sci-biology:qrna-2.0.3c-r3:20221204-082951.log

sci-biology:qrna-2.0.3c-r3:20221204-082951.log (text/plain), 53.65 KB, created by Toralf Förster on 2022-12-04 11:27:54 UTC

 * Package:    sci-biology/qrna-2.0.3c-r3:0
 * Repository: gentoo
 * Maintainer: [e-mail]
 * 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'