Invalid MEX-file '/home/aiserver/Downloads/mexopencv-3.3.1/+cv/private/VideoCapture_.mexa64': Missing symbol 'sqlite3_auto_extension' required by

[fybaft2012]

Hi kyamagu,
I installed mexopencv (for 3.3.1 branch) on ubuntu 16.04 with opencv 3.3.1, and compiled mexopencv with MATLAB R2017b, following the instruction. First, when I compiled mexopencv, it gave the gcc version warning (matlab 2017 supported gcc 4.9.4), but it can compile successfully anyway. When I call cv.VideoCapture(), it gives the following errors:

Invalid MEX-file '/home/aiserver/Downloads/mexopencv-3.3.1/+cv/private/VideoCapture_.mexa64':
Missing symbol 'sqlite3_auto_extension'
Missing symbol 'sqlite3_bind_blob'
Missing symbol 'sqlite3_bind_double'
Missing symbol 'sqlite3_bind_int'
Missing symbol 'sqlite3_bind_int64'
Missing symbol 'sqlite3_bind_null'
Missing symbol 'sqlite3_bind_text'
Missing symbol 'sqlite3_changes'
Missing symbol 'sqlite3_clear_bindings'
Missing symbol 'sqlite3_close'
Missing symbol 'sqlite3_column_blob'
Missing symbol 'sqlite3_column_bytes'
Missing symbol 'sqlite3_column_count'
Missing symbol 'sqlite3_column_decltype'
Missing symbol 'sqlite3_column_double'
Missing symbol 'sqlite3_column_int'
Missing symbol 'sqlite3_column_int64'
Missing symbol 'sqlite3_column_name'
Missing symbol 'sqlite3_column_table_name'
Missing symbol 'sqlite3_column_text'
Missing symbol 'sqlite3_column_type'
Missing symbol 'sqlite3_create_function'
Missing symbol 'sqlite3_create_module'
Missing symbol 'sqlite3_create_module_v2'
Missing symbol 'sqlite3_declare_vtab'
Missing symbol 'sqlite3_errcode'
Missing symbol 'sqlite3_errmsg'
Missing symbol 'sqlite3_exec'
Missing symbol 'sqlite3_finalize'
Missing symbol 'sqlite3_free'
Missing symbol 'sqlite3_free_table'
Missing symbol 'sqlite3_get_table'
Missing symbol 'sqlite3_last_insert_rowid'
Missing symbol 'sqlite3_libversion_number'
Missing symbol 'sqlite3_malloc'
Missing symbol 'sqlite3_mprintf'
Missing symbol 'sqlite3_open'
Missing symbol 'sqlite3_open_v2'
Missing symbol 'sqlite3_prepare'
Missing symbol 'sqlite3_prepare_v2'
Missing symbol 'sqlite3_realloc'
Missing symbol 'sqlite3_reset'
Missing symbol 'sqlite3_result_blob'
Missing symbol 'sqlite3_result_double'
Missing symbol 'sqlite3_result_error'
Missing symbol 'sqlite3_result_int'
Missing symbol 'sqlite3_result_int64'
Missing symbol 'sqlite3_result_null'
Missing symbol 'sqlite3_result_text'
Missing symbol 'sqlite3_result_value'
Missing symbol 'sqlite3_snprintf'
Missing symbol 'sqlite3_step'
Missing symbol 'sqlite3_total_changes'
Missing symbol 'sqlite3_user_data'
Missing symbol 'sqlite3_value_blob'
Missing symbol 'sqlite3_value_bytes'
Missing symbol 'sqlite3_value_double'
Missing symbol 'sqlite3_value_int'
Missing symbol 'sqlite3_value_int64'
Missing symbol 'sqlite3_value_numeric_type'
Missing symbol 'sqlite3_value_text'
Missing symbol 'sqlite3_value_type'
Missing symbol 'sqlite3_vfs_find'
Missing symbol 'sqlite3_vfs_register'
Missing symbol 'sqlite3_vfs_unregister'
Missing symbol 'sqlite3_vmprintf'
Missing symbol '_ZN11xercesc_3_111InputSource11setEncodingEPKt'
Missing symbol '_ZN11xercesc_3_111InputSource11setPublicIdEPKt'
Missing symbol '_ZN11xercesc_3_111InputSource11setSystemIdEPKt'
Missing symbol '_ZN11xercesc_3_125DOMImplementationRegistry20getDOMImplementationEPKt'
Missing symbol '_ZN11xercesc_3_19XMLString7releaseEPPtPNS_13MemoryManagerE'
Missing symbol '_ZN11xercesc_3_19XMLString9transcodeEPKtPNS_13MemoryManagerE'
required by
'/usr/lib/libgdal.so.1
->/usr/local/lib/libopencv_imgcodecs.so.3.3
->/usr/local/lib/libopencv_videoio.so.3.3
->/usr/local/lib/libopencv_highgui.so.3.3
->/usr/local/lib/libopencv_features2d.so.3.3
->/usr/local/lib/libopencv_calib3d.so.3.3
->/usr/local/lib/libopencv_cudalegacy.so.3.3
->/usr/local/lib/libopencv_cudaobjdetect.so.3.3
->/home/aiserver/Downloads/mexopencv-3.3.1/+cv/private/VideoCapture_.mexa64'

Missing symbol 'dlclose'
Missing symbol 'dlopen'
Missing symbol 'dlsym'
Missing symbol 'heim_abort'
required by
'/usr/lib/x86_64-linux-gnu/libgssapi.so.3
->/usr/lib/x86_64-linux-gnu/libldap_r-2.4.so.2
->/usr/lib/x86_64-linux-gnu/libcurl-gnutls.so.4
->/usr/lib/x86_64-linux-gnu/libnetcdf.so.11
->/usr/lib/libgdal.so.1
->/usr/local/lib/libopencv_imgcodecs.so.3.3
->/usr/local/lib/libopencv_videoio.so.3.3
->/usr/local/lib/libopencv_highgui.so.3.3
->/usr/local/lib/libopencv_features2d.so.3.3
->/usr/local/lib/libopencv_calib3d.so.3.3
->/usr/local/lib/libopencv_cudalegacy.so.3.3
->/usr/local/lib/libopencv_cudaobjdetect.so.3.3
->/home/aiserver/Downloads/mexopencv-3.3.1/+cv/private/VideoCapture_.mexa64'

Missing symbol '_et_list'
required by
'/usr/lib/x86_64-linux-gnu/libheimntlm.so.0
->/usr/lib/x86_64-linux-gnu/libgssapi.so.3
->/usr/lib/x86_64-linux-gnu/libldap_r-2.4.so.2
->/usr/lib/x86_64-linux-gnu/libcurl-gnutls.so.4
->/usr/lib/x86_64-linux-gnu/libnetcdf.so.11
->/usr/lib/libgdal.so.1
->/usr/local/lib/libopencv_imgcodecs.so.3.3
->/usr/local/lib/libopencv_videoio.so.3.3
->/usr/local/lib/libopencv_highgui.so.3.3
->/usr/local/lib/libopencv_features2d.so.3.3
->/usr/local/lib/libopencv_calib3d.so.3.3
->/usr/local/lib/libopencv_cudalegacy.so.3.3
->/usr/local/lib/libopencv_cudaobjdetect.so.3.3
->/home/aiserver/Downloads/mexopencv-3.3.1/+cv/private/VideoCapture_.mexa64'

Missing symbol 'ANannlen'
Missing symbol 'ANannlist'
Missing symbol 'ANend'
Missing symbol 'ANendaccess'
Missing symbol 'ANfileinfo'
Missing symbol 'ANgetdatainfo'
Missing symbol 'ANnumann'
Missing symbol 'ANreadann'
Missing symbol 'ANselect'
Missing symbol 'ANstart'
Missing symbol 'DFdiget'
Missing symbol 'DFdiput'
Missing symbol 'DFdiread'
Missing symbol 'DFdisetup'
Missing symbol 'DFdiwrite'
Missing symbol 'DFKconvert'
Missing symbol 'DFKgetPNSC'
Missing symbol 'DFKislitendNT'
Missing symbol 'DFKisnativeNT'
Missing symbol 'DFKNTsize'
Missing symbol 'DFKsetNT'
Missing symbol 'error_top'
Missing symbol 'HCcreate'
Missing symbol 'HCget_config_info'
Missing symbol 'Hclose'
Missing symbol 'HCPgetcompinfo'
Missing symbol 'HCPgetcompress'
Missing symbol 'HCPgetcomptype'
Missing symbol 'HCPgetdatasize'
Missing symbol 'HDcheck_empty'
Missing symbol 'Hdeldd'
Missing symbol 'HDgetdatainfo'
Missing symbol 'HDget_special_info'
Missing symbol 'HDmemfill'
Missing symbol 'Hendaccess'
Missing symbol 'HEPclear'
Missing symbol 'HEpush'
Missing symbol 'HEvalue'
Missing symbol 'Hgetelement'
Missing symbol 'Hinquire'
Missing symbol 'Hishdf'
Missing symbol 'HLcreate'
Missing symbol 'Hlength'
Missing symbol 'HLgetblockinfo'
Missing symbol 'HMCcreate'
Missing symbol 'HMCreadChunk'
Missing symbol 'HMCsetMaxcache'
Missing symbol 'HMCwriteChunk'
Missing symbol 'Hnewref'
Missing symbol 'Hnextread'
Missing symbol 'Hoffset'
Missing symbol 'Hopen'
Missing symbol 'HPisfile_in_use'
Missing symbol 'HPregister_term_func'
Missing symbol 'Hputelement'
Missing symbol 'Hread'
Missing symbol 'Hseek'
Missing symbol 'Hsetaccesstype'
Missing symbol 'Hsetlength'
Missing symbol 'Hstartaccess'
Missing symbol 'Hstartread'
Missing symbol 'Hwrite'
Missing symbol 'HXcreate'
Missing symbol 'Vaddtagref'
Missing symbol 'Vattach'
Missing symbol 'Vdelete'
Missing symbol 'Vdetach'
Missing symbol 'vexistvg'
Missing symbol 'vexistvs'
Missing symbol 'VFfieldorder'
Missing symbol 'VFfieldtype'
Missing symbol 'Vfindclass'
Missing symbol 'Vfinish'
Missing symbol 'Vgetclass'
Missing symbol 'Vgetnext'
Missing symbol 'Vgettagref'
Missing symbol 'VHmakegroup'
Missing symbol 'VHstoredata'
Missing symbol 'VHstoredatam'
Missing symbol 'Vinitialize'
Missing symbol 'Vinquire'
Missing symbol 'Visvg'
Missing symbol 'Visvs'
Missing symbol 'Vntagrefs'
Missing symbol 'VSattach'
Missing symbol 'VSdelete'
Missing symbol 'VSdetach'
Missing symbol 'VSfdefine'
Missing symbol 'VSgetclass'
Missing symbol 'VSgetdatainfo'
Missing symbol 'VSgetname'
Missing symbol 'VSinquire'
Missing symbol 'VSQueryref'
Missing symbol 'VSread'
Missing symbol 'VSseek'
Missing symbol 'VSsetclass'
Missing symbol 'VSsetfields'
Missing symbol 'VSwrite'
required by
'/usr/lib/libmfhdfalt.so.0
->/usr/lib/libgdal.so.1
->/usr/local/lib/libopencv_imgcodecs.so.3.3
->/usr/local/lib/libopencv_videoio.so.3.3
->/usr/local/lib/libopencv_highgui.so.3.3
->/usr/local/lib/libopencv_features2d.so.3.3
->/usr/local/lib/libopencv_calib3d.so.3.3
->/usr/local/lib/libopencv_cudalegacy.so.3.3
->/usr/local/lib/libopencv_cudaobjdetect.so.3.3
->/home/aiserver/Downloads/mexopencv-3.3.1/+cv/private/VideoCapture_.mexa64'

Missing symbol 'th_comment_add'
Missing symbol 'th_comment_add_tag'
Missing symbol 'th_comment_clear'
Missing symbol 'th_comment_init'
Missing symbol 'th_comment_query'
Missing symbol 'th_comment_query_count'
required by
'/usr/lib/x86_64-linux-gnu/libtheoraenc.so.1
->/usr/lib/x86_64-linux-gnu/libavcodec-ffmpeg.so.56
->/usr/local/lib/libopencv_videoio.so.3.3
->/usr/local/lib/libopencv_highgui.so.3.3
->/usr/local/lib/libopencv_features2d.so.3.3
->/usr/local/lib/libopencv_calib3d.so.3.3
->/usr/local/lib/libopencv_cudalegacy.so.3.3
->/usr/local/lib/libopencv_cudaobjdetect.so.3.3
->/home/aiserver/Downloads/mexopencv-3.3.1/+cv/private/VideoCapture_.mexa64'

Could you give any help, thanks!

[amroamroamro]

Errors are about missing symbols originating from the GDAL library and its dependencies
(sqlite, xerces, hdf, ...). I also see a couple missing symbols regarding theora codec used by ffmpeg.

GDAL is turned off by default, so I assume you enabled it during cmake configuration. You need to make sure it's properly installed as well as all of its run-time dependencies.

But more importantly, you need to check for any conflicts with MATLAB's own libraries (as explained in my other post you commented on). Use ldd both in a terminal and within MATLAB and look for differences, which you'll want to preload with LD_PRELOAD.

You'll find more explanation in the wiki

[fybaft2012]

Hi amroamroamro,
As you pointed out that it is because that I enabled GDAL library during cmake configuration. So I recompile Opencv again without GDAL library, now it works perfectly!
Thank you very much! I will close this issues.