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Genetics library: Volunteers needed
by Andy Thomason 23 Jul '15

23 Jul '15

Hi All, I am recruiting users for the putative genetics library. https://github.com/andy-thomason/genetics We have a few simple examples of gene searching and I am working on a more complete aligner example and some performance improvements to the index data structure. For data, you can obtain the human genome from: ftp://ftp.ensembl.org/pub/release-81/fasta/homo_sapiens/dna/Homo_sapiens.GR… Interesting problems we would like to solve: Given a 20 character sequence with up to six errors, what is the fastest way to list all possibilities other than a brute force search (CRISPR). Can we use JNI to connect the library to Hadoop and other distributed seach systems? Can we construct a database of all known viral genomes including recombination? Can we detect variations in MHC VDJ regions within a single sample? Many other interesting puzzles are there to be found... Andy. --- This email has been checked for viruses by Avast antivirus software. http://www.avast.com

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Trouble with Boost.Test on ESXi
by William Winder 23 Jul '15

23 Jul '15

I'm using Boost.Test and Boost v1.55 to unit test an application on Windows/Linux/ESXi. The ESXi build is done on a CentOS 5.10 machine, this has been working well for the main application, but the Boost.Test binary hits an assert before running any tests: /tmp # ./MyTests Test setup error: system_error produced by: ::sigaltstack( 0, &sigstk ) != -1: Function not implemented The "Function not implemented" problem has been a recurring problem for me while making my application compatible with ESXi. My basic understanding is that ESXi implements a subset of glibc. I saw a similar issue here: http://comments.gmane.org/gmane.comp.lib.boost.testing/7782 I'm wondering how I can disable this assert and what the repercussions would be. Thanks

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Re: [boost] Genetics Library:Volunteers Needed
by Mudit Sharma 23 Jul '15

23 Jul '15

Hi! I am deeply interested in volunteering for genetics library in Boost. I have sound knowledge of boost libraries. Note:This project can help me personally. Thanks! M

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gcc 5.1/6.0 warnings with smart_ptr
by Gennadiy Rozental 23 Jul '15

23 Jul '15

Hi, There are bunch of warnings like these: ../boost/smart_ptr/shared_ptr.hpp:249:65: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations] Any chance we can shut these down? Maybe update toolset config? Gennadiy

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[boost.test] Assertion/crash
by Philip Bennefall 23 Jul '15

23 Jul '15

Hi all, I am having an issue where boost.test is triggering an assert when I make a BOOST_REQUIRE_EQUAL check. It always gives me the same assert. I am on Windows 7 with Visual C++ 2013, compiling a 32 bit application. This error happens both with boost_1_57_0 and boost_1_58_0. The assert says: Debug Assertion Failed! Program: C:\Windows\system32\MSVCP120D.dll File: C:\Program Files (x86)\Microsoft Visual Studio 12.0\VC\INCLUDE\xstring Line: 168 Expression: string iterator + offset out of range Here's the stack: 0041ef44 0149ca07 015c08f0 015c07e0 000000a8 MSVCP120D!std::_Debug_message+0x26 0041ef60 0149ca93 00000053 0041ef80 0041efa0 my_tests!std::_String_const_iterator<std::_String_val<std::_Simple_types<char> > >::operator+=+0x77 0041ef70 0149c91e 00000053 d4f524ac 07d2cff0 my_tests!std::_String_iterator<std::_String_val<std::_Simple_types<char> > >::operator+=+0x13 0041efa0 0149be76 0041efb4 00000053 d4f524ec my_tests!std::_String_iterator<std::_String_val<std::_Simple_types<char> > >::operator++0x4e 0041efe0 0149bdf6 0041f100 07d2ef28 07d2ef7b my_tests!std::_Transform1<char *,std::_String_iterator<std::_String_val<std::_Simple_types<char> > >,char (__cdecl*)(char)>+0x46 0041f034 0149c1b1 0041f100 07d2ef28 07d2ef7b my_tests!std::_Transform1<char *,std::_String_iterator<std::_String_val<std::_Simple_types<char> > >,char (__cdecl*)(char)>+0x96 0041f0c8 0149b5bf 0041f100 07d2cff0 0041f0e0 my_tests!std::transform<std::_String_iterator<std::_String_val<std::_Simple_types<char> > >,std::_String_iterator<std::_String_val<std::_Simple_types<char> > >,char (__cdecl*)(char)>+0x191 0041f148 0149d6e2 0041f18c 00000000 015c0d18 my_tests!boost::unit_test::unit_test_log_t::operator<<+0x10f 0041f2c8 014315dc 0041f320 0041f3f4 015aa770 my_tests!boost::test_tools::tt_detail::check_impl+0x372 0041f364 01404626 00000000 0041f3f4 015aa770 my_tests!boost::test_tools::tt_detail::check_frwd<boost::test_tools::tt_detail::equal_impl_frwd,int,enum my_error_codes>+0xec 0041f458 014050af 000d7550 d4f53c34 00000000 my_tests!basic_operations::playback_decoders::pull_samples+0x146 0041f738 014053e6 015b223c 015b2234 00000000 my_tests!basic_operations::playback_decoders::iteration+0x8cf 0041f758 01405451 d4f53c70 cccccccc cccccccc my_tests!basic_operations::playback_decoders::playback_decoders_mono::test_method+0x26 0041f77c 014399d1 00000000 cccccccc 0041f7a3 my_tests!basic_operations::playback_decoders::playback_decoders_mono_invoker+0x51 0041f790 0148a54f 0041f7cf 076ecff4 00cccccc my_tests!boost::unit_test::ut_detail::invoker<boost::unit_test::ut_detail::unused>::invoke<void (__cdecl*)(void)>+0x21 0041f7a8 01522cc5 0041f7cf 078c4ff0 076ecff0 my_tests!boost::unit_test::ut_detail::callback0_impl_t<boost::unit_test::ut_detail::unused,void (__cdecl*)(void)>::invoke+0x2f 0041f7bc 01522ce7 0041f7cf 0a66aff4 00000000 my_tests!boost::unit_test::callback0<boost::unit_test::ut_detail::unused>::operator()+0x25 0041f7d0 01522a1f 0041f7ef 0041f7f0 01522dbd my_tests!boost::unit_test::`anonymous namespace'::zero_return_wrapper_t<boost::unit_test::callback0<boost::unit_test::ut_detail::unused> >::operator()+0x17 0041f7dc 01522dbd 0a66aff4 0a66aff0 0041f918 my_tests!boost::unit_test::ut_detail::invoker<int>::invoke<boost::unit_test::`anonymous namespace'::zero_return_wrapper_t<boost::unit_test::callback0<boost::unit_test::ut_detail::unused> > >+0xf 0041f7f0 01521e31 0041f918 0a66aff0 0041f810 my_tests!boost::unit_test::ut_detail::callback0_impl_t<int,boost::unit_test::`anonymous namespace'::zero_return_wrapper_t<boost::unit_test::callback0<boost::unit_test::ut_detail::unused> > >::invoke+0x1d 0041f800 01521b6e 0041f814 538d1e44 0041f87c my_tests!boost::unit_test::callback0<int>::operator()+0x21 0041f810 01521312 01620790 0041f918 d4f53370 my_tests!boost::detail::do_invoke<boost::scoped_ptr<boost::detail::translate_exception_base>,boost::unit_test::callback0<int> >+0x3e 0041f87c 01520dc4 0041f918 d4f533f0 00000000 my_tests!boost::execution_monitor::catch_signals+0xd2 0041f8fc 0152259d 0041f918 d4f53268 00000000 my_tests!boost::execution_monitor::execute+0x54 0041f964 014b6723 078c4fa8 d4f5316c 01574668 my_tests!boost::unit_test::unit_test_monitor_t::execute_and_translate+0xad 0041fa60 014a2565 078c4fa8 0041fa7c 014a259a my_tests!boost::unit_test::framework_impl::visit+0x3c3 0041fa6c 014a259a 078c4fa8 01620750 0041fb38 my_tests!boost::unit_test::traverse_test_tree+0x25 0041fa7c 014a22b2 00010040 01620750 d4f53034 my_tests!boost::unit_test::traverse_test_tree+0x2a 0041fb38 014a25b5 06258fa0 01620750 0041fc04 my_tests!boost::unit_test::traverse_test_tree+0x1e2 0041fb48 014a22b2 00000004 01620750 d4f53708 my_tests!boost::unit_test::traverse_test_tree+0x45 0041fc04 014a25b5 07388f98 01620750 0041fdc0 my_tests!boost::unit_test::traverse_test_tree+0x1e2 0041fc14 014a9ccb 00000001 01620750 d4f536cc my_tests!boost::unit_test::traverse_test_tree+0x45 0041fdc0 014b6bc3 00000001 00000001 d4f53538 my_tests!boost::unit_test::framework::run+0x5db 0041fe34 014b6d5c 013b346d 00000001 066fafb0 my_tests!boost::unit_test::unit_test_main+0xb3 0041fe4c 014996f9 00000001 066fafb0 05f44f28 my_tests!main+0x1c 0041fe9c 0149983d 0041feb0 74e4337a 7efde000 my_tests!__tmainCRTStartup+0x199 0041fea4 74e4337a 7efde000 0041fef0 773892e2 my_tests!mainCRTStartup+0xd 0041feb0 773892e2 7efde000 74959ac7 00000000 kernel32!BaseThreadInitThunk+0x12 0041fef0 773892b5 01499830 7efde000 00000000 ntdll!RtlInitializeExceptionChain+0x63 0041ff08 00000000 01499830 7efde000 00000000 ntdll!RtlInitializeExceptionChain+0x36 Does anyone have any tips for things I might try? Thanks in advance for any help on this! Kind regards, Philip Bennefall

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Boost release 1.59.0 beta 1 is now available from SourceForge
by Marshall Clow 22 Jul '15

22 Jul '15

Boost release 1.59.0 beta 1 is now available from SourceForge See http://sourceforge.net/projects/boost/files/boost/1.59.0.beta.1/ For details of what's in the release, see http://www.boost.org/users/history/version_1_59_0.html. Note that the links to files on this web page are for the final release - use the SourceForge link above to get the beta files. Please download the beta, give it a try, and report any problems you encounter. Thanks, -- The Boost Release Team

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[container] [1.59.0b1] Behavioral (runtime) breakage with flat_xxx + ordered_unique_range + non-default comparator
by Adam Merz 21 Jul '15

21 Jul '15

I've encountered a serious behavioral breakage for code using flat_xxx in conjunction with ordered_unique_range and a non-default comparator in 1.59.0b1. Here is a small repro: #include <initializer_list> #include <algorithm> #include <functional> #include <iterator> #include <iostream> #include <boost/container/flat_set.hpp> int main() { namespace bcont = boost::container; auto const p = [](auto const& desc, auto const& s) { std::cout << desc << ": "; std::copy( s.cbegin(), s.cend(), std::ostream_iterator<int>(std::cout, " ") ); std::cout << '\n'; }; auto const r = {4, 3, 2}; bcont::flat_set<int, std::greater<int>> const s{3, 2, 1}; p("orig set", s); auto s1{s}; s1.insert(r.begin(), r.end()); p("without\tordered_unique_range (expected output)", s1); auto s2{s}; s2.insert(bcont::ordered_unique_range, r.begin(), r.end()); p("with\tordered_unique_range (erroneous output)", s2); } I've worked around this locally by rerouting the ordered_unique_range codepath to the default codepath, but this seems like a showstopper for 1.59.0 as the code's behavior has broken entirely silently. Regards, Adam Merz

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Python bindings for Boost.Interprocess
by Edison Gustavo Muenz 21 Jul '15

21 Jul '15

Hi all, this is my first e-mail on the list, so please be nice, I’m new here. I have this problem in which I need to communicate between two processes, one written in C++ (it’s actually a .so) and one written in python. They need to share large arrays. I’ve searched on the internet for a way to use shared-memory in python, and the only alternative I found was POSIX IPC for Python <http://semanchuk.com/philip/posix_ipc/> (which looks good, but it is *nix only). Also, I find the Boost.Interprocess library to be a joy to use, it worked for the problem I had, so I wanted to use it. Since I didn’t find python bindings for Boost.Interprocess is it desirable to have this? I started writing some code which uses a tiny part of Boost.Interprocess that is necessary to solve my problem. It is working already. I’m asking here to know what do boost experts think about this idea, if it unreasonable or if other developers already had this need. Feedback would be greatly appreciated. Thanks, Edison Gustavo Muenz

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[mpl] Updated fixes on 'master'
by Edward Diener 18 Jul '15

18 Jul '15

A number of fixes in mpl, by Bruno Dutra and Deniz Bahadir, had been tested on 'develop' for quite a long time but had not been merged to 'master' for the upcoming release. The regression tests on 'develop' had shown that the fixes were working properly and I have taken the responsibility of merging them now to 'master' for the upcoming release. I will be checking the 'master' regression tests. If there are any problems I will revert this merge but I am 99.99% certain that the changes are correct, so I take full responsibility for merging. The fixes come from Trac items so I feel that correcting these bugs is important for the upcoming release else I would not have performed the merge and the push to Boost.

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[string_ref] [utility] Add string_view?
by Beman Dawes 18 Jul '15

18 Jul '15

Boost has shipped string_ref since 1.53. See www.boost.org/doc/libs/1_58_0/libs/utility/doc/html/string_ref.html In the meantime, the C++ committee has shipped a final version, named string_view, in the Library Fundamentals TS. See http://www.open-std.org/jtc1/sc22/wg21/docs/papers/2015/n4480.html#string.v… In addition to the name change, the interface in the TS more closely mimics the std::basic_string interface. I'd really like to see the final TS basic_string_view added to Boost so I can start using it now. Using basic_string_ref, and then later having to rename all uses, is less attractive. I suspect others may feel the same way. Because a Boost basic_string_view would be an implementation of a standard library TS class, and because basic_string_ref is already in Boost, it seems a min-review would be sufficient rather than a formal review. So what I'm proposing here is to create a basic_string_view branch of the utility repo, and start working on basic_string_view there. Once it is reasonably compliant with the TS and Boost doc requirements we would hold a mini-review and then merge the branch to develop, and once stable, to release. Comments? --Beman

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