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blast+ build error

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Feb 28th, 2018
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  1. /usr/bin/g++  -std=gnu++11 -c -Wall -Wno-format-y2k  -pthread -fopenmp -march=native -Ofast -pipe --param=ssp-buffer-size=4 -fPIC  -O   -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE  -D_FORTIFY_SOURCE=2 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/ReleaseMT/inc -I/tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/include   /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/teamcity_messages.cpp -o teamcity_messages.o
  2. /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp: In constructor ‘ncbi::CNcbiTestApplication::CNcbiTestApplication()’:
  3. /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:925:39: error: invalid new-expression of abstract class type ‘ncbi::CNcbiBoostLogger’
  4.      m_Logger   = new CNcbiBoostLogger();
  5.                                        ^
  6. /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:224:7: note:   because the following virtual functions are pure within ‘ncbi::CNcbiBoostLogger’:
  7.  class CNcbiBoostLogger : public TBoostLogFormatter
  8.        ^~~~~~~~~~~~~~~~
  9. In file included from /usr/include/boost/test/output/compiler_log_formatter.hpp:17:0,
  10.                  from /usr/include/boost/test/impl/compiler_log_formatter.ipp:19,
  11.                  from /usr/include/boost/test/included/unit_test.hpp:18,
  12.                  from /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:70:
  13. /usr/include/boost/test/unit_test_log_formatter.hpp:267:25: note:   virtual void boost::unit_test::unit_test_log_formatter::log_entry_context(std::ostream&, boost::unit_test::log_level, boost::unit_test::const_string)
  14.      virtual void        log_entry_context( std::ostream& os, log_level l, const_string value ) = 0;
  15.                          ^~~~~~~~~~~~~~~~~
  16. /usr/include/boost/test/unit_test_log_formatter.hpp:274:25: note:   virtual void boost::unit_test::unit_test_log_formatter::entry_context_finish(std::ostream&, boost::unit_test::log_level)
  17.      virtual void        entry_context_finish( std::ostream& os, log_level l ) = 0;
  18.                          ^~~~~~~~~~~~~~~~~~~~
  19. /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp: In member function ‘void ncbi::CNcbiTestApplication::SetTestDisabled(boost::unit_test::test_unit*)’:
  20. /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:116:37: error: ‘RUN_FILTERS’ is not a member of ‘boost::unit_test::runtime_config’
  21.      RTCFG(std::vector<std::string>, RUN_FILTERS, test_to_run)
  22.                                      ^
  23. /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:99:58: note: in definition of macro ‘RTCFG’
  24.      but::runtime_config::get<type >(but::runtime_config::new_name)
  25.                                                           ^~~~~~~~
  26. /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:997:9: note: in expansion of macro ‘CONFIGURED_FILTERS’
  27.      if (CONFIGURED_FILTERS.empty()) {
  28.          ^
  29. /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp: In member function ‘void ncbi::CNcbiTestApplication::x_SetupBoostReporters()’:
  30. /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:1665:59: error: ‘REPORT_FORMAT’ is not a member of ‘boost::unit_test::runtime_config’
  31.      but::output_format format = RTCFG(but::output_format, REPORT_FORMAT,
  32.                                                            ^
  33. /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:99:58: note: in definition of macro ‘RTCFG’
  34.      but::runtime_config::get<type >(but::runtime_config::new_name)
  35.                                                           ^~~~~~~~
  36. /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:1693:57: error: ‘LOG_FORMAT’ is not a member of ‘boost::unit_test::runtime_config’
  37.      m_Logger->SetOutputFormat(RTCFG(but::output_format, LOG_FORMAT,
  38.                                                          ^
  39. /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:99:58: note: in definition of macro ‘RTCFG’
  40.      but::runtime_config::get<type >(but::runtime_config::new_name)
  41.                                                           ^~~~~~~~
  42. /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp: In member function ‘boost::unit_test::test_suite* ncbi::CNcbiTestApplication::InitTestFramework(int, char**)’:
  43. /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:116:37: error: ‘RUN_FILTERS’ is not a member of ‘boost::unit_test::runtime_config’
  44.      RTCFG(std::vector<std::string>, RUN_FILTERS, test_to_run)
  45.                                      ^
  46. /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:99:58: note: in definition of macro ‘RTCFG’
  47.      but::runtime_config::get<type >(but::runtime_config::new_name)
  48.                                                           ^~~~~~~~
  49. /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:1815:19: note: in expansion of macro ‘CONFIGURED_FILTERS’
  50.              &&  (!CONFIGURED_FILTERS.empty()  ||  x_ReadConfiguration()))
  51.                    ^
  52. /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp: In member function ‘virtual void ncbi::CNcbiBoostLogger::log_entry_context(std::ostream&, boost::unit_test::const_string)’:
  53. /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:2130:43: error: no matching function for call to ‘boost::unit_test::unit_test_log_formatter::log_entry_context(std::ostream&, boost::unit_test::const_string&)
  54.      m_Upper->log_entry_context(ostr, value);
  55.                                            ^
  56. In file included from /usr/include/boost/test/output/compiler_log_formatter.hpp:17:0,
  57.                  from /usr/include/boost/test/impl/compiler_log_formatter.ipp:19,
  58.                  from /usr/include/boost/test/included/unit_test.hpp:18,
  59.                  from /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:70:
  60. /usr/include/boost/test/unit_test_log_formatter.hpp:267:25: note: candidate: virtual void boost::unit_test::unit_test_log_formatter::log_entry_context(std::ostream&, boost::unit_test::log_level, boost::unit_test::const_string)
  61.      virtual void        log_entry_context( std::ostream& os, log_level l, const_string value ) = 0;
  62.                          ^~~~~~~~~~~~~~~~~
  63. /usr/include/boost/test/unit_test_log_formatter.hpp:267:25: note:   candidate expects 3 arguments, 2 provided
  64. /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp: In member function ‘virtual void ncbi::CNcbiBoostLogger::entry_context_finish(std::ostream&)’:
  65. /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:2135:39: error: no matching function for call to ‘boost::unit_test::unit_test_log_formatter::entry_context_finish(std::ostream&)
  66.      m_Upper->entry_context_finish(ostr);
  67.                                        ^
  68. In file included from /usr/include/boost/test/output/compiler_log_formatter.hpp:17:0,
  69.                  from /usr/include/boost/test/impl/compiler_log_formatter.ipp:19,
  70.                  from /usr/include/boost/test/included/unit_test.hpp:18,
  71.                  from /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:70:
  72. /usr/include/boost/test/unit_test_log_formatter.hpp:274:25: note: candidate: virtual void boost::unit_test::unit_test_log_formatter::entry_context_finish(std::ostream&, boost::unit_test::log_level)
  73.      virtual void        entry_context_finish( std::ostream& os, log_level l ) = 0;
  74.                          ^~~~~~~~~~~~~~~~~~~~
  75. /usr/include/boost/test/unit_test_log_formatter.hpp:274:25: note:   candidate expects 2 arguments, 1 provided
  76. In file included from /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:2227:0:
  77. /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/teamcity_boost.cpp: In constructor ‘jetbrains::teamcity::TeamcityFormatterRegistrar::TeamcityFormatterRegistrar()’:
  78. /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/teamcity_boost.cpp:92:89: error: invalid new-expression of abstract class type ‘jetbrains::teamcity::TeamcityBoostLogFormatter’
  79.              boost::unit_test::unit_test_log.set_formatter(new TeamcityBoostLogFormatter());
  80.                                                                                          ^
  81. /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/teamcity_boost.cpp:44:7: note:   because the following virtual functions are pure within ‘jetbrains::teamcity::TeamcityBoostLogFormatter’:
  82.  class TeamcityBoostLogFormatter: public boost::unit_test::unit_test_log_formatter {
  83.        ^~~~~~~~~~~~~~~~~~~~~~~~~
  84. In file included from /usr/include/boost/test/output/compiler_log_formatter.hpp:17:0,
  85.                  from /usr/include/boost/test/impl/compiler_log_formatter.ipp:19,
  86.                  from /usr/include/boost/test/included/unit_test.hpp:18,
  87.                  from /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:70:
  88. /usr/include/boost/test/unit_test_log_formatter.hpp:267:25: note:   virtual void boost::unit_test::unit_test_log_formatter::log_entry_context(std::ostream&, boost::unit_test::log_level, boost::unit_test::const_string)
  89.      virtual void        log_entry_context( std::ostream& os, log_level l, const_string value ) = 0;
  90.                          ^~~~~~~~~~~~~~~~~
  91. /usr/include/boost/test/unit_test_log_formatter.hpp:274:25: note:   virtual void boost::unit_test::unit_test_log_formatter::entry_context_finish(std::ostream&, boost::unit_test::log_level)
  92.      virtual void        entry_context_finish( std::ostream& os, log_level l ) = 0;
  93.                          ^~~~~~~~~~~~~~~~~~~~
  94. /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/teamcity_boost.cpp:94:40: error: ‘LOG_LEVEL’ is not a member of ‘boost::unit_test::runtime_config’
  95.                  (RTCFG(but::log_level, LOG_LEVEL, log_level));
  96.                                         ^
  97. /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:99:58: note: in definition of macro ‘RTCFG’
  98.      but::runtime_config::get<type >(but::runtime_config::new_name)
  99.                                                           ^~~~~~~~
  100. /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp: In function ‘int main(int, char**)’:
  101. /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:2266:25: error: ‘WAIT_FOR_DEBUGGER’ is not a member of ‘boost::unit_test::runtime_config’
  102.          if( RTCFG(bool, WAIT_FOR_DEBUGGER, wait_for_debugger) ) {
  103.                          ^
  104. /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:99:58: note: in definition of macro ‘RTCFG’
  105.      but::runtime_config::get<type >(but::runtime_config::new_name)
  106.                                                           ^~~~~~~~
  107. /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:2275:56: error: ‘LIST_CONTENT’ is not a member of ‘boost::unit_test::runtime_config’
  108.          output_format list_cont = RTCFG(output_format, LIST_CONTENT,
  109.                                                         ^
  110. /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:99:58: note: in definition of macro ‘RTCFG’
  111.      but::runtime_config::get<type >(but::runtime_config::new_name)
  112.                                                           ^~~~~~~~
  113. /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:2292:25: error: ‘LIST_LABELS’ is not a member of ‘boost::unit_test::runtime_config’
  114.          if( RTCFG(bool, LIST_LABELS, list_labels) ) {
  115.                          ^
  116. /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:99:58: note: in definition of macro ‘RTCFG’
  117.      but::runtime_config::get<type >(but::runtime_config::new_name)
  118.                                                           ^~~~~~~~
  119. /tmp/yaourt-tmp-anadon/aur-blast+/src/ncbi-blast-2.7.1+-src/c++/src/corelib/test_boost.cpp:2319:56: error: ‘RESULT_CODE’ is not a member of ‘boost::unit_test::runtime_config’
  120.              runtime_config::get<bool>( runtime_config::RESULT_CODE )
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