Hi Nat, I don't know but I will check - there is a good chance that this is to blame. The build worked fine with the compilers etc. until just now - build tag for boost is 73458, I will try a new version. Best wishes, Graeme -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Nathaniel Echols Sent: 28 September 2012 14:21 To: cctbx mailing list Subject: Re: [cctbxbb] Build failing How old are your boost sources? These aren't part of the SVN tree (we distribute a snapshot of the boost SVN), so they won't be updated unless you get a new bundle. (I can just give you the current Boost we're using if you want, which is now the release branch.) -Nat On Fri, Sep 28, 2012 at 3:51 AM, wrote:

Hi Folks,

Following an svn update and several attempts to build, I am still getting this compile error

/Users/graeme/svn/cctbx/sources/boost/boost/math/special_functions/det ail/bessel_jy.hpp:346:11: error: 'bessel_y_small_z_series' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] In file included from /Users/graeme/svn/cctbx/sources/boost/boost/math/special_functions/detail/bessel_jn.hpp:17:0, from /Users/graeme/svn/cctbx/sources/boost/boost/math/special_functions/bessel.hpp:18, from /Users/graeme/svn/cctbx/sources/cctbx_project/scitbx/math/bessel.h:9, from /Users/graeme/svn/cctbx/sources/cctbx_project/scitbx/math/boost_python/math_ext.cpp:3: /Users/graeme/svn/cctbx/sources/boost/boost/math/special_functions/det ail/bessel_jy_series.hpp:139:10: note: 'template T boost::math::detail::bessel_y_small_z_series(T, T, T*, const Policy&)' declared here, later in the translation unit In file included from /Users/graeme/svn/cctbx/sources/boost/boost/math/special_functions/bessel.hpp:17:0, from /Users/graeme/svn/cctbx/sources/cctbx_project/scitbx/math/bessel.h:9, from /Users/graeme/svn/cctbx/sources/cctbx_project/scitbx/math/boost_python/math_ext.cpp:3: /Users/graeme/svn/cctbx/sources/boost/boost/math/special_functions/det ail/bessel_jy.hpp:356:11: error: 'bessel_j_small_z_series' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] In file included from /Users/graeme/svn/cctbx/sources/boost/boost/math/special_functions/detail/bessel_jn.hpp:17:0, from /Users/graeme/svn/cctbx/sources/boost/boost/math/special_functions/bessel.hpp:18, from /Users/graeme/svn/cctbx/sources/cctbx_project/scitbx/math/bessel.h:9, from /Users/graeme/svn/cctbx/sources/cctbx_project/scitbx/math/boost_python/math_ext.cpp:3: /Users/graeme/svn/cctbx/sources/boost/boost/math/special_functions/det ail/bessel_jy_series.hpp:47:10: note: 'template T boost::math::detail::bessel_j_small_z_series(T, T, const Policy&)' declared here, later in the translation unit In file included from /Users/graeme/svn/cctbx/sources/boost/boost/math/special_functions/bessel.hpp:17:0, from /Users/graeme/svn/cctbx/sources/cctbx_project/scitbx/math/bessel.h:9, from /Users/graeme/svn/cctbx/sources/cctbx_project/scitbx/math/boost_python/math_ext.cpp:3: /Users/graeme/svn/cctbx/sources/boost/boost/math/special_functions/det ail/bessel_jy.hpp:363:11: error: 'bessel_yn_small_z' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] In file included from /Users/graeme/svn/cctbx/sources/boost/boost/math/special_functions/detail/bessel_jn.hpp:17:0, from /Users/graeme/svn/cctbx/sources/boost/boost/math/special_functions/bessel.hpp:18, from /Users/graeme/svn/cctbx/sources/cctbx_project/scitbx/math/bessel.h:9, from /Users/graeme/svn/cctbx/sources/cctbx_project/scitbx/math/boost_python/math_ext.cpp:3: /Users/graeme/svn/cctbx/sources/boost/boost/math/special_functions/det ail/bessel_jy_series.hpp:213:3: note: 'template T boost::math::detail::bessel_yn_small_z(int, T, T*, const Policy&)' declared here, later in the translation unit scons: *** [scitbx/math/boost_python/math_ext.o] Error 1 scons: building terminated because of errors. usr+sys time: 26.64 seconds, ticks: 51849408, micro-seconds/tick: usr+0.514 wall clock time: 8 minutes 5.55 seconds (485.55 seconds total) make: *** [default] Error 2

OS X Lion machine

Graemes-MacBook-Pro:build graeme$ uname -a Darwin Graemes-MacBook-Pro.local 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr 9 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64 Graemes-MacBook-Pro:build graeme$ gcc --version gcc (GCC) 4.7.0 20120314 (prerelease) Copyright (C) 2012 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Have I missed something? Nightly builds seem to be OK.

Commands

../../cctbx_plus/base/Python.framework/Versions/2.7/Resources/Python.a pp/Contents/MacOS/Python ../sources/cctbx_project/libtbx/configure.py --compiler=gcc labelit cctbx bpcx_regression rstbx . setpaths.sh make

Thanks,

Graeme

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On Sat, Sep 29, 2012 at 10:41 AM, William G. Scott wrote:

...

Graemes-MacBook-Pro:build graeme$ gcc --version gcc (GCC) 4.7.0 20120314 (prerelease)

I can't get cctbx to compile with that compiler, but, oddly, with an uncompiled cctbx, I can get phaser to compile with that compiler (see my open-mp thread).

Where are you getting gcc 4.7 from, fink or somewhere else? We are planning to buy a 4-core Mac Mini to do additional build tests on, since our official support is still stuck at 10.6 and Xcode 3.2, and it might be worthwhile trying the latest gcc as well as the latest Xcode tools (currently clang 4.1, which also appears to have issues). -Nat

Ah painful - taking the boost directory from a recent download I get /Library/Python/2.7/site-packages Traceback (most recent call last): File "compare_bpcx_xds.py", line 7, in <module> from cctbx.array_family import flex File "/Users/graeme/svn/cctbx/sources/cctbx_project/cctbx/array_family/flex.py", line 2, in <module> import scitbx.array_family.flex File "/Users/graeme/svn/cctbx/sources/cctbx_project/scitbx/array_family/flex.py", line 2, in <module> import boost.optional # import dependency File "/Users/graeme/svn/cctbx/sources/cctbx_project/boost_adaptbx/boost/optional.py", line 2, in <module> import boost.python File "/Users/graeme/svn/cctbx/sources/cctbx_project/boost_adaptbx/boost/python.py", line 57, in <module> ext = import_ext("boost_python_meta_ext") File "/Users/graeme/svn/cctbx/sources/cctbx_project/boost_adaptbx/boost/python.py", line 36, in import_ext + [" "+p for p in sys.path])) ImportError: __import__("boost_python_meta_ext"): dlopen(/Users/graeme/svn/cctbx/build/lib/boost_python_meta_ext.so, 2): Symbol not found: std::range_error::~range_error() still - which is a problem. I specially constructed the base Python for this with extra stuff in :o( which worked just fine until last week. Have I done something wrong? I have never seen this before. This was the same error I got using the boost from their svn. Thanks, Graeme On 1 Oct 2012, at 09:19, wrote:

Hi Folks,

I got this compiler with XCode (which is now a pain to get) but it is vanilla so makes making portable code a little easier.

Nat, I pulled the boost sources from their subversion, my build worked but on running I now get errors importing boost_python_meta_ext

I will start from a fresh download, unless you keep boost in your svn tree somewhere I should use?

Thanks,

Graeme

-----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Nathaniel Echols Sent: 30 September 2012 21:42 To: cctbx mailing list Subject: Re: [cctbxbb] Build failing

On Sat, Sep 29, 2012 at 10:41 AM, William G. Scott wrote:

...

...

Graemes-MacBook-Pro:build graeme$ gcc --version gcc (GCC) 4.7.0 20120314 (prerelease)

I can't get cctbx to compile with that compiler, but, oddly, with an uncompiled cctbx, I can get phaser to compile with that compiler (see my open-mp thread).

Where are you getting gcc 4.7 from, fink or somewhere else? We are planning to buy a 4-core Mac Mini to do additional build tests on, since our official support is still stuck at 10.6 and Xcode 3.2, and it might be worthwhile trying the latest gcc as well as the latest Xcode tools (currently clang 4.1, which also appears to have issues).

-Nat _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

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On Mon, Oct 1, 2012 at 2:32 AM, wrote:

Compiler change

I now need to use clang and stop overriding it to use gcc with --compiler=gcc.

Now appears to work right. Is this correct?

Yes, this should work - although we're finding clang to be a bit buggy too, I'm afraid. -Nat