* Package: sci-biology/qrna-2.0.3c-r3:0 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking qrna-2.0.3c.tar.bz2 to /var/tmp/portage/sci-biology/qrna-2.0.3c-r3/work >>> Source unpacked in /var/tmp/portage/sci-biology/qrna-2.0.3c-r3/work >>> Preparing source in /var/tmp/portage/sci-biology/qrna-2.0.3c-r3/work/qrna-2.0.3c ... * Applying qrna-2.0.3c-glibc-2.10.patch ... [ ok ] * Applying qrna-2.0.3c-ldflags.patch ... [ ok ] removed 'squid02/libsquid.a' >>> Source prepared. * Clang 16 testing: this build is using a /etc/portage/bashrc hook (2022-11-24T21:47)! * Clang 16 testing: see https://wiki.gentoo.org/wiki/Modern_C_porting for more info. >>> Configuring source in /var/tmp/portage/sci-biology/qrna-2.0.3c-r3/work/qrna-2.0.3c ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/qrna-2.0.3c-r3/work/qrna-2.0.3c ... make -j4 -C squid make: Entering directory '/var/tmp/portage/sci-biology/qrna-2.0.3c-r3/work/qrna-2.0.3c/squid' clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c dayhoff.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c sqerror.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c types.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c revcomp.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c interleaved.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c iupac.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c sre_string.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c translate.c interleaved.c:157:82: warning: size argument in 'strncmp' call is a comparison [-Wmemsize-comparison] ...!= NULL && strncmp(buf, expected_name, strlen(expected_name) == 0)) ~~~~~~~~~~~~~~~~~~~~~~^~~~ interleaved.c:157:32: note: did you mean to compare the result of 'strncmp' instead? ...!= NULL && strncmp(buf, expected_name, strlen(expected_name) == 0)) ^ ~ ) interleaved.c:157:60: note: explicitly cast the argument to size_t to silence this warning ...!= NULL && strncmp(buf, expected_name, strlen(expected_name) == 0)) ^ (size_t)( ) interleaved.c:232:82: warning: size argument in 'strncmp' call is a comparison [-Wmemsize-comparison] ...!= NULL && strncmp(buf, expected_name, strlen(expected_name) == 0)) ~~~~~~~~~~~~~~~~~~~~~~^~~~ interleaved.c:232:32: note: did you mean to compare the result of 'strncmp' instead? ...!= NULL && strncmp(buf, expected_name, strlen(expected_name) == 0)) ^ ~ ) interleaved.c:232:60: note: explicitly cast the argument to size_t to silence this warning ...!= NULL && strncmp(buf, expected_name, strlen(expected_name) == 0)) ^ (size_t)( ) clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c aligneval.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c file.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c msf.c 2 warnings generated. clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c weight.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c sre_ctype.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c selex.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c seqencode.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c gnuregex.c gnuregex.c:795:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] re_set_syntax (syntax) ^ gnuregex.c:1175:37: warning: passing arguments to 'at_begline_loc_p' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] || at_begline_loc_p (pattern, p, syntax)) ^ gnuregex.c:1190:37: warning: passing arguments to 'at_endline_loc_p' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] || at_endline_loc_p (p, pend, syntax)) ^ gnuregex.c:1296:21: warning: passing arguments to 'store_op1' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] STORE_JUMP (jump, b, laststart); ^ gnuregex.c:903:13: note: expanded from macro 'STORE_JUMP' store_op1 (op, loc, (to) - (loc) - 3) ^ gnuregex.c:1301:19: warning: passing arguments to 'store_op1' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] STORE_JUMP (maybe_pop_jump, b, laststart - 3); ^ gnuregex.c:903:13: note: expanded from macro 'STORE_JUMP' store_op1 (op, loc, (to) - (loc) - 3) ^ gnuregex.c:1310:13: warning: passing arguments to 'insert_op1' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] INSERT_JUMP (keep_string_p ? on_failure_keep_string_jump ^ gnuregex.c:911:14: note: expanded from macro 'INSERT_JUMP' insert_op1 (op, loc, (to) - (loc) - 3, b) ^ gnuregex.c:1324:17: warning: passing arguments to 'insert_op1' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] INSERT_JUMP (dummy_failure_jump, laststart, laststart + 6); ^ gnuregex.c:911:14: note: expanded from macro 'INSERT_JUMP' insert_op1 (op, loc, (to) - (loc) - 3, b) ^ gnuregex.c:1407:39: warning: passing arguments to 'compile_range' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] = compile_range (&p, pend, translate, syntax, b); ^ gnuregex.c:1418:41: warning: passing arguments to 'compile_range' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] ret = compile_range (&p, pend, translate, syntax, b); ^ gnuregex.c:1616:17: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ gnuregex.c:1629:19: warning: passing arguments to 'store_op1' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] STORE_JUMP (jump_past_alt, fixup_alt_jump, b - 1); ^ gnuregex.c:903:13: note: expanded from macro 'STORE_JUMP' store_op1 (op, loc, (to) - (loc) - 3) ^ gnuregex.c:1636:17: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ gnuregex.c:1686:15: warning: passing arguments to 'insert_op1' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] INSERT_JUMP (on_failure_jump, begalt, b + 6); ^ gnuregex.c:911:14: note: expanded from macro 'INSERT_JUMP' insert_op1 (op, loc, (to) - (loc) - 3, b) ^ gnuregex.c:1707:17: warning: passing arguments to 'store_op1' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] STORE_JUMP (jump_past_alt, fixup_alt_jump, b); ^ gnuregex.c:903:13: note: expanded from macro 'STORE_JUMP' store_op1 (op, loc, (to) - (loc) - 3) ^ gnuregex.c:1801:22: warning: passing arguments to 'insert_op1' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] INSERT_JUMP (jump, laststart, b + 3); ^ gnuregex.c:911:14: note: expanded from macro 'INSERT_JUMP' insert_op1 (op, loc, (to) - (loc) - 3, b) ^ gnuregex.c:1826:22: warning: passing arguments to 'insert_op2' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] INSERT_JUMP2 (succeed_n, laststart, ^ gnuregex.c:915:14: note: expanded from macro 'INSERT_JUMP2' insert_op2 (op, loc, (to) - (loc) - 3, arg, b) ^ gnuregex.c:1835:33: warning: passing arguments to 'insert_op2' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] insert_op2 (set_number_at, laststart, 5, lower_bound, b); ^ gnuregex.c:1846:26: warning: passing arguments to 'store_op2' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] STORE_JUMP2 (jump_n, b, laststart + 5, ^ gnuregex.c:907:13: note: expanded from macro 'STORE_JUMP2' store_op2 (op, loc, (to) - (loc) - 3, arg) ^ gnuregex.c:1864:37: warning: passing arguments to 'insert_op2' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] insert_op2 (set_number_at, laststart, b - laststart, ^ gnuregex.c:1958:42: warning: passing arguments to 'group_in_compile_stack' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] if (group_in_compile_stack (compile_stack, c1)) ^ gnuregex.c:2024:5: warning: passing arguments to 'store_op1' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] STORE_JUMP (jump_past_alt, fixup_alt_jump, b); ^ gnuregex.c:903:13: note: expanded from macro 'STORE_JUMP' store_op1 (op, loc, (to) - (loc) - 3) ^ gnuregex.c:1049:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regex_compile (pattern, size, syntax, bufp) ^ gnuregex.c:2050:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] store_op1 (op, loc, arg) ^ gnuregex.c:2063:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] store_op2 (op, loc, arg1, arg2) ^ gnuregex.c:2078:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] insert_op1 (op, loc, arg, end) ^ gnuregex.c:2097:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] insert_op2 (op, loc, arg1, arg2, end) ^ gnuregex.c:2118:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] at_begline_loc_p (pattern, p, syntax) ^ gnuregex.c:2137:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] at_endline_loc_p (p, pend, syntax) ^ gnuregex.c:2159:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] group_in_compile_stack (compile_stack, regnum) ^ gnuregex.c:2187:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] compile_range (p_ptr, pend, translate, syntax, b) ^ gnuregex.c:2519:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] re_compile_fastmap (bufp) ^ gnuregex.c:2804:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] re_set_registers (bufp, regs, num_regs, starts, ends) ^ gnuregex.c:2821:33: warning: expression which evaluates to zero treated as a null pointer constant of type 'regoff_t *' (aka 'int *') [-Wnon-literal-null-conversion] regs->start = regs->end = (regoff_t) 0; ^~~~~~~~~~~~ gnuregex.c:2831:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] re_search (bufp, string, size, startpos, range, regs) ^ gnuregex.c:2864:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] re_search_2 (bufp, string1, size1, string2, size2, startpos, range, regs, stop) ^ gnuregex.c:3123:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] re_match (bufp, string, size, pos, regs) ^ gnuregex.c:3148:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] re_match_2 (bufp, string1, size1, string2, size2, pos, regs, stop) ^ gnuregex.c:3604:43: warning: passing arguments to 'group_match_null_string_p' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] = group_match_null_string_p (&p1, pend, reg_info); ^ gnuregex.c:3752:31: warning: cast to smaller integer type 'int' from 'char *' [-Wpointer-to-int-cast] if ((int) old_regend[r] >= (int) regstart[r]) ^~~~~~~~~~~~~~~~~~~ gnuregex.c:3752:54: warning: cast to smaller integer type 'int' from 'char *' [-Wpointer-to-int-cast] if ((int) old_regend[r] >= (int) regstart[r]) ^~~~~~~~~~~~~~~~~ gnuregex.c:3758:19: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] PUSH_FAILURE_POINT (p1 + mcnt, d, -2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2394:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:3758:19: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] PUSH_FAILURE_POINT (p1 + mcnt, d, -2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2397:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (highest_active_reg); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:3822:38: warning: passing arguments to 'bcmp_translate' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] ? bcmp_translate (d, d2, mcnt, translate) ^ gnuregex.c:3905:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] PUSH_FAILURE_POINT (p + mcnt, NULL, -2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2394:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:3905:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] PUSH_FAILURE_POINT (p + mcnt, NULL, -2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2397:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (highest_active_reg); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:3958:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] PUSH_FAILURE_POINT (p + mcnt, d, -2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2394:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:3958:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] PUSH_FAILURE_POINT (p + mcnt, d, -2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2397:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (highest_active_reg); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4064:13: warning: cast to smaller integer type 'unsigned int' from 'fail_stack_elt_t' (aka 'unsigned char *') [-Wpointer-to-int-cast] POP_FAILURE_POINT (sdummy, pdummy, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2482:14: note: expanded from macro 'POP_FAILURE_POINT' high_reg = (unsigned) POP_FAILURE_ITEM (); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4064:13: warning: cast to smaller integer type 'unsigned int' from 'fail_stack_elt_t' (aka 'unsigned char *') [-Wpointer-to-int-cast] POP_FAILURE_POINT (sdummy, pdummy, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2485:13: note: expanded from macro 'POP_FAILURE_POINT' low_reg = (unsigned) POP_FAILURE_ITEM (); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4097:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] PUSH_FAILURE_POINT (0, 0, -2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2394:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4097:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] PUSH_FAILURE_POINT (0, 0, -2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2397:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (highest_active_reg); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4110:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] PUSH_FAILURE_POINT (0, 0, -2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2394:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4110:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] PUSH_FAILURE_POINT (0, 0, -2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2397:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (highest_active_reg); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4278:11: warning: cast to smaller integer type 'unsigned int' from 'fail_stack_elt_t' (aka 'unsigned char *') [-Wpointer-to-int-cast] POP_FAILURE_POINT (d, p, ^~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2482:14: note: expanded from macro 'POP_FAILURE_POINT' high_reg = (unsigned) POP_FAILURE_ITEM (); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4278:11: warning: cast to smaller integer type 'unsigned int' from 'fail_stack_elt_t' (aka 'unsigned char *') [-Wpointer-to-int-cast] POP_FAILURE_POINT (d, p, ^~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2485:13: note: expanded from macro 'POP_FAILURE_POINT' low_reg = (unsigned) POP_FAILURE_ITEM (); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4394:48: warning: passing arguments to 'alt_match_null_string_p' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] if (!alt_match_null_string_p (p1, p1 + mcnt - 3, ^ gnuregex.c:4424:44: warning: passing arguments to 'alt_match_null_string_p' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] if (!alt_match_null_string_p (p1, p1 + mcnt, reg_info)) ^ gnuregex.c:4439:46: warning: passing arguments to 'common_op_match_null_string_p' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] if (!common_op_match_null_string_p (&p1, end, reg_info)) ^ gnuregex.c:4344:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] group_match_null_string_p (p, end, reg_info) ^ gnuregex.c:4475:46: warning: passing arguments to 'common_op_match_null_string_p' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] if (!common_op_match_null_string_p (&p1, end, reg_info)) ^ gnuregex.c:4453:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] alt_match_null_string_p (p, end, reg_info) ^ gnuregex.c:4490:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] common_op_match_null_string_p (p, end, reg_info) ^ gnuregex.c:4578:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] bcmp_translate (s1, s2, len, translate) ^ gnuregex.c:4720:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regcomp (preg, pattern, cflags) ^ gnuregex.c:4795:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regexec (preg, string, nmatch, pmatch, eflags) ^ gnuregex.c:4860:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regerror (errcode, preg, errbuf, errbuf_size) ^ gnuregex.c:4904:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regfree (preg) ^ clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c sre_math.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c rk.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c getopt.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c cluster.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c stack.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c sqio.c sqio.c:1279:9: warning: comparison of array 'sp' equal to a null pointer is always false [-Wtautological-pointer-compare] if (sp==NULL || *sp=='\0') ^~ ~~~~ clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -c alignio.c 1 warning generated. 67 warnings generated. x86_64-pc-linux-gnu-ar rcv libsquid.a aligneval.o alignio.o cluster.o dayhoff.o file.o getopt.o interleaved.o sqerror.o gnuregex.o sqio.o iupac.o msf.o revcomp.o rk.o selex.o seqencode.o sre_ctype.o sre_math.o sre_string.o stack.o translate.o types.o weight.o a - aligneval.o a - alignio.o a - cluster.o a - dayhoff.o a - file.o a - getopt.o a - interleaved.o a - sqerror.o a - gnuregex.o a - sqio.o a - iupac.o a - msf.o a - revcomp.o a - rk.o a - selex.o a - seqencode.o a - sre_ctype.o a - sre_math.o a - sre_string.o a - stack.o a - translate.o a - types.o a - weight.o if test -x /bin/ranlib; then /bin/ranlib libsquid.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libsquid.a; else exit 0; fi if test -x x86_64-pc-linux-gnu-ranlib; then x86_64-pc-linux-gnu-ranlib libsquid.a; else exit 0; fi chmod 644 libsquid.a make: Leaving directory '/var/tmp/portage/sci-biology/qrna-2.0.3c-r3/work/qrna-2.0.3c/squid' make -j4 -C squid02 make: Entering directory '/var/tmp/portage/sci-biology/qrna-2.0.3c-r3/work/qrna-2.0.3c/squid02' clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c sqerror.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c translate.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c sre_ctype.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c clustal.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c msf.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c gki.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c sre_math.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c getopt.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c phylip.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c gsi.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c msa.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c aligneval.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c file.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c vectorops.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c sreformat_main.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c types.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c cluster.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c selex.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c iupac.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c alignio.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c hsregex.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c weight.c hsregex.c:331:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] sqd_regcomp(exp) ^ hsregex.c:420:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] reg(cp, paren, flagp) ^ hsregex.c:420:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] hsregex.c:490:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regbranch(cp, flagp) ^ hsregex.c:490:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] hsregex.c:531:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regpiece(cp, flagp) ^ hsregex.c:531:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] hsregex.c:600:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regatom(cp, flagp) ^ hsregex.c:600:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] hsregex.c:709:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regnode(cp, op) ^ hsregex.c:709:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] hsregex.c:734:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regc(cp, b) ^ hsregex.c:734:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] hsregex.c:750:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] reginsert(cp, op, opnd) ^ hsregex.c:750:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] hsregex.c:775:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regtail(cp, p, val) ^ hsregex.c:775:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] hsregex.c:800:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regoptail(cp, p, val) ^ hsregex.c:800:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] hsregex.c:842:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] sqd_regexec(prog, str) ^ hsregex.c:896:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regtry(ep, prog, string) ^ hsregex.c:896:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] hsregex.c:932:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regmatch(ep, prog) ^ hsregex.c:932:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] hsregex.c:1087:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regrepeat(ep, node) ^ hsregex.c:1087:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] hsregex.c:1124:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regnext(p) ^ hsregex.c:1124:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] hsregex.c:1270:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] sqd_regsub(rp, source, dest) ^ hsregex.c:1319:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] sqd_regerror(s) ^ clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c revcomp.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c a2m.c 30 warnings generated. clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c stopwatch.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c seqencode.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c sqio.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c shuffle.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c stack.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c sre_string.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c sre_random.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c stockholm.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c eps.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c dayhoff.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c squidcore.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c rk.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c ssi.c ssi.c:748:35: warning: comparison between pointer and integer ('unsigned long long' and 'void *') [-Wpointer-integer-compare] (unsigned long long) d_off == NULL? 0 : d_off->off.i64, ~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~ clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c afetch_main.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c alistat_main.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c sindex_main.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c revcomp_main.c sindex_main.c:175:58: warning: comparison of array 'sqinfo.desc' not equal to a null pointer is always true [-Wtautological-pointer-compare] if (do_pfamseq && sfp->format == SQFILE_FASTA && sqinfo.desc != NULL) { ~~~~~~~^~~~ ~~~~ 1 warning generated. clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c shuffle_main.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c seqsplit_main.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c seqstat_main.c 1 warning generated. clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c weight_main.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c compalign_main.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c translate_main.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c sfetch_main.c x86_64-pc-linux-gnu-ar rcv libsquid.a a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o a - a2m.o a - aligneval.o a - alignio.o a - clustal.o a - cluster.o a - dayhoff.o a - eps.o a - file.o a - getopt.o a - gki.o a - gsi.o a - hsregex.o a - iupac.o a - msa.o a - msf.o a - phylip.o a - revcomp.o a - rk.o a - selex.o a - seqencode.o a - shuffle.o a - sqerror.o a - sqio.o a - squidcore.o a - sre_ctype.o a - sre_math.o a - sre_random.o a - sre_string.o a - ssi.o a - stack.o a - stockholm.o a - stopwatch.o a - translate.o a - types.o a - vectorops.o a - weight.o clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c compstruct_main.c x86_64-pc-linux-gnu-ranlib libsquid.a clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DHAVE_CONFIG_H -o sreformat sreformat_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm chmod 644 libsquid.a clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DHAVE_CONFIG_H -o afetch afetch_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DHAVE_CONFIG_H -o alistat alistat_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DHAVE_CONFIG_H -o sindex sindex_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DHAVE_CONFIG_H -o revcomp revcomp_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DHAVE_CONFIG_H -o shuffle shuffle_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DHAVE_CONFIG_H -o seqsplit seqsplit_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DHAVE_CONFIG_H -o seqstat seqstat_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DHAVE_CONFIG_H -o weight weight_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DHAVE_CONFIG_H -o compalign compalign_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DHAVE_CONFIG_H -o translate translate_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DHAVE_CONFIG_H -o sfetch sfetch_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DHAVE_CONFIG_H -o compstruct compstruct_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o -lm make: Leaving directory '/var/tmp/portage/sci-biology/qrna-2.0.3c-r3/work/qrna-2.0.3c/squid02' make -j4 -C src make: Entering directory '/var/tmp/portage/sci-biology/qrna-2.0.3c-r3/work/qrna-2.0.3c/src' clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DASSERT -I../squid -c ../src/evolnullmodel.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DASSERT -I../squid -c ../src/qrnaversion.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DASSERT -I../squid -c ../src/evolemissions.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DASSERT -I../squid -c ../src/evolscorewithmodels.c ../src/evolscorewithmodels.c:422:3: error: call to undeclared function 'EvolScoreWithRNA'; ISO C99 and later do not support implicit function declarations [-Werror,-Wimplicit-function-declaration] EvolScoreWithRNA(ofp, sqinfoX, isegX, sqinfoY, isegY, gss, 0, win, emo... ^ ../src/evolscorewithmodels.c:422:3: note: did you mean 'ScoreWithRNA'? ../src/funcs.h:868:15: note: 'ScoreWithRNA' declared here extern void ScoreWithRNA(FILE *ofp, SQINFO sqinfoX, int *sX, SQINFO sq... ^ ../src/evolscorewithmodels.c:494:3: error: call to undeclared function 'EvolViterbiRNADiag'; ISO C99 and later do not support implicit function declarations [-Werror,-Wimplicit-function-declaration] EvolViterbiRNADiag(ofp, sqinfoX, isegX, sqinfoY, isegY, gss, 0, win, e... ^ ../src/evolscorewithmodels.c:494:3: note: did you mean 'ViterbiRNADiag'? ../src/funcs.h:792:24: note: 'ViterbiRNADiag' declared here extern void ViterbiRNADiag(FILE *ofp, SQINFO sqinfoX, int *se... ^ ../src/evolscorewithmodels.c:551:3: error: call to undeclared function 'EvolForwardRNADiag'; ISO C99 and later do not support implicit function declarations [-Werror,-Wimplicit-function-declaration] EvolForwardRNADiag(ofp, sqinfoX, isegX, sqinfoY, isegY, gss, 0, win, e... ^ ../src/evolscorewithmodels.c:551:3: note: did you mean 'ForwardRNADiag'? ../src/funcs.h:781:24: note: 'ForwardRNADiag' declared here extern void ForwardRNADiag(FILE *ofp, SQINFO sqinfoX, int *se... ^ ../src/evolscorewithmodels.c:627:7: error: call to undeclared function 'EvolViterbiRNADiag'; ISO C99 and later do not support implicit function declarations [-Werror,-Wimplicit-function-declaration] EvolViterbiRNADiag(ofp, sqinfoX, iseqX, sqinfoY, iseqY, gss, 0, le... ^ ../src/evolscorewithmodels.c:654:7: error: call to undeclared function 'EvolForwardRNADiag'; ISO C99 and later do not support implicit function declarations [-Werror,-Wimplicit-function-declaration] EvolForwardRNADiag(ofp, sqinfoX, iseqX, sqinfoY, iseqY, gss, 0, le... ^ 5 errors generated. make: *** [Makefile:194: evolscorewithmodels.o] Error 1 shuffle=4225741661 make: *** Waiting for unfinished jobs.... ../src/evolemissions.c:4804:3: warning: '/*' within block comment [-Wcomment] /* the diagonal */ ^ 1 warning generated. make: Leaving directory '/var/tmp/portage/sci-biology/qrna-2.0.3c-r3/work/qrna-2.0.3c/src' * ERROR: sci-biology/qrna-2.0.3c-r3::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/qrna-2.0.3c-r3::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/qrna-2.0.3c-r3::gentoo'`. * The complete build log is located at '/var/log/portage/sci-biology:qrna-2.0.3c-r3:20221204-082951.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/qrna-2.0.3c-r3/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/qrna-2.0.3c-r3/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/qrna-2.0.3c-r3/work/qrna-2.0.3c' * S: '/var/tmp/portage/sci-biology/qrna-2.0.3c-r3/work/qrna-2.0.3c'