP
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/site-packages/fiona/_geometry.cpython-36m-darwin.so
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/site-packages/fiona/_err.cpython-36m-darwin.so
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/lib-dynload/math.cpython-36m-darwin.so
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/lib-dynload/_datetime.cpython-36m-darwin.so
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/lib-dynload/_json.cpython-36m-darwin.so
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/lib-dynload/_ctypes.cpython-36m-darwin.so
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/lib-dynload/zlib.cpython-36m-darwin.so
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/lib-dynload/_bz2.cpython-36m-darwin.so
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/lib-dynload/_lzma.cpython-36m-darwin.so
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/lib-dynload/grp.cpython-36m-darwin.so
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/lib-dynload/_posixsubprocess.cpython-36m-darwin.so
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/lib-dynload/select.cpython-36m-darwin.so
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/site-packages/fiona/_drivers.cpython-36m-darwin.so
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/lib-dynload/binascii.cpython-36m-darwin.so
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/lib-dynload/pyexpat.cpython-36m-darwin.so
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/lib-dynload/_hashlib.cpython-36m-darwin.so
dyld: loaded: /Library/Frameworks/Python.framework/Versions/3.6/lib/libssl.1.0.0.dylib
dyld: loaded: /Library/Frameworks/Python.framework/Versions/3.6/lib/libcrypto.1.0.0.dylib
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/lib-dynload/_blake2.cpython-36m-darwin.so
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/lib-dynload/_sha3.cpython-36m-darwin.so
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/lib-dynload/_bisect.cpython-36m-darwin.so
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/lib-dynload/_random.cpython-36m-darwin.so
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/lib-dynload/_socket.cpython-36m-darwin.so
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/lib-dynload/_opcode.cpython-36m-darwin.so
dyld: loaded: /Users/sean/envs/sqlite3/lib/python3.6/site-packages/fiona/_transform.cpython-36m-darwin.so
{"driver": "ESRI Shapefile", "schema": {"properties": {"PERIMETER": "float:24.15", "FEATURE2": "str:80", "NAME": "str:80", "FEATURE1": "str:80", "URL": "str:101", "AGBUR": "str:80", "AREA": "float:24.15", "STATE_FIPS": "str:80", "WILDRNP020": "int:10", "STATE": "str:80"}, "geometry": "Polygon"}, "crs": "EPSG:4326", "crs_wkt": "GEOGCS[\"GCS_WGS_1984\",DATUM[\"WGS_1984\",SPHEROID[\"WGS_84\",6378137,298.257223563]],PRIMEM[\"Greenwich\",0],UNIT[\"Degree\",0.017453292519943295],AUTHORITY[\"EPSG\",\"4326\"]]", "bounds": [-113.56424713134766, 37.0689811706543, -104.97087097167969, 41.99627685546875], "name": "coutwildrnp", "count": 67}

Can you try this environmental variable and check if some other libsqlite3 library is being loaded instead? I've seen some mentions on the web about Homebrew's GDAL and spatialite recipes being broken, and I think it's quite possible that your system is affected.

[miccferr]

Here's the output from a new virtualenv with fiona1.7.10post2

DYLD_PRINT_LIBRARIES=YES  python -c "import fiona"
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili2/bin/python
dyld: loaded: /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili2/bin/../.Python
dyld: loaded: /usr/lib/libSystem.B.dylib
dyld: loaded: /usr/lib/libauto.dylib
dyld: loaded: /usr/lib/libDiagnosticMessagesClient.dylib
dyld: loaded: /usr/lib/libicucore.A.dylib
dyld: loaded: /usr/lib/libobjc.A.dylib
dyld: loaded: /usr/lib/libz.1.dylib
dyld: loaded: /usr/lib/libc++.1.dylib
dyld: loaded: /usr/lib/libc++abi.dylib
dyld: loaded: /usr/lib/system/libcache.dylib
dyld: loaded: /usr/lib/system/libcommonCrypto.dylib
dyld: loaded: /usr/lib/system/libcompiler_rt.dylib
dyld: loaded: /usr/lib/system/libcopyfile.dylib
dyld: loaded: /usr/lib/system/libcorecrypto.dylib
dyld: loaded: /usr/lib/system/libdispatch.dylib
dyld: loaded: /usr/lib/system/libdyld.dylib
dyld: loaded: /usr/lib/system/libkeymgr.dylib
dyld: loaded: /usr/lib/system/liblaunch.dylib
dyld: loaded: /usr/lib/system/libmacho.dylib
dyld: loaded: /usr/lib/system/libquarantine.dylib
dyld: loaded: /usr/lib/system/libremovefile.dylib
dyld: loaded: /usr/lib/system/libsystem_asl.dylib
dyld: loaded: /usr/lib/system/libsystem_blocks.dylib
dyld: loaded: /usr/lib/system/libsystem_c.dylib
dyld: loaded: /usr/lib/system/libsystem_configuration.dylib
dyld: loaded: /usr/lib/system/libsystem_coreservices.dylib
dyld: loaded: /usr/lib/system/libsystem_coretls.dylib
dyld: loaded: /usr/lib/system/libsystem_dnssd.dylib
dyld: loaded: /usr/lib/system/libsystem_info.dylib
dyld: loaded: /usr/lib/system/libsystem_kernel.dylib
dyld: loaded: /usr/lib/system/libsystem_m.dylib
dyld: loaded: /usr/lib/system/libsystem_malloc.dylib
dyld: loaded: /usr/lib/system/libsystem_network.dylib
dyld: loaded: /usr/lib/system/libsystem_networkextension.dylib
dyld: loaded: /usr/lib/system/libsystem_notify.dylib
dyld: loaded: /usr/lib/system/libsystem_platform.dylib
dyld: loaded: /usr/lib/system/libsystem_pthread.dylib
dyld: loaded: /usr/lib/system/libsystem_sandbox.dylib
dyld: loaded: /usr/lib/system/libsystem_secinit.dylib
dyld: loaded: /usr/lib/system/libsystem_trace.dylib
dyld: loaded: /usr/lib/system/libunc.dylib
dyld: loaded: /usr/lib/system/libunwind.dylib
dyld: loaded: /usr/lib/system/libxpc.dylib
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili2/lib/python3.6/lib-dynload/_heapq.cpython-36m-darwin.so
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili2/lib/python3.6/lib-dynload/_struct.cpython-36m-darwin.so
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili2/lib/python3.6/site-packages/fiona/ogrext.cpython-36m-darwin.so
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili2/lib/python3.6/site-packages/fiona/.dylibs/libgdal.20.dylib
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili2/lib/python3.6/site-packages/fiona/.dylibs/libproj.12.dylib
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili2/lib/python3.6/site-packages/fiona/.dylibs/libjson-c.2.dylib
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili2/lib/python3.6/site-packages/fiona/.dylibs/libwebp.7.dylib
dyld: loaded: /usr/lib/libsqlite3.dylib
dyld: loaded: /usr/lib/libexpat.1.dylib
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili2/lib/python3.6/site-packages/fiona/.dylibs/libopenjp2.2.3.0.dylib
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili2/lib/python3.6/site-packages/fiona/.dylibs/libnetcdf.11.dylib
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili2/lib/python3.6/site-packages/fiona/.dylibs/libhdf5_hl.100.dylib
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili2/lib/python3.6/site-packages/fiona/.dylibs/libhdf5.101.dylib
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili2/lib/python3.6/site-packages/fiona/.dylibs/libtiff.5.dylib
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili2/lib/python3.6/site-packages/fiona/.dylibs/libjpeg.9.dylib
dyld: loaded: /usr/lib/libpcre.0.dylib
dyld: loaded: /usr/lib/libcurl.4.dylib
dyld: loaded: /usr/lib/libiconv.2.dylib
dyld: loaded: /usr/lib/libxml2.2.dylib
dyld: loaded: /System/Library/Frameworks/Security.framework/Versions/A/Security
dyld: loaded: /System/Library/Frameworks/LDAP.framework/Versions/A/LDAP
dyld: loaded: /System/Library/Frameworks/Kerberos.framework/Versions/A/Kerberos
dyld: loaded: /usr/lib/libbsm.0.dylib
dyld: loaded: /usr/lib/libxar.1.dylib
dyld: loaded: /usr/lib/libpam.2.dylib
dyld: loaded: /System/Library/Frameworks/IOKit.framework/Versions/A/IOKit
dyld: loaded: /usr/lib/libOpenScriptingUtil.dylib
dyld: loaded: /usr/lib/libbz2.1.0.dylib
dyld: loaded: /usr/lib/libenergytrace.dylib
dyld: loaded: /usr/lib/system/libkxld.dylib
dyld: loaded: /usr/lib/libsasl2.2.dylib
dyld: loaded: /System/Library/PrivateFrameworks/CoreDaemon.framework/Versions/B/CoreDaemon
dyld: loaded: /usr/lib/libresolv.9.dylib
dyld: loaded: /System/Library/Frameworks/SystemConfiguration.framework/Versions/A/SystemConfiguration
dyld: loaded: /usr/lib/libcrypto.0.9.8.dylib
dyld: loaded: /System/Library/PrivateFrameworks/AppleSRP.framework/Versions/A/AppleSRP
dyld: loaded: /System/Library/Frameworks/ServiceManagement.framework/Versions/A/ServiceManagement
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices
dyld: loaded: /System/Library/PrivateFrameworks/TrustEvaluationAgent.framework/Versions/A/TrustEvaluationAgent
dyld: loaded: /System/Library/Frameworks/CFNetwork.framework/Versions/A/CFNetwork
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/FSEvents.framework/Versions/A/FSEvents
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CarbonCore.framework/Versions/A/CarbonCore
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/Metadata.framework/Versions/A/Metadata
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/OSServices.framework/Versions/A/OSServices
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/SearchKit.framework/Versions/A/SearchKit
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/AE.framework/Versions/A/AE
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/LaunchServices
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/DictionaryServices.framework/Versions/A/DictionaryServices
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/SharedFileList.framework/Versions/A/SharedFileList
dyld: loaded: /System/Library/Frameworks/DiskArbitration.framework/Versions/A/DiskArbitration
dyld: loaded: /System/Library/Frameworks/NetFS.framework/Versions/A/NetFS
dyld: loaded: /System/Library/PrivateFrameworks/NetAuth.framework/Versions/A/NetAuth
dyld: loaded: /System/Library/PrivateFrameworks/login.framework/Versions/A/Frameworks/loginsupport.framework/Versions/A/loginsupport
dyld: loaded: /System/Library/PrivateFrameworks/TCC.framework/Versions/A/TCC
dyld: loaded: /usr/lib/libmecabra.dylib
dyld: loaded: /System/Library/Frameworks/Foundation.framework/Versions/C/Foundation
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices
dyld: loaded: /System/Library/Frameworks/CoreGraphics.framework/Versions/A/CoreGraphics
dyld: loaded: /System/Library/Frameworks/CoreText.framework/Versions/A/CoreText
dyld: loaded: /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/ATS
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ColorSync.framework/Versions/A/ColorSync
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/HIServices.framework/Versions/A/HIServices
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/LangAnalysis.framework/Versions/A/LangAnalysis
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/PrintCore.framework/Versions/A/PrintCore
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/QD.framework/Versions/A/QD
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/SpeechSynthesis.framework/Versions/A/SpeechSynthesis
dyld: loaded: /System/Library/Frameworks/IOSurface.framework/Versions/A/IOSurface
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
dyld: loaded: /System/Library/PrivateFrameworks/MultitouchSupport.framework/Versions/A/MultitouchSupport
dyld: loaded: /System/Library/Frameworks/Metal.framework/Versions/A/Metal
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/vecLib
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvDSP.dylib
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvMisc.dylib
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLinearAlgebra.dylib
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libSparseBLAS.dylib
dyld: loaded: /System/Library/PrivateFrameworks/GPUCompiler.framework/libmetal_timestamp.dylib
dyld: loaded: /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreFSCache.dylib
dyld: loaded: /System/Library/PrivateFrameworks/IOAccelerator.framework/Versions/A/IOAccelerator
dyld: loaded: /usr/lib/libextension.dylib
dyld: loaded: /usr/lib/libarchive.2.dylib
dyld: loaded: /usr/lib/liblangid.dylib
dyld: loaded: /usr/lib/libCRFSuite.dylib
dyld: loaded: /usr/lib/liblzma.5.dylib
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontParser.dylib
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontRegistry.dylib
dyld: loaded: /System/Library/PrivateFrameworks/AppleVPA.framework/Versions/A/AppleVPA
dyld: loaded: /System/Library/PrivateFrameworks/AppleJPEG.framework/Versions/A/AppleJPEG
dyld: loaded: /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJPEG.dylib
dyld: loaded: /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libTIFF.dylib
dyld: loaded: /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libPng.dylib
dyld: loaded: /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libGIF.dylib
dyld: loaded: /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJP2.dylib
dyld: loaded: /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libRadiance.dylib
dyld: loaded: /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL
dyld: loaded: /System/Library/Frameworks/CoreVideo.framework/Versions/A/CoreVideo
dyld: loaded: /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib
dyld: loaded: /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib
dyld: loaded: /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib
dyld: loaded: /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib
dyld: loaded: /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.dylib
dyld: loaded: /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib
dyld: loaded: /usr/lib/libcompression.dylib
dyld: loaded: /usr/lib/libcups.2.dylib
dyld: loaded: /System/Library/Frameworks/GSS.framework/Versions/A/GSS
dyld: loaded: /System/Library/PrivateFrameworks/Heimdal.framework/Versions/A/Heimdal
dyld: loaded: /usr/lib/libheimdal-asn1.dylib
dyld: loaded: /System/Library/Frameworks/OpenDirectory.framework/Versions/A/OpenDirectory
dyld: loaded: /System/Library/PrivateFrameworks/CommonAuth.framework/Versions/A/CommonAuth
dyld: loaded: /System/Library/Frameworks/OpenDirectory.framework/Versions/A/Frameworks/CFOpenDirectory.framework/Versions/A/CFOpenDirectory
dyld: loaded: /System/Library/Frameworks/SecurityFoundation.framework/Versions/A/SecurityFoundation
dyld: loaded: /System/Library/Frameworks/CoreAudio.framework/Versions/A/CoreAudio
dyld: loaded: /System/Library/Frameworks/AudioToolbox.framework/Versions/A/AudioToolbox
dyld: loaded: /System/Library/PrivateFrameworks/LanguageModeling.framework/Versions/A/LanguageModeling
dyld: loaded: /usr/lib/libmarisa.dylib
dyld: loaded: /usr/lib/libChineseTokenizer.dylib
dyld: loaded: /usr/lib/libcmph.dylib
dyld: loaded: /System/Library/Frameworks/CoreData.framework/Versions/A/CoreData
dyld: loaded: /usr/lib/libxslt.1.dylib
dyld: unloaded: /Users/mferretti/.virtualenvs/ciclabili2/lib/python3.6/site-packages/fiona/ogrext.cpython-36m-darwin.so
dyld: unloaded: /Users/mferretti/.virtualenvs/ciclabili2/lib/python3.6/site-packages/fiona/.dylibs/libgdal.20.dylib
dyld: unloaded: /Users/mferretti/.virtualenvs/ciclabili2/lib/python3.6/site-packages/fiona/.dylibs/libproj.12.dylib
dyld: unloaded: /Users/mferretti/.virtualenvs/ciclabili2/lib/python3.6/site-packages/fiona/.dylibs/libjson-c.2.dylib
dyld: unloaded: /Users/mferretti/.virtualenvs/ciclabili2/lib/python3.6/site-packages/fiona/.dylibs/libwebp.7.dylib
dyld: unloaded: /usr/lib/libexpat.1.dylib
dyld: unloaded: /Users/mferretti/.virtualenvs/ciclabili2/lib/python3.6/site-packages/fiona/.dylibs/libopenjp2.2.3.0.dylib
dyld: unloaded: /Users/mferretti/.virtualenvs/ciclabili2/lib/python3.6/site-packages/fiona/.dylibs/libnetcdf.11.dylib
dyld: unloaded: /Users/mferretti/.virtualenvs/ciclabili2/lib/python3.6/site-packages/fiona/.dylibs/libhdf5_hl.100.dylib
dyld: unloaded: /Users/mferretti/.virtualenvs/ciclabili2/lib/python3.6/site-packages/fiona/.dylibs/libhdf5.101.dylib
dyld: unloaded: /Users/mferretti/.virtualenvs/ciclabili2/lib/python3.6/site-packages/fiona/.dylibs/libtiff.5.dylib
dyld: unloaded: /Users/mferretti/.virtualenvs/ciclabili2/lib/python3.6/site-packages/fiona/.dylibs/libjpeg.9.dylib
dyld: unloaded: /usr/lib/libpcre.0.dylib
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Users/mferretti/.virtualenvs/ciclabili2/lib/python3.6/site-packages/fiona/__init__.py", line 69, in <module>
    from fiona.collection import Collection, BytesCollection, vsi_path
  File "/Users/mferretti/.virtualenvs/ciclabili2/lib/python3.6/site-packages/fiona/collection.py", line 9, in <module>
    from fiona.ogrext import Iterator, ItemsIterator, KeysIterator
ImportError: dlopen(/Users/mferretti/.virtualenvs/ciclabili2/lib/python3.6/site-packages/fiona/ogrext.cpython-36m-darwin.so, 2): Symbol not found: _sqlite3_column_table_name
  Referenced from: /Users/mferretti/.virtualenvs/ciclabili2/lib/python3.6/site-packages/fiona/.dylibs/libgdal.20.dylib
  Expected in: /usr/lib/libsqlite3.dylib
 in /Users/mferretti/.virtualenvs/ciclabili2/lib/python3.6/site-packages/fiona/.dylibs/libgdal.20.dylib

Here's from the working virtualenv with fiona1.7.10post1

➔ DYLD_PRINT_LIBRARIES=YES  python -c "import fiona"
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili/bin/python
dyld: loaded: /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili/bin/../.Python
dyld: loaded: /usr/lib/libSystem.B.dylib
dyld: loaded: /usr/lib/libauto.dylib
dyld: loaded: /usr/lib/libDiagnosticMessagesClient.dylib
dyld: loaded: /usr/lib/libicucore.A.dylib
dyld: loaded: /usr/lib/libobjc.A.dylib
dyld: loaded: /usr/lib/libz.1.dylib
dyld: loaded: /usr/lib/libc++.1.dylib
dyld: loaded: /usr/lib/libc++abi.dylib
dyld: loaded: /usr/lib/system/libcache.dylib
dyld: loaded: /usr/lib/system/libcommonCrypto.dylib
dyld: loaded: /usr/lib/system/libcompiler_rt.dylib
dyld: loaded: /usr/lib/system/libcopyfile.dylib
dyld: loaded: /usr/lib/system/libcorecrypto.dylib
dyld: loaded: /usr/lib/system/libdispatch.dylib
dyld: loaded: /usr/lib/system/libdyld.dylib
dyld: loaded: /usr/lib/system/libkeymgr.dylib
dyld: loaded: /usr/lib/system/liblaunch.dylib
dyld: loaded: /usr/lib/system/libmacho.dylib
dyld: loaded: /usr/lib/system/libquarantine.dylib
dyld: loaded: /usr/lib/system/libremovefile.dylib
dyld: loaded: /usr/lib/system/libsystem_asl.dylib
dyld: loaded: /usr/lib/system/libsystem_blocks.dylib
dyld: loaded: /usr/lib/system/libsystem_c.dylib
dyld: loaded: /usr/lib/system/libsystem_configuration.dylib
dyld: loaded: /usr/lib/system/libsystem_coreservices.dylib
dyld: loaded: /usr/lib/system/libsystem_coretls.dylib
dyld: loaded: /usr/lib/system/libsystem_dnssd.dylib
dyld: loaded: /usr/lib/system/libsystem_info.dylib
dyld: loaded: /usr/lib/system/libsystem_kernel.dylib
dyld: loaded: /usr/lib/system/libsystem_m.dylib
dyld: loaded: /usr/lib/system/libsystem_malloc.dylib
dyld: loaded: /usr/lib/system/libsystem_network.dylib
dyld: loaded: /usr/lib/system/libsystem_networkextension.dylib
dyld: loaded: /usr/lib/system/libsystem_notify.dylib
dyld: loaded: /usr/lib/system/libsystem_platform.dylib
dyld: loaded: /usr/lib/system/libsystem_pthread.dylib
dyld: loaded: /usr/lib/system/libsystem_sandbox.dylib
dyld: loaded: /usr/lib/system/libsystem_secinit.dylib
dyld: loaded: /usr/lib/system/libsystem_trace.dylib
dyld: loaded: /usr/lib/system/libunc.dylib
dyld: loaded: /usr/lib/system/libunwind.dylib
dyld: loaded: /usr/lib/system/libxpc.dylib
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili/lib/python3.6/lib-dynload/_heapq.cpython-36m-darwin.so
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili/lib/python3.6/lib-dynload/_struct.cpython-36m-darwin.so
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili/lib/python3.6/site-packages/fiona/ogrext.cpython-36m-darwin.so
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili/lib/python3.6/site-packages/fiona/.dylibs/libgdal.20.dylib
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili/lib/python3.6/site-packages/fiona/.dylibs/libproj.12.dylib
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili/lib/python3.6/site-packages/fiona/.dylibs/libjson-c.2.dylib
dyld: loaded: /usr/lib/libsqlite3.dylib
dyld: loaded: /usr/lib/libexpat.1.dylib
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili/lib/python3.6/site-packages/fiona/.dylibs/libopenjp2.2.3.0.dylib
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili/lib/python3.6/site-packages/fiona/.dylibs/libnetcdf.11.dylib
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili/lib/python3.6/site-packages/fiona/.dylibs/libhdf5_hl.100.dylib
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili/lib/python3.6/site-packages/fiona/.dylibs/libhdf5.101.dylib
dyld: loaded: /usr/lib/libpcre.0.dylib
dyld: loaded: /usr/lib/libcurl.4.dylib
dyld: loaded: /usr/lib/libiconv.2.dylib
dyld: loaded: /usr/lib/libxml2.2.dylib
dyld: loaded: /System/Library/Frameworks/Security.framework/Versions/A/Security
dyld: loaded: /System/Library/Frameworks/LDAP.framework/Versions/A/LDAP
dyld: loaded: /System/Library/Frameworks/Kerberos.framework/Versions/A/Kerberos
dyld: loaded: /usr/lib/libbsm.0.dylib
dyld: loaded: /usr/lib/libxar.1.dylib
dyld: loaded: /usr/lib/libpam.2.dylib
dyld: loaded: /System/Library/Frameworks/IOKit.framework/Versions/A/IOKit
dyld: loaded: /usr/lib/libOpenScriptingUtil.dylib
dyld: loaded: /usr/lib/libbz2.1.0.dylib
dyld: loaded: /usr/lib/libenergytrace.dylib
dyld: loaded: /usr/lib/system/libkxld.dylib
dyld: loaded: /usr/lib/libsasl2.2.dylib
dyld: loaded: /System/Library/PrivateFrameworks/CoreDaemon.framework/Versions/B/CoreDaemon
dyld: loaded: /usr/lib/libresolv.9.dylib
dyld: loaded: /System/Library/Frameworks/SystemConfiguration.framework/Versions/A/SystemConfiguration
dyld: loaded: /usr/lib/libcrypto.0.9.8.dylib
dyld: loaded: /System/Library/PrivateFrameworks/AppleSRP.framework/Versions/A/AppleSRP
dyld: loaded: /System/Library/Frameworks/ServiceManagement.framework/Versions/A/ServiceManagement
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices
dyld: loaded: /System/Library/PrivateFrameworks/TrustEvaluationAgent.framework/Versions/A/TrustEvaluationAgent
dyld: loaded: /System/Library/Frameworks/CFNetwork.framework/Versions/A/CFNetwork
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/FSEvents.framework/Versions/A/FSEvents
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CarbonCore.framework/Versions/A/CarbonCore
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/Metadata.framework/Versions/A/Metadata
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/OSServices.framework/Versions/A/OSServices
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/SearchKit.framework/Versions/A/SearchKit
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/AE.framework/Versions/A/AE
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/LaunchServices
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/DictionaryServices.framework/Versions/A/DictionaryServices
dyld: loaded: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/SharedFileList.framework/Versions/A/SharedFileList
dyld: loaded: /System/Library/Frameworks/DiskArbitration.framework/Versions/A/DiskArbitration
dyld: loaded: /System/Library/Frameworks/NetFS.framework/Versions/A/NetFS
dyld: loaded: /System/Library/PrivateFrameworks/NetAuth.framework/Versions/A/NetAuth
dyld: loaded: /System/Library/PrivateFrameworks/login.framework/Versions/A/Frameworks/loginsupport.framework/Versions/A/loginsupport
dyld: loaded: /System/Library/PrivateFrameworks/TCC.framework/Versions/A/TCC
dyld: loaded: /usr/lib/libmecabra.dylib
dyld: loaded: /System/Library/Frameworks/Foundation.framework/Versions/C/Foundation
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices
dyld: loaded: /System/Library/Frameworks/CoreGraphics.framework/Versions/A/CoreGraphics
dyld: loaded: /System/Library/Frameworks/CoreText.framework/Versions/A/CoreText
dyld: loaded: /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/ATS
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ColorSync.framework/Versions/A/ColorSync
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/HIServices.framework/Versions/A/HIServices
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/LangAnalysis.framework/Versions/A/LangAnalysis
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/PrintCore.framework/Versions/A/PrintCore
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/QD.framework/Versions/A/QD
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/SpeechSynthesis.framework/Versions/A/SpeechSynthesis
dyld: loaded: /System/Library/Frameworks/IOSurface.framework/Versions/A/IOSurface
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
dyld: loaded: /System/Library/PrivateFrameworks/MultitouchSupport.framework/Versions/A/MultitouchSupport
dyld: loaded: /System/Library/Frameworks/Metal.framework/Versions/A/Metal
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/vecLib
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvDSP.dylib
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvMisc.dylib
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLinearAlgebra.dylib
dyld: loaded: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libSparseBLAS.dylib
dyld: loaded: /System/Library/PrivateFrameworks/GPUCompiler.framework/libmetal_timestamp.dylib
dyld: loaded: /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreFSCache.dylib
dyld: loaded: /System/Library/PrivateFrameworks/IOAccelerator.framework/Versions/A/IOAccelerator
dyld: loaded: /usr/lib/libextension.dylib
dyld: loaded: /usr/lib/libarchive.2.dylib
dyld: loaded: /usr/lib/liblangid.dylib
dyld: loaded: /usr/lib/libCRFSuite.dylib
dyld: loaded: /usr/lib/liblzma.5.dylib
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontParser.dylib
dyld: loaded: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontRegistry.dylib
dyld: loaded: /System/Library/PrivateFrameworks/AppleVPA.framework/Versions/A/AppleVPA
dyld: loaded: /System/Library/PrivateFrameworks/AppleJPEG.framework/Versions/A/AppleJPEG
dyld: loaded: /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJPEG.dylib
dyld: loaded: /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libTIFF.dylib
dyld: loaded: /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libPng.dylib
dyld: loaded: /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libGIF.dylib
dyld: loaded: /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJP2.dylib
dyld: loaded: /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libRadiance.dylib
dyld: loaded: /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL
dyld: loaded: /System/Library/Frameworks/CoreVideo.framework/Versions/A/CoreVideo
dyld: loaded: /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib
dyld: loaded: /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib
dyld: loaded: /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib
dyld: loaded: /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib
dyld: loaded: /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.dylib
dyld: loaded: /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib
dyld: loaded: /usr/lib/libcompression.dylib
dyld: loaded: /usr/lib/libcups.2.dylib
dyld: loaded: /System/Library/Frameworks/GSS.framework/Versions/A/GSS
dyld: loaded: /System/Library/PrivateFrameworks/Heimdal.framework/Versions/A/Heimdal
dyld: loaded: /usr/lib/libheimdal-asn1.dylib
dyld: loaded: /System/Library/Frameworks/OpenDirectory.framework/Versions/A/OpenDirectory
dyld: loaded: /System/Library/PrivateFrameworks/CommonAuth.framework/Versions/A/CommonAuth
dyld: loaded: /System/Library/Frameworks/OpenDirectory.framework/Versions/A/Frameworks/CFOpenDirectory.framework/Versions/A/CFOpenDirectory
dyld: loaded: /System/Library/Frameworks/SecurityFoundation.framework/Versions/A/SecurityFoundation
dyld: loaded: /System/Library/Frameworks/CoreAudio.framework/Versions/A/CoreAudio
dyld: loaded: /System/Library/Frameworks/AudioToolbox.framework/Versions/A/AudioToolbox
dyld: loaded: /System/Library/PrivateFrameworks/LanguageModeling.framework/Versions/A/LanguageModeling
dyld: loaded: /usr/lib/libmarisa.dylib
dyld: loaded: /usr/lib/libChineseTokenizer.dylib
dyld: loaded: /usr/lib/libcmph.dylib
dyld: loaded: /System/Library/Frameworks/CoreData.framework/Versions/A/CoreData
dyld: loaded: /usr/lib/libxslt.1.dylib
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili/lib/python3.6/site-packages/fiona/_geometry.cpython-36m-darwin.so
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili/lib/python3.6/site-packages/fiona/_err.cpython-36m-darwin.so
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili/lib/python3.6/lib-dynload/math.cpython-36m-darwin.so
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili/lib/python3.6/lib-dynload/_datetime.cpython-36m-darwin.so
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili/lib/python3.6/lib-dynload/_json.cpython-36m-darwin.so
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili/lib/python3.6/lib-dynload/_ctypes.cpython-36m-darwin.so
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili/lib/python3.6/lib-dynload/zlib.cpython-36m-darwin.so
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili/lib/python3.6/lib-dynload/_bz2.cpython-36m-darwin.so
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili/lib/python3.6/lib-dynload/_lzma.cpython-36m-darwin.so
dyld: loaded: /usr/local/opt/xz/lib/liblzma.5.dylib
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili/lib/python3.6/lib-dynload/grp.cpython-36m-darwin.so
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili/lib/python3.6/lib-dynload/_posixsubprocess.cpython-36m-darwin.so
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili/lib/python3.6/lib-dynload/select.cpython-36m-darwin.so
dyld: loaded: /Users/mferretti/.virtualenvs/ciclabili/lib/python3.6/site-packages/fiona/_drivers.cpython-36m-darwin.so

It seems like libsqlite is the same in both cases, i.e. dyld: loaded: /usr/lib/libsqlite3.dylib

[sgillies]

Ok, so it looks like there is no "foreign" libsqlite3 on your library path path. I'm stumped. I wonder if my binary distributions are incompatible with 10.11?

Another workaround: avoid the binary distributions by doing this:

`pip install --no-binary fiona fiona

This will fetch a source distribution, call your system's gdal-config program (if /usr/local/bin/gdal-config from homebrew is on your path) and compile all the extension modules.

[miccferr]

Woohoo! Installing fiona as you suggested actually works. So I guess there is a problem with your binary distribution?

[sgillies]

Apparently so. I guess I'm going to get to learn more about libsqlite3 on different versions of OS X 😂

[nine9ths]

I'm on 10.12 and running into a similar issue, post1 works, post2 fails missing sqlite3, although suggested workaround also fails for me with the following:

...
running build_ext
    building 'fiona._transform' extension
    creating build/temp.macosx-10.12-x86_64-3.6
    creating build/temp.macosx-10.12-x86_64-3.6/fiona
    clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Cellar/gdal/2.3.0/include -I/usr/local/Cellar/python/3.6.5/Frameworks/Python.framework/Versions/3.6/include/python3.6m -c fiona/_transform.cpp -o build/temp.macosx-10.12-x86_64-3.6/fiona/_transform.o
    In file included from fiona/_transform.cpp:605:
    In file included from /usr/local/Cellar/gdal/2.3.0/include/cpl_conv.h:35:
    /usr/local/Cellar/gdal/2.3.0/include/cpl_port.h:187:6: error: Must have C++11 or newer.
    #    error Must have C++11 or newer.
         ^
...

[simonhuwiler]

Same problems here like @miccferr and @nine9ths
Mac 10.12.6, Python 3.6.5

After installing gdal with brew install gdal and avoiding binary with pip install --no-binary fiona fiona, I got this error

/usr/local/Cellar/gdal/2.3.0/include/cpl_conv.h:354:70: warning: deleted function definitions are a C++11 extension [-Wc++11-extensions] CPLConfigOptionSetter& operator=(const CPLConfigOptionSetter&) = delete; ^ /usr/local/Cellar/gdal/2.3.0/include/cpl_conv.h:372:10: fatal error: 'type_traits' file not found #include <type_traits> // for std::is_base_of ^~~~~~~~~~~~~ 6 warnings and 2 errors generated. error: command 'gcc' failed with exit status 1

[simonhuwiler]

Is there a way to helping you finding the problem? We're stuck on this IOS-Version and would like to further use fiona.

[sgillies]

All: I'm building new wheels with sqlite 3.24.0 included for Fiona 1.7.12 and am optimistic that they will resolve this. Look for them on PyPI tomorrow. I'd love to hear that they work!

[simonhuwiler]

Could install, import and run fiona. Thank you very much!

[sgillies]

Solution: pip install fiona>=1.7.12.