Hi!

> It is most deterministic to set the variables controlling which version of 
> everything is used. It us also important to use the same compiler (gcc vs 
> clang) that was used to build your version of python.

Got it.  I’m using the stock compiler with Xcode 5.1 (Clang) and the stock 
Python 2.7 distribution (which I hope/assume was also compiled with Clang).  I 
might try installing GCC and roll with that.

> You still have a mismatch somewhere.
> But I can't see what version of the jdk you're linking against ?

Here is the full output, building against JDK 1.7.0 update 51.  The CFLAGS and 
CPPFLAGS are needed because the Xcode compiler does not observe the 
-mno-fused-madd argument and will stop with a hard error unless 
-Qunused-arguments is specified.

$ export CFLAGS=-Qunused-arguments
$ export CPPFLAGS=-Qunused-arguments
$ export LDFLAGS=-v
$ python setup.py build

found JAVAHOME = 
/Library/Java/JavaVirtualMachines/jdk1.7.0_51.jdk/Contents/Home/
found JAVAFRAMEWORKS = 
/Library/Java/JavaVirtualMachines/jdk1.7.0_51.jdk/Contents/Home/include/
Loading source files for package org.apache.jcc...
Constructing Javadoc information...
Standard Doclet version 1.8.0
Building tree for all the packages and classes...
Generating javadoc/org/apache/jcc/PythonException.html...
Generating javadoc/org/apache/jcc/PythonVM.html...
Generating javadoc/org/apache/jcc/package-frame.html...
Generating javadoc/org/apache/jcc/package-summary.html...
Generating javadoc/org/apache/jcc/package-tree.html...
Generating javadoc/constant-values.html...
Generating javadoc/serialized-form.html...
Building index for all the packages and classes...
Generating javadoc/overview-tree.html...
Generating javadoc/index-all.html...
Generating javadoc/deprecated-list.html...
Building index for all classes...
Generating javadoc/allclasses-frame.html...
Generating javadoc/allclasses-noframe.html...
Generating javadoc/index.html...
Generating javadoc/help-doc.html...
running build
running build_py
writing /Users/mike/Desktop/modelica/install/jcc/jcc/config.py
copying jcc/config.py -> build/lib.macosx-10.9-intel-2.7/jcc
copying jcc/classes/org/apache/jcc/PythonVM.class -> 
build/lib.macosx-10.9-intel-2.7/jcc/classes/org/apache/jcc
copying jcc/classes/org/apache/jcc/PythonException.class -> 
build/lib.macosx-10.9-intel-2.7/jcc/classes/org/apache/jcc
running build_ext
building 'jcc' extension
cc -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -Qunused-arguments 
-Qunused-arguments -dynamiclib -D_jcc_lib -DJCC_VER="2.19" 
-I/Library/Java/JavaVirtualMachines/jdk1.7.0_51.jdk/Contents/Home//include 
-I/Library/Java/JavaVirtualMachines/jdk1.7.0_51.jdk/Contents/Home//include/darwin
 -I_jcc -Ijcc/sources 
-I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c 
jcc/sources/jcc.cpp -o build/temp.macosx-10.9-intel-2.7/jcc/sources/jcc.o 
-DPYTHON -fno-strict-aliasing -Wno-write-strings
cc -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -Qunused-arguments 
-Qunused-arguments -dynamiclib -D_jcc_lib -DJCC_VER="2.19" 
-I/Library/Java/JavaVirtualMachines/jdk1.7.0_51.jdk/Contents/Home//include 
-I/Library/Java/JavaVirtualMachines/jdk1.7.0_51.jdk/Contents/Home//include/darwin
 -I_jcc -Ijcc/sources 
-I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c 
jcc/sources/JCCEnv.cpp -o build/temp.macosx-10.9-intel-2.7/jcc/sources/JCCEnv.o 
-DPYTHON -fno-strict-aliasing -Wno-write-strings
c++ -Wl,-x -dynamiclib -undefined dynamic_lookup -v -Qunused-arguments 
-Qunused-arguments build/temp.macosx-10.9-intel-2.7/jcc/sources/jcc.o 
build/temp.macosx-10.9-intel-2.7/jcc/sources/JCCEnv.o -o 
build/lib.macosx-10.9-intel-2.7/libjcc.dylib 
-L/Library/Java/JavaVirtualMachines/jdk1.7.0_51.jdk/Contents/Home//jre/lib 
-ljava 
-L/Library/Java/JavaVirtualMachines/jdk1.7.0_51.jdk/Contents/Home//jre/lib/server
 -ljvm -Wl,-rpath 
-Wl,/Library/Java/JavaVirtualMachines/jdk1.7.0_51.jdk/Contents/Home//jre/lib 
-Wl,-rpath 
-Wl,/Library/Java/JavaVirtualMachines/jdk1.7.0_51.jdk/Contents/Home//jre/lib/server
 -Wl,-S -install_name @rpath/libjcc.dylib -current_version 2.19 
-compatibility_version 2.19
Apple LLVM version 5.1 (clang-503.0.38) (based on LLVM 3.4svn)
Target: x86_64-apple-darwin13.1.0
Thread model: posix
 
"/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld"
 -demangle -dynamic -dylib -dylib_compatibility_version 2.19 
-dylib_current_version 2.19 -arch x86_64 -dylib_install_name 
@rpath/libjcc.dylib -macosx_version_min 10.9.0 -undefined dynamic_lookup 
-undefined dynamic_lookup -o build/lib.macosx-10.9-intel-2.7/libjcc.dylib 
-L/Library/Java/JavaVirtualMachines/jdk1.7.0_51.jdk/Contents/Home//jre/lib 
-L/Library/Java/JavaVirtualMachines/jdk1.7.0_51.jdk/Contents/Home//jre/lib/server
 -x build/temp.macosx-10.9-intel-2.7/jcc/sources/jcc.o 
build/temp.macosx-10.9-intel-2.7/jcc/sources/JCCEnv.o -ljava -ljvm -rpath 
/Library/Java/JavaVirtualMachines/jdk1.7.0_51.jdk/Contents/Home//jre/lib -rpath 
/Library/Java/JavaVirtualMachines/jdk1.7.0_51.jdk/Contents/Home//jre/lib/server 
-S -lc++ -lSystem 
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/lib/darwin/libclang_rt.osx.a
ld: internal error: atom not found in 
symbolIndex(__ZN7JNIEnv_13CallIntMethodEP8_jobjectP10_jmethodIDz) for 
architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
error: command 'c++' failed with exit status 1

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