October 2012 - cctbxbb - phenix-online.org

Re: [cctbxbb] RE : cctbx debian package: new commit
by Radostan Riedel 04 Oct '12

04 Oct '12

On Wed, 03. Oct 11:11, Baptiste Carvello wrote: > 2) there are a few C++ applications which depend on cctbx, the one I > know is FOX ( http://vincefn.net/Fox/ , objcryst-fox in Debian). For > those use cases, should we still build a libcctbx-dev package with the > headers and static libs (for those we don't need to care about ABI > stability)? I think this is a very important point here. Let's assume I want to extent the cctbx by adding a module, for let's say absorbtion correction and I want to implement a method called "multiscan" and I want to make a fast python boost extension to integrate with my python code. I need some symbols from any of the shared libs in cctbx. How could this be done in Debian or in any other distribution? About the check for version: In my patch I did this with SCons[1]. What this does is to compile and link a test program and check for success. I saw in your code that you are doing similar things and we could write some simple c++ program that for example includes boost/version and check some "BOOST_VERSION"? This way it checks globally for the availability of a shared library. [1] http://www.scons.org/doc/2.0.1/HTML/scons-user/x4146.html

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Explicit import for iotbx.pdb.amino_acid_codes
by Claudia Millán Nebot 01 Oct '12

01 Oct '12

Hello everyone :) I've just started to look into the cctbx facilities, and as i'm a newbie in both object oriented programming and in general to the system, i'm tryng to play around and find by myself how things are working. Using the cctbx.python, i realised that it is necessary to import explicitly the module amino_acid_codes, while for others like atom_name_interpretation this is done straigthforward if you do an import from a lower level (like from iotbx.pdb import *). Is there some good reason because this has to be like that? Thanks in advance for the answer, and excuse me if is it is a question too simple! Claudia Millán (cmncri(a)ibmb.csic.es) Institut de Biologia Molecular de Barcelona (IBMB-CSIC) Barcelona, Spain

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Build failing
by Graeme.Winter＠diamond.ac.uk 01 Oct '12

01 Oct '12

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/detail/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/detail/bessel_jy_series.hpp:139:10: note: 'template<class T, class Policy> 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/detail/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/detail/bessel_jy_series.hpp:47:10: note: 'template<class T, class Policy> 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/detail/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/detail/bessel_jy_series.hpp:213:3: note: 'template<class T, class Policy> 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: 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.app/Contents/MacOS/Python ../sources/cctbx_project/libtbx/configure.py --compiler=gcc labelit cctbx bpcx_regression rstbx . setpaths.sh make Thanks, Graeme -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. 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