multiple compiler issue

[kemin711]

When I have multiple compilers, the make step fails.
It seems that cmake finds the compiler in /usr/bin

I configured my computer to have /usr/local/bin before /usr/bin in the PATH environment variable.

[~/Downloads/bamtools-master/build]$ cmake ..
-- The C compiler identification is GNU 4.4.7
-- The CXX compiler identification is GNU 4.4.7
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Configuring done
-- Generating done
-- Build files have been written to: /home/zhouke/Downloads/bamtools-master/build

But the make process is using the newer version of gcc 4.8.1 and is having trouble.

[~/Downloads/bamtools-master/build]$ make
Scanning dependencies of target SharedHeaders
[ 1%] Exporting SharedHeaders
[ 1%] Built target SharedHeaders
Scanning dependencies of target APIHeaders
[ 2%] Exporting APIHeaders
[ 2%] Built target APIHeaders
Scanning dependencies of target AlgorithmsHeaders
[ 3%] Exporting AlgorithmsHeaders
[ 3%] Built target AlgorithmsHeaders
Scanning dependencies of target BamTools
[ 4%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o
In file included from /home/zhouke/Downloads/bamtools-master/src/api/BamAux.h:14,
from /home/zhouke/Downloads/bamtools-master/src/api/BamAlignment.h:14,
from /home/zhouke/Downloads/bamtools-master/src/api/BamAlignment.cpp:10:
/usr/local/include/c++/4.8.1/cstring:71: error: expected ‘{’ before ‘_GLIBCXX_VISIBILITY’
/usr/local/include/c++/4.8.1/cstring:71: error: expected constructor, destructor, or type conversion before ‘(’ token
In file included from /usr/local/include/c++/4.8.1/bits/stringfwd.h:40,
from /usr/local/include/c++/4.8.1/iosfwd:39,
from /usr/local/include/c++/4.8.1/ios:38,
from /usr/local/include/c++/4.8.1/istream:38,
from /usr/local/include/c++/4.8.1/fstream:38,
from /home/zhouke/Downloads/bamtools-master/src/api/BamAux.h:15,
from /home/zhouke/Downloads/bamtools-master/src/api/BamAlignment.h:14,
from /home/zhouke/Downloads/bamtools-master/src/api/BamAlignment.cpp:10:
/usr/local/include/c++/4.8.1/bits/memoryfwd.h:50: error: expected ‘{’ before ‘_GLIBCXX_VISIBILITY’
/usr/local/include/c++/4.8.1/bits/memoryfwd.h:50: error: expected constructor, destructor, or type conversion before ‘(’ token
In file included from /usr/local/include/c++/4.8.1/iosfwd:39,
from /usr/local/include/c++/4.8.1/ios:38,
from /usr/local/include/c++/4.8.1/istream:38,
from /usr/local/include/c++/4.8.1/fstream:38,
from /home/zhouke/Downloads/bamtools-master/src/api/BamAux.h:15,
from /home/zhouke/Downloads/bamtools-master/src/api/BamAlignment.h:14,
from /home/zhouke/Downloads/bamtools-master/src/api/BamAlignment.cpp:10:
/usr/local/include/c++/4.8.1/bits/stringfwd.h:42: error: expected ‘{’ before ‘_GLIBCXX_VISIBILITY’
/usr/local/include/c++/4.8.1/bits/stringfwd.h:42: error: expected constructor, destructor, or type conversion before ‘(’ token
In file included from /usr/local/include/c++/4.8.1/bits/postypes.h:40,
from /usr/local/include/c++/4.8.1/iosfwd:40,
from /usr/local/include/c++/4.8.1/ios:38,
from /usr/local/include/c++/4.8.1/istream:38,
from /usr/local/include/c++/4.8.1/fstream:38,
from /home/zhouke/Downloads/bamtools-master/src/api/BamAux.h:15,
from /home/zhouke/Downloads/bamtools-master/src/api/BamAlignment.h:14,
from /home/zhouke/Downloads/bamtools-master/src/api/BamAlignment.cpp:10:
/usr/local/include/c++/4.8.1/cwchar:64: error: ‘::mbstate_t’ has not been declared
/usr/local/include/c++/4.8.1/cwchar:135: error: expected ‘{’ before ‘_GLIBCXX_VISIBILITY’
/usr/local/include/c++/4.8.1/cwchar:135: error: expected constructor, destructor, or type conversion before ‘(’ token
/usr/local/include/c++/4.8.1/cwchar:248: error: ‘::wcstold’ has not been declared
/usr/local/include/c++/4.8.1/cwchar:257: error: ‘::wcstoll’ has not been declared
/usr/local/include/c++/4.8.1/cwchar:258: error: ‘::wcstoull’ has not been declared
/usr/local/include/c++/4.8.1/cwchar:264: error: ‘::__gnu_cxx’ has not been declared
/usr/local/include/c++/4.8.1/cwchar:265: error: ‘::__gnu_cxx’ has not been declared
/usr/local/include/c++/4.8.1/cwchar:266: error: ‘::__gnu_cxx’ has not been declared
In file included from /usr/local/include/c++/4.8.1/iosfwd:40,
from /usr/local/include/c++/4.8.1/ios:38,
from /usr/local/include/c++/4.8.1/istream:38,
from /usr/local/include/c++/4.8.1/fstream:38,
from /home/zhouke/Downloads/bamtools-master/src/api/BamAux.h:15,
from /home/zhouke/Downloads/bamtools-master/src/api/BamAlignment.h:14,
from /home/zhouke/Downloads/bamtools-master/src/api/BamAlignment.cpp:10:
/usr/local/include/c++/4.8.1/bits/postypes.h:68: error: expected ‘{’ before ‘_GLIBCXX_VISIBILITY’
/usr/local/include/c++/4.8.1/bits/postypes.h:68: error: expected constructor, destructor, or type conversion before ‘(’ token
In file included from /usr/local/include/c++/4.8.1/ios:39,
from /usr/local/include/c++/4.8.1/istream:38,
from /usr/local/include/c++/4.8.1/fstream:38,
from /home/zhouke/Downloads/bamtools-master/src/api/BamAux.h:15,
from /home/zhouke/Downloads/bamtools-master/src/api/BamAlignment.h:14,
from /home/zhouke/Downloads/bamtools-master/src/api/BamAlignment.cpp:10:
/usr/local/include/c++/4.8.1/exception:35: error: expected ‘}’ before end of line
/usr/local/include/c++/4.8.1/exception:35: error: expected ‘}’ before end of line
/usr/local/include/c++/4.8.1/exception:35: error: expected ‘}’ before end of line
/usr/local/include/c++/4.8.1/exception:35: error: expected ‘}’ before end of line
/usr/local/include/c++/4.8.1/exception:35: error: expected ‘}’ before end of line
/usr/local/include/c++/4.8.1/exception:35: error: expected declaration before end of line
make[2]: *** [src/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o] Error 1
make[1]: *** [src/api/CMakeFiles/BamTools.dir/all] Error 2
make: *** [all] Error 2

I am not sure these errors are caused by the source code of bamtools not compatible with the newer versions of GCC or what. I am not an expert in cmake. Any one can help here?

[leecbaker]

CMake defaults to using the compiler at /usr/bin/c++. To select a different compiler, you'll want to set environment variables when calling CMake. Something like this should work:

 CC=/usr/local/bin/gcc CXX=/usr/local/bin/g++ cmake ..

Substitute in the path for the compiler you want to actually use. The CC variable specifies the C compiler, while the CXX variable specifies the C++ compiler.

[kemin711]

Multi compiler does pose a big problem. This is not particular to bamtools. It is related to cmake. I had a situation when bamtools is made with compiler GCC 4.8. when I compile and link with GCC 5.2 I got linking errors:
-L/usr/local/lib/bamtools -lbamtools The LDFLAGS are set properly, and this used to work fine.
So the above posting is very useful to relieve this problem.