Homebrew build fails: ld: symbol(s) not found for architecture x86_64 #1957

nextstopsun · 2013-07-20T07:42:21Z

I'm trying to solve an issue with cairo https://groups.google.com/forum/#!topic/mapnik/wDCZx9232FE

So I've decided to reinstall everything (cairo, boost, mapnik) from scratch.
But I get an error when installing mapnik.

brew install --with-cairo --with-gdal --with-geos --with-postgresql mapnik
==> Downloading http://mapnik.s3.amazonaws.com/dist/v2.2.0/mapnik-v2.2.0.tar.bz2
Already downloaded: /Library/Caches/Homebrew/mapnik-2.2.0.tar.bz2
==> /usr/local/opt/python/bin/python2 scons/scons.py configure CC="cc" CXX="c++" JOBS=4 PREFIX=/usr/local/Cellar/mapnik/2.2.0 ICU_INCLUDES=/usr/local/opt/icu4c/include ICU_LIBS=/usr/local/opt/icu4c/lib PY
==> /usr/local/opt/python/bin/python2 scons/scons.py install
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
"c++" -o plugins/input/csv/csv_datasource.os -c -ansi -Wall -ftemplate-depth-300 -O3 -fno-strict-aliasing -finline-functions -Wno-inline -Wno-parentheses -Wno-char-subscripts -fPIC -DHAVE_JPEG -DMAPNIK_USE_PROJ4 -DHAVE_PNG -DHAVE_TIFF -DBIGINT -DBOOST_REGEX_HAS_ICU -DDARWIN -DMAPNIK_THREADSAFE -DNDEBUG -Ideps -Ideps/clipper/include -Ideps/agg/include -I. -Iinclude -I/usr/local/Cellar/gdal/1.10.0/include -I/usr/local/Cellar/postgresql/9.2.4/include -I/usr/local/Cellar/libtiff/4.0.3/include -I/usr/local/Cellar/proj/4.8.0/include -I/usr/local/Cellar/jpeg/8d/include -I/usr/local/Cellar/libxml2/2.9.1/include/libxml2 -I/usr/local/Cellar/freetype/2.4.11/include -I/usr/local/Cellar/freetype/2.4.11/include/freetype2 -I/usr/local/Cellar/icu4c/51.1/include -I/usr/local/Cellar/boost/1.54.0/include -I/usr/include plugins/input/csv/csv_datasource.cpp
scons: *** [src/libmapnik.dylib] Error 1
scons: building terminated because of errors.

How to resolve this?
OS X version is 10.8.4

springmeyer · 2013-07-20T15:55:31Z

The actual undefined symbols is not showing up in that error output. It looks like you need to rerun the install with the --verbose flag. The problem is likely not Mapnik but rather one of the dependencies is broken and needs rebuilt. You will not know which one until you can get an error indicating the particular symbol that is missing.

nextstopsun · 2013-07-22T07:38:23Z

Dane, thanks for reply.

When doing
brew install --with-cairo --with-gdal --with-geos --with-postgresql --verbose mapnik

I have a verbose output of an error:

Install file: "deps/agg/include/agg_vpgen_segmentator.h" as "/usr/local/Cellar/mapnik/2.2.0/include/mapnik/agg/agg_vpgen_segmentator.h"
Undefined symbols for architecture x86_64:
"boost::filesystem::path_traits::dispatch(boost::filesystem::directory_entry const&, std::string&, std::codecvt<wchar_t, char, __mbstate_t> const&)", referenced from:
mapnik::datasource_cache::register_datasources(std::string const&) in datasource_cache.os
mapnik::freetype_engine::register_fonts(std::string const&, bool) in font_engine_freetype.os
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
"c++" -o plugins/input/csv/csv_datasource.os -c -ansi -Wall -ftemplate-depth-300 -O3 -fno-strict-aliasing -finline-functions -Wno-inline -Wno-parentheses -Wno-char-subscripts -fPIC -DHAVE_JPEG -DMAPNIK_USE_PROJ4 -DHAVE_PNG -DHAVE_TIFF -DBIGINT -DBOOST_REGEX_HAS_ICU -DDARWIN -DMAPNIK_THREADSAFE -DNDEBUG -Ideps -Ideps/clipper/include -Ideps/agg/include -I. -Iinclude -I/usr/local/Cellar/gdal/1.10.0/include -I/usr/local/Cellar/postgresql/9.2.4/include -I/usr/local/Cellar/libtiff/4.0.3/include -I/usr/local/Cellar/proj/4.8.0/include -I/usr/local/Cellar/jpeg/8d/include -I/usr/local/Cellar/libxml2/2.9.1/include/libxml2 -I/usr/local/Cellar/freetype/2.4.11/include -I/usr/local/Cellar/freetype/2.4.11/include/freetype2 -I/usr/local/Cellar/icu4c/51.1/include -I/usr/local/Cellar/boost/1.54.0/include -I/usr/include plugins/input/csv/csv_datasource.cpp
scons: *** [src/libmapnik.dylib] Error 1
"c++" -o plugins/input/gdal/gdal_datasource.os -c -ansi -Wall -ftemplate-depth-300 -O3 -fno-strict-aliasing -finline-functions -Wno-inline -Wno-parentheses -Wno-char-subscripts -fPIC -DHAVE_JPEG -DMAPNIK_USE_PROJ4 -DHAVE_PNG -DHAVE_TIFF -DBIGINT -DBOOST_REGEX_HAS_ICU -DDARWIN -DMAPNIK_THREADSAFE -DNDEBUG -Ideps -Ideps/clipper/include -Ideps/agg/include -I. -Iinclude -I/usr/local/Cellar/gdal/1.10.0/include -I/usr/local/Cellar/postgresql/9.2.4/include -I/usr/local/Cellar/libtiff/4.0.3/include -I/usr/local/Cellar/proj/4.8.0/include -I/usr/local/Cellar/jpeg/8d/include -I/usr/local/Cellar/libxml2/2.9.1/include/libxml2 -I/usr/local/Cellar/freetype/2.4.11/include -I/usr/local/Cellar/freetype/2.4.11/include/freetype2 -I/usr/local/Cellar/icu4c/51.1/include -I/usr/local/Cellar/boost/1.54.0/include -I/usr/include plugins/input/gdal/gdal_datasource.cpp
scons: building terminated because of errors.

I guess that has something to do with freetype lib. I reinstalled it from Homebrew, but that doesn't help. Any clues?

springmeyer · 2013-07-22T14:46:07Z

No you have a problem with boost. Likely duplicate versions on your system. Remove boost and reinstall it.

On Jul 22, 2013, at 12:38 AM, Nikolai Lebedev notifications@github.com wrote:

Dane, thanks for reply.

When doing
brew install --with-cairo --with-gdal --with-geos --with-postgresql --verbose mapnik

I have a verbose output of an error:

Install file: "deps/agg/include/agg_vpgen_segmentator.h" as "/usr/local/Cellar/mapnik/2.2.0/include/mapnik/agg/agg_vpgen_segmentator.h"
Undefined symbols for architecture x86_64:
"boost::filesystem::path_traits::dispatch(boost::filesystem::directory_entry const&, std::string&, std::codecvt const&)", referenced from:
mapnik::datasource_cache::register_datasources(std::string const&) in datasource_cache.os
mapnik::freetype_engine::register_fonts(std::string const&, bool) in font_engine_freetype.os
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
"c++" -o plugins/input/csv/csv_datasource.os -c -ansi -Wall -ftemplate-depth-300 -O3 -fno-strict-aliasing -finline-functions -Wno-inline -Wno-parentheses -Wno-char-subscripts -fPIC -DHAVE_JPEG -DMAPNIK_USE_PROJ4 -DHAVE_PNG -DHAVE_TIFF -DBIGINT -DBOOST_REGEX_HAS_ICU -DDARWIN -DMAPNIK_THREADSAFE -DNDEBUG -Ideps -Ideps/clipper/include -Ideps/agg/include -I. -Iinclude -I/usr/local/Cellar/gdal/1.10.0/include -I/usr/local/Cellar/postgresql/9.2.4/include -I/usr/local/Cellar/libtiff/4.0.3/include -I/usr/local/Cellar/proj/4.8.0/include -I/usr/local/Cellar/jpeg/8d/include -I/usr/local/Cellar/libxml2/2.9.1/include/libxml2 -I/usr/local/Cellar/freetype/2.4.11/include -I/usr/local/Cellar/freetype/2.4.11/include/freetype2 -I/usr/local/Cellar/icu4c/51.1/include -I/usr/local/Cellar/boost/1.54.0/include -I/usr/include plugins/input/csv/csv_datasource.cpp
scons: *** [src/libmapnik.dylib] Error 1
"c++" -o plugins/input/gdal/gdal_datasource.os -c -ansi -Wall -ftemplate-depth-300 -O3 -fno-strict-aliasing -finline-functions -Wno-inline -Wno-parentheses -Wno-char-subscripts -fPIC -DHAVE_JPEG -DMAPNIK_USE_PROJ4 -DHAVE_PNG -DHAVE_TIFF -DBIGINT -DBOOST_REGEX_HAS_ICU -DDARWIN -DMAPNIK_THREADSAFE -DNDEBUG -Ideps -Ideps/clipper/include -Ideps/agg/include -I. -Iinclude -I/usr/local/Cellar/gdal/1.10.0/include -I/usr/local/Cellar/postgresql/9.2.4/include -I/usr/local/Cellar/libtiff/4.0.3/include -I/usr/local/Cellar/proj/4.8.0/include -I/usr/local/Cellar/jpeg/8d/include -I/usr/local/Cellar/libxml2/2.9.1/include/libxml2 -I/usr/local/Cellar/freetype/2.4.11/include -I/usr/local/Cellar/freetype/2.4.11/include/freetype2 -I/usr/local/Cellar/icu4c/51.1/include -I/usr/local/Cellar/boost/1.54.0/include -I/usr/include plugins/input/gdal/gdal_datasource.cpp
scons: building terminated because of errors.

I guess that has something to do with freetype lib. I reinstalled it from Homebrew, but that doesn't help. Any clues?

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nextstopsun · 2013-07-22T15:18:32Z

I did that several times already, but it didn't help. Is it obligatory for mapnik to build boost with --with-mpi flag? Although I've built open-mpi from scratch, boost doesn't get built with this option. Is it somehow related to this issue? Homebrew/legacy-homebrew#21304

springmeyer · 2013-07-22T16:04:07Z

no, Mapnik does not need boost build with mpi so that is unrelated. But it does look like some change in the boost build with homebrew is breaking things (or maybe just the upgrade to boost 1.54).

springmeyer · 2013-07-22T16:04:45Z

btw, can you paste more of your verbose output? You cut off the actual line that links libmapnik.dylib.

nextstopsun · 2013-07-22T17:06:54Z

Sure, here is the full output https://gist.github.com/nlebedev/6055590
Dane, thank you very very much for your help.

springmeyer · 2013-07-22T17:14:23Z

do you maybe have a folder at /usr/include/boost ? I doubt you do, but let me know.

springmeyer · 2013-07-22T17:21:48Z

also what does the output of brew unlink boost give?

nextstopsun · 2013-07-22T18:24:05Z

Checked for boost folder in /usr/include - nope, don't have it.
brew unlink boost seems ok to me:
bash-3.2$ brew unlink boost
Unlinking /usr/local/Cellar/boost/1.54.0... 116 links removed

springmeyer · 2013-07-22T19:40:33Z

okay, sounds good. So, this is mysterious then. I cannot replicate - the exact above command you ran brew install --with-cairo --with-gdal --with-geos --with-postgresql --verbose mapnik works fine for me.

What does brew doctor report for you?

nextstopsun · 2013-07-22T22:11:26Z

$ brew doctor Your system is ready to brew.

What does your brew info boost report?

Maybe reinstalling python helps?
Do you build against system or homebrew python?

springmeyer · 2013-07-22T22:16:28Z

system python. I refuse to use homebrew'ed python as it creates too many problems currently: #1838

springmeyer · 2013-07-22T22:17:20Z

$ brew info boost
boost: stable 1.54.0 (bottled), HEAD
http://www.boost.org
/usr/local/Cellar/boost/1.54.0 (9811 files, 346M) *
  Poured from bottle
From: https://github.com/mxcl/homebrew/commits/master/Library/Formula/boost.rb
==> Options
--universal
    Build a universal binary
--with-c++11
    Compile using Clang, std=c++11 and stdlib=libc++
--with-icu
    Build regexp engine with icu support
--with-mpi
    Build with mpi support
--without-python
    Build without python support
--without-single
    Disable building single-threading variant
--without-static
    Disable building static library variant

nextstopsun · 2013-07-22T23:25:29Z

Thanks, Dane, nailed it. I reinstalled boost without any flags, so it reports boost: stable 1.54.0 (bottled), HEAD.
Mapnik installed fine after that.
Is it the --with-icu flag that crashes the installation, or anything else special about bottled boost?

springmeyer · 2013-07-22T23:28:18Z

--with-c++11 could surely break things (for the time being). Not sure about the other flags. --with-icu ideally would work because for proper unicode support in mapnik you ideally want boost built with icu support (although I rarely ever attempt this with homebrew boost).

nextstopsun · 2013-07-23T16:23:07Z

Yes, you're right! It's --with-c++11 that breaks stuff. --with-mpi doesn't work anyway, so the only option for mapnik is to brew install --with-icu boost. Maybe mapnik should be built with c++11 too?

springmeyer · 2013-07-23T16:39:58Z

@NLebedev - mapnik will soon (in master) move to requiring it be built with c++11, but the v2.2.0 still needs to be build with normally (aka with -ansi)

springmeyer mentioned this issue Jul 22, 2013

Tilemill 2 on OS X install fails at npm install mapbox/mapbox-studio-classic#48

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springmeyer closed this as completed Jul 23, 2013

rmjarvis mentioned this issue Nov 1, 2013

Problems linking boost library: Undefined symbols for architecture x86_64 GalSim-developers/GalSim#483

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zy6p mentioned this issue Feb 24, 2022

base path of datasource was influenced by xml config path #4145

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Homebrew build fails: ld: symbol(s) not found for architecture x86_64 #1957

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Homebrew build fails: ld: symbol(s) not found for architecture x86_64 #1957

Homebrew build fails: ld: symbol(s) not found for architecture x86_64 #1957

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