BIO-DIKU / SeqScan

Pattern matching in biological sequences
GNU General Public License v2.0
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make of parser Makefile breaks #21

Closed maasha closed 9 years ago

maasha commented 9 years ago
maasha@edna:~/install/src/SeqScan/parser$ make
bison -d seq_par.y
flex seq_lex.l
g++ -std=c++11 ../src/modifiers.cc ../src/match.cc ../src/pu/backtrack_unit.cc ../src/pu/pattern_unit.cc punit_list.cpp seq_par.tab.c lex.yy.c -L/usr/local/opt/flex/lib -lfl -o seqscan
clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated
clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated
seq_lex.l:14:61: warning: '/*' within block comment [-Wcomment]
/* Combined: ABCDEFGHIKLMNPQRSTUVWXYabcdefghiklmnpqrstuvwyx /*
                                                            ^
seq_lex.l:16:1: warning: '/*' within block comment [-Wcomment]
/* All observed chars in README examples: */
^
lex.yy.c:669:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
        register yy_state_type yy_current_state;
        ^~~~~~~~~
lex.yy.c:670:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
        register char *yy_cp, *yy_bp;
        ^~~~~~~~~
lex.yy.c:670:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
        register char *yy_cp, *yy_bp;
        ^~~~~~~~~
lex.yy.c:671:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
        register int yy_act;
        ^~~~~~~~~
lex.yy.c:719:4: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
                        register YY_CHAR yy_c = yy_ec[YY_SC_TO_UI(*yy_cp)];
                        ^~~~~~~~~
lex.yy.c:1005:6: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
        register char *dest = YY_CURRENT_BUFFER_LVALUE->yy_ch_buf;
        ^~~~~~~~~
lex.yy.c:1006:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
        register char *source = (yytext_ptr);
        ^~~~~~~~~
lex.yy.c:1007:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
        register int number_to_move, i;
        ^~~~~~~~~
lex.yy.c:1007:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
        register int number_to_move, i;
        ^~~~~~~~~
lex.yy.c:1139:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
        register yy_state_type yy_current_state;
        ^~~~~~~~~
lex.yy.c:1140:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
        register char *yy_cp;
        ^~~~~~~~~
lex.yy.c:1146:3: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
                register YY_CHAR yy_c = (*yy_cp ? yy_ec[YY_SC_TO_UI(*yy_cp)] : 1);
                ^~~~~~~~~
lex.yy.c:1171:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
        register int yy_is_jam;
        ^~~~~~~~~
lex.yy.c:1172:6: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
        register char *yy_cp = (yy_c_buf_p);
        ^~~~~~~~~
lex.yy.c:1174:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
        register YY_CHAR yy_c = 1;
        ^~~~~~~~~
lex.yy.c:1194:2: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
        register char *yy_cp;
        ^~~~~~~~~
lex.yy.c:1204:3: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
                register yy_size_t number_to_move = (yy_n_chars) + 2;
                ^~~~~~~~~
lex.yy.c:1205:3: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
                register char *dest = &YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[
                ^~~~~~~~~
lex.yy.c:1207:3: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
                register char *source =
                ^~~~~~~~~
21 warnings generated.
Undefined symbols for architecture x86_64:
  "ParseTreeList::get_parse_unit(int)", referenced from:
      _main in seq_par-2356cc.o
  "ParseTreeList::get_size()", referenced from:
      _main in seq_par-2356cc.o
  "ParseTreeList::push_back(ParseTreeUnit*)", referenced from:
      _yyparse in seq_par-2356cc.o
  "ParseTreeList::ParseTreeList()", referenced from:
      _yyparse in seq_par-2356cc.o
      ___cxx_global_var_init1 in seq_par-2356cc.o
  "ParseTreeUnit::init_or_units()", referenced from:
      _yyparse in seq_par-2356cc.o
  "ParseTreeUnit::insert_or_units(ParseTreeUnit*, ParseTreeUnit*)", referenced from:
      _yyparse in seq_par-2356cc.o
  "ParseTreeUnit::pprint()", referenced from:
      _main in seq_par-2356cc.o
  "ParseTreeUnit::ParseTreeUnit()", referenced from:
      _yyparse in seq_par-2356cc.o
      ___cxx_global_var_init in seq_par-2356cc.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [all] Error 1
maasha commented 9 years ago

Fixed with parser-generator