Running on OSX (circa 3.0.5)

[DaveRoe]

The latest release is 3.0.5 and the source won't build on OSX. The latest binary is 2.1.1. Have you effectively dropped support for OSX or will it be supported in the future.

Thank you. I love your software.

[iminkin]

Hi Dave,

We didn't drop the support of OSX, we just have regular problems with build on OSX. The last time we even encountered a bug in clang. The last binary on the Source Forge for OSX is 3.0.4, I will add a binary of 3.0.5 for OSX very soon.

[iminkin]

Dave,

Could you post the error message that you get?

[DaveRoe]

I'm using Xcode 6.0.1 and OSX 10.9.5.

In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/sibelia.cpp:9:
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/util.h:10:
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/blockfinder.h:11:
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/indexedsequence.h:10:
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/hashing.h:10:
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/dnasequence.h:10:
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/fasta.h:10:
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/common.h:33:
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/include/boost/function.hpp:24:
In file included from /usr/local/include/boost/function/detail/prologue.hpp:17:
In file included from /usr/local/include/boost/function/function_base.hpp:22:
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/include/boost/type_traits/has_trivial_copy.hpp:14:
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/include/boost/type_traits/is_volatile.hpp:28:
/Users/daver/tmp/Sibelia-3.0.5-Source/src/include/boost/type_traits/detail/cv_traits_impl.hpp:37:33: error: C++ requires a type specifier for all declarations
BOOST_STATIC_CONSTANT(bool, is_const = false);
^~~~~~~~
/Users/daver/tmp/Sibelia-3.0.5-Source/src/include/boost/type_traits/detail/cv_traits_impl.hpp:37:5: error: C++ requires a type specifier for all declarations
BOOST_STATIC_CONSTANT(bool, is_const = false);
^~~~~~~~~~~~~~~~~~~~~
/Users/daver/tmp/Sibelia-3.0.5-Source/src/include/boost/type_traits/detail/cv_traits_impl.hpp:38:33: error: C++ requires a type specifier for all declarations
BOOST_STATIC_CONSTANT(bool, is_volatile = false);
^~~~~~~~~~~
/Users/daver/tmp/Sibelia-3.0.5-Source/src/include/boost/type_traits/detail/cv_traits_impl.hpp:38:5: error: C++ requires a type specifier for all declarations
BOOST_STATIC_CONSTANT(bool, is_volatile = false);
^~~~~~~~~~~~~~~~~~~~~
/Users/daver/tmp/Sibelia-3.0.5-Source/src/include/boost/type_traits/detail/cv_traits_impl.hpp:45:33: error: C++ requires a type specifier for all declarations
BOOST_STATIC_CONSTANT(bool, is_const = true);
^~~~~~~~
/Users/daver/tmp/Sibelia-3.0.5-Source/src/include/boost/type_traits/detail/cv_traits_impl.hpp:45:5: error: C++ requires a type specifier for all declarations
BOOST_STATIC_CONSTANT(bool, is_const = true);
^~~~~~~~~~~~~~~~~~~~~
/Users/daver/tmp/Sibelia-3.0.5-Source/src/include/boost/type_traits/detail/cv_traits_impl.hpp:46:33: error: C++ requires a type specifier for all declarations
BOOST_STATIC_CONSTANT(bool, is_volatile = false);
^~~~~~~~~~~
/Users/daver/tmp/Sibelia-3.0.5-Source/src/include/boost/type_traits/detail/cv_traits_impl.hpp:46:5: error: C++ requires a type specifier for all declarations
BOOST_STATIC_CONSTANT(bool, is_volatile = false);
^~~~~~~~~~~~~~~~~~~~~
/Users/daver/tmp/Sibelia-3.0.5-Source/src/include/boost/type_traits/detail/cv_traits_impl.hpp:53:33: error: C++ requires a type specifier for all declarations
BOOST_STATIC_CONSTANT(bool, is_const = false);
^~~~~~~~
/Users/daver/tmp/Sibelia-3.0.5-Source/src/include/boost/type_traits/detail/cv_traits_impl.hpp:53:5: error: C++ requires a type specifier for all declarations
BOOST_STATIC_CONSTANT(bool, is_const = false);
^~~~~~~~~~~~~~~~~~~~~
/Users/daver/tmp/Sibelia-3.0.5-Source/src/include/boost/type_traits/detail/cv_traits_impl.hpp:54:33: error: C++ requires a type specifier for all declarations
BOOST_STATIC_CONSTANT(bool, is_volatile = true);
^~~~~~~~~~~
/Users/daver/tmp/Sibelia-3.0.5-Source/src/include/boost/type_traits/detail/cv_traits_impl.hpp:54:5: error: C++ requires a type specifier for all declarations
BOOST_STATIC_CONSTANT(bool, is_volatile = true);
^~~~~~~~~~~~~~~~~~~~~
/Users/daver/tmp/Sibelia-3.0.5-Source/src/include/boost/type_traits/detail/cv_traits_impl.hpp:61:33: error: C++ requires a type specifier for all declarations
BOOST_STATIC_CONSTANT(bool, is_const = true);
^~~~~~~~
/Users/daver/tmp/Sibelia-3.0.5-Source/src/include/boost/type_traits/detail/cv_traits_impl.hpp:61:5: error: C++ requires a type specifier for all declarations
BOOST_STATIC_CONSTANT(bool, is_const = true);
^~~~~~~~~~~~~~~~~~~~~
/Users/daver/tmp/Sibelia-3.0.5-Source/src/include/boost/type_traits/detail/cv_traits_impl.hpp:62:33: error: C++ requires a type specifier for all declarations
BOOST_STATIC_CONSTANT(bool, is_volatile = true);
^~~~~~~~~~~
/Users/daver/tmp/Sibelia-3.0.5-Source/src/include/boost/type_traits/detail/cv_traits_impl.hpp:62:5: error: C++ requires a type specifier for all declarations
BOOST_STATIC_CONSTANT(bool, is_volatile = true);
^~~~~~~~~~~~~~~~~~~~~
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/sibelia.cpp:9:
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/util.h:10:
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/blockfinder.h:11:
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/indexedsequence.h:10:
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/hashing.h:10:
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/dnasequence.h:10:
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/fasta.h:10:
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/common.h:33:
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/include/boost/function.hpp:24:
In file included from /usr/local/include/boost/function/detail/prologue.hpp:17:
In file included from /usr/local/include/boost/function/function_base.hpp:22:
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/include/boost/type_traits/has_trivial_copy.hpp:14:
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/include/boost/type_traits/is_volatile.hpp:40:
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/include/boost/type_traits/detail/bool_trait_def.hpp:14:
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/include/boost/type_traits/detail/template_arity_spec.hpp:10:
In file included from /usr/local/include/boost/mpl/int.hpp:20:
In file included from /usr/local/include/boost/mpl/aux_/integral_wrapper.hpp:16:
/usr/local/include/boost/mpl/integral_c_tag.hpp:22:52: error: C++ requires a type specifier for all declarations
struct integral_c_tag { BOOST_STATIC_CONSTANT(int, value = 0); };
^~~~~
/usr/local/include/boost/mpl/integral_c_tag.hpp:22:25: error: C++ requires a type specifier for all declarations
struct integral_c_tag { BOOST_STATIC_CONSTANT(int, value = 0); };
^~~~~~~~~~~~~~~~~~~~~
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/sibelia.cpp:9:
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/util.h:10:
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/blockfinder.h:11:
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/indexedsequence.h:10:
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/hashing.h:10:
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/dnasequence.h:10:
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/fasta.h:10:
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/common.h:33:
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/include/boost/function.hpp:24:
In file included from /usr/local/include/boost/function/detail/prologue.hpp:17:
In file included from /usr/local/include/boost/function/function_base.hpp:22:
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/include/boost/type_traits/has_trivial_copy.hpp:14:
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/include/boost/type_traits/is_volatile.hpp:40:
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/include/boost/type_traits/detail/bool_trait_def.hpp:14:
In file included from /Users/daver/tmp/Sibelia-3.0.5-Source/src/include/boost/type_traits/detail/template_arity_spec.hpp:10:
In file included from /usr/local/include/boost/mpl/int.hpp:20:
/usr/local/include/boost/mpl/aux_/integral_wrapper.hpp:45:51: error: C++ requires a type specifier for all declarations
BOOST_STATIC_CONSTANT(AUX_WRAPPER_VALUE_TYPE, value = N);
^~~~~
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make[2]: *** [CMakeFiles/Sibelia.dir/sibelia.cpp.o] Error 1
make[1]: *** [CMakeFiles/Sibelia.dir/all] Error 2
make: *** [all] Error 2

[iminkin]

Thank you, I will investigate that

[DaveRoe]

See the attached file and the notes below. I hope that tells you what you
want to know.

c++ -v
Apple LLVM version 6.0 (clang-600.0.51) (based on LLVM 3.5svn)
Target: x86_64-apple-darwin13.4.0
Thread model: posix

cc -v
Apple LLVM version 6.0 (clang-600.0.51) (based on LLVM 3.5svn)
Target: x86_64-apple-darwin13.4.0
Thread model: posix

brew info boost
boost: stable 1.55.0 (bottled), HEAD
http://www.boost.org
/usr/local/Cellar/boost/1.55.0_1 (10036 files, 452M)
Poured from bottle
/usr/local/Cellar/boost/1.55.0_2 (10036 files, 452M) *
Poured from bottle
From:
https://github.com/Homebrew/homebrew/blob/master/Library/Formula/boost.rb
==> Options
--c++11
Build using C++11 mode
--universal
Build a universal binary
--with-icu
Build regexp engine with icu support
--with-mpi
Build with MPI support
--with-python
Build with python support
--with-python3
Build with python3 support
--without-single
Disable building single-threading variant
--without-static
Disable building static library variant
--HEAD
install HEAD version

Dave

On Tue, Oct 14, 2014 at 11:51 PM, Ilya Minkin [email protected]
wrote:

Which compiler are you using? It is very strange that there is an error in
Boost.

—
Reply to this email directly or view it on GitHub
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[iminkin]

Although I didn't resolve this particular issue (I will investigate it later), we compiled a binary for Mac OS: https://sourceforge.net/projects/sibelia-bio/upload/3.0.5/