build.log

build.log (text/plain), 40.15 KB, created by Agostino Sarubbo on 2020-07-09 11:51:12 UTC

 * Package:    sci-biology/t-coffee-11.00-r2
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox


@@@@@ PLEASE PAY ATTENTION HERE!!! @@@@@
This information may help you to understand if this is a duplicate or if this bug exists after you pushed a fix;
This ebuild was merged at the following commit:
https://github.com/gentoo-mirror/gentoo/commit/0afe8006b19e05f59e53463eaadc1ed26dafd2be
@@@@@ END @@@@@

>>> Unpacking source...
>>> Unpacking T-COFFEE_distribution_Version_11.00.4466924.tar.gz to /var/tmp/portage/sci-biology/t-coffee-11.00-r2/work
>>> Source unpacked in /var/tmp/portage/sci-biology/t-coffee-11.00-r2/work
>>> Preparing source in /var/tmp/portage/sci-biology/t-coffee-11.00-r2/work/T-COFFEE_distribution_Version_11.00.4466924 ...
 * Applying t-coffee-11.00-mayhem.patch ...
 [ ok ]
 * Applying t-coffee-11.00-set_proper_dir_permissions.patch ...
 [ ok ]
 * Applying t-coffee-11.00-cxx11.patch ...
 [ ok ]
 * Applying t-coffee-11.00-gcc7.patch ...
 [ ok ]
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/t-coffee-11.00-r2/work/T-COFFEE_distribution_Version_11.00.4466924 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/t-coffee-11.00-r2/work/T-COFFEE_distribution_Version_11.00.4466924 ...
make -j2 V=1 V=1 CC=x86_64-pc-linux-gnu-clang++ 'CFLAGS=-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wno-write-strings -Wno-unused-result' -C t_coffee_source t_coffee 
make: Entering directory '/var/tmp/portage/sci-biology/t-coffee-11.00-r2/work/T-COFFEE_distribution_Version_11.00.4466924/t_coffee_source'
x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_domain_dp_drivers.deps -c -o dp_lib/util_domain_dp_drivers.o dp_lib/util_domain_dp_drivers.c
x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_dp_sim.deps -c -o dp_lib/util_dp_sim.o dp_lib/util_dp_sim.c
clang-10clang-10: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
In file included from dp_lib/util_domain_dp_drivers.c:34:
In file included from ./util_lib_header.hIn file included from dp_lib/util_dp_sim.c:33:
In file included from ./util_lib_header.h:30:
./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment]
/*                                                                   */
^
:30:
./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment]
/*                                                                   */
^
dp_lib/util_dp_sim.c:173:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register int d;
  ^~~~~~~~~
dp_lib/util_dp_sim.c:248:20: warning: empty parentheses interpreted as a
      function declaration [-Wvexing-parse]
  vertexptr findmax();                  /* return the largest score node */
                   ^~
dp_lib/util_dp_sim.c:248:20: note: replace parentheses with an initializer to
      declare a variable
  vertexptr findmax();                  /* return the largest score node */
                   ^~
                    = nullptr
dp_lib/util_dp_sim.c:481:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
{ register  int  i, j;                  /* row and column indices */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:481:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
{ register  int  i, j;                  /* row and column indices */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:482:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  c;                     /* best score at current point */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:483:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  f;                     /* best score ending with insertion */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:484:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  d;                     /* best score ending with deletion */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:485:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  p;                     /* best score at (i-1, j-1) */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:486:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  ci, cj;                /* end-point associated with c */ 
  ^~~~~~~~~
dp_lib/util_dp_sim.c:486:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  ci, cj;                /* end-point associated with c */ 
  ^~~~~~~~~
dp_lib/util_dp_sim.c:487:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  di, dj;                /* end-point associated with d */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:487:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  di, dj;                /* end-point associated with d */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:488:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  fi, fj;                /* end-point associated with f */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:488:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  fi, fj;                /* end-point associated with f */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:489:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  pi, pj;                /* end-point associated with p */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:489:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  pi, pj;                /* end-point associated with p */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:562:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
{ register  int  i, j;                  /* row and column indices */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:562:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
{ register  int  i, j;                  /* row and column indices */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:563:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  c;                     /* best score at current point */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:564:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  f;                     /* best score ending with insertion */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:565:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  d;                     /* best score ending with deletion */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:566:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  p;                     /* best score at (i-1, j-1) */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:567:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  ci, cj;                /* end-point associated with c */ 
  ^~~~~~~~~
dp_lib/util_dp_sim.c:567:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  ci, cj;                /* end-point associated with c */ 
  ^~~~~~~~~
dp_lib/util_dp_sim.c:568:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  di=0, dj=0;            /* end-point associated with d */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:568:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  di=0, dj=0;            /* end-point associated with d */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:569:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  fi, fj;                /* end-point associated with f */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:569:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  fi, fj;                /* end-point associated with f */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:570:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  pi, pj;                /* end-point associated with p */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:570:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  pi, pj;                /* end-point associated with p */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:572:16: warning: empty parentheses interpreted as a
      function declaration [-Wvexing-parse]
  int   addnode();                      /* function for inserting a node */
               ^~
dp_lib/util_dp_sim.c:572:16: note: replace parentheses with an initializer to
      declare a variable
  int   addnode();                      /* function for inserting a node */
               ^~
                = 0
dp_lib/util_dp_sim.c:786:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
{ register  int  i, j;                  /* row and column indices */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:786:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
{ register  int  i, j;                  /* row and column indices */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:787:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  c;                     /* best score at current point */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:788:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  f;                     /* best score ending with insertion */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:789:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  d;                     /* best score ending with deletion */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:790:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  p;                     /* best score at (i-1, j-1) */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:791:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  ci, cj;                /* end-point associated with c */ 
  ^~~~~~~~~
dp_lib/util_dp_sim.c:791:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  ci, cj;                /* end-point associated with c */ 
  ^~~~~~~~~
dp_lib/util_dp_sim.c:792:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  di, dj;                /* end-point associated with d */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:792:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  di, dj;                /* end-point associated with d */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:793:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  fi, fj;                /* end-point associated with f */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:793:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  fi, fj;                /* end-point associated with f */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:794:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  pi, pj;                /* end-point associated with p */
  ^~~~~~~~~
dp_lib/util_dp_sim.c:794:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register  int  pi, pj;                /* end-point associated with p */
  ^~~~~~~~~
dp_lib/util_domain_dp_drivers.c:590:16: warning: using thedp_lib/util_dp_sim.c:864:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register int i, j;
  ^~~~~~~~~
dp_lib/util_dp_sim.c:864:3: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register int i, j;
  ^~~~~~~~~
 result of an
      assignment as a condition without parentheses [-Wparentheses]
   while (entry=extract_entry (CL))
          ~~~~~^~~~~~~~~~~~~~~~~~~
dp_lib/util_dp_sim.cdp_lib/util_domain_dp_drivers.c:590:16: note: place parentheses around the
      assignment to silence this warning
:883:3: warning   while (entry=extract_entry (CL))
               ^
          (                       )
: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
  register int i;
dp_lib/util_domain_dp_drivers.c:590:16: note: use '==' to turn this assignment
      into an equality comparison
  ^~~~~~~~~
   while (entry=extract_entry (CL))
               ^
               ==
dp_lib/util_dp_sim.c:911:5: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int   i, j;
    ^~~~~~~~~
dp_lib/util_dp_sim.c:911:5: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int   i, j;
    ^~~~~~~~~
dp_lib/util_dp_sim.c:912:5: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int c, e, d, s;
    ^~~~~~~~~
dp_lib/util_dp_sim.c:912:5: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int c, e, d, s;
    ^~~~~~~~~
dp_lib/util_dp_sim.c:912:5: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int c, e, d, s;
    ^~~~~~~~~
dp_lib/util_dp_sim.c:912:5: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int c, e, d, s;
    ^~~~~~~~~
2 warnings generated.
x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_domain_dp.deps -c -o dp_lib/util_domain_dp.o dp_lib/util_domain_dp.c
clang-10: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
In file included from dp_lib/util_domain_dp.c:34:
In file included from ./util_lib_header.h:30:
./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment]
/*                                                                   */
^
1 warning generated.
x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/fsa_dp.deps -c -o dp_lib/fsa_dp.o dp_lib/fsa_dp.c
clang-10: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
In file included from dp_lib/fsa_dp.c:34:
In file included from ./util_lib_header.h:30:
./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment]
/*                                                                   */
^
55 warnings generated.
x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_dp_generic_fasta_nw.deps -c -o dp_lib/util_dp_generic_fasta_nw.o dp_lib/util_dp_generic_fasta_nw.c
clang-10: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
In file included from dp_lib/util_dp_generic_fasta_nw.c:35:
In file included from ./util_lib_header.h:30:
./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment]
/*                                                                   */
^
1 warning generated.
x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/pavie_dp.deps -c -o dp_lib/pavie_dp.o dp_lib/pavie_dp.c
clang-10: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
In file included from dp_lib/pavie_dp.c:34:
In file included from ./util_lib_header.h:30:
./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment]
/*                                                                   */
^
dp_lib/pavie_dp.c:1144:58: warning: operator '?:' has lower precedence than '*';
      '*' will be evaluated first [-Wparentheses]
          gap_inY= F[i-1][j]   + (CL->M[x[i-1]-'A'][gap]*(j==YL)?factor:1);
                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
dp_lib/pavie_dp.c:1144:58: note: place parentheses around the '*' expression to
      silence this warning
          gap_inY= F[i-1][j]   + (CL->M[x[i-1]-'A'][gap]*(j==YL)?factor:1);
                                                                ^
                                  (                             )
dp_lib/pavie_dp.c:1144:58: note: place parentheses around the '?:' expression to
      evaluate it first
          gap_inY= F[i-1][j]   + (CL->M[x[i-1]-'A'][gap]*(j==YL)?factor:1);
                                                                ^
                                                         (               )
dp_lib/pavie_dp.c:1145:58: warning: operator '?:' has lower precedence than '*';
      '*' will be evaluated first [-Wparentheses]
          gap_inX= F[i][j-1]   + (CL->M[y[j-1]-'A'][gap]*(i==XL)?factor:1);
                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
dp_lib/pavie_dp.c:1145:58: note: place parentheses around the '*' expression to
      silence this warning
          gap_inX= F[i][j-1]   + (CL->M[y[j-1]-'A'][gap]*(i==XL)?factor:1);
                                                                ^
                                  (                             )
dp_lib/pavie_dp.c:1145:58: note: place parentheses around the '?:' expression to
      evaluate it first
          gap_inX= F[i][j-1]   + (CL->M[y[j-1]-'A'][gap]*(i==XL)?factor:1);
                                                                ^
                                                         (               )
3 warnings generated.
x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_dp_mm_nw.deps -c -o dp_lib/util_dp_mm_nw.o dp_lib/util_dp_mm_nw.c
1 warning generated.
x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_dp_cdna_fasta_nw.deps -c -o dp_lib/util_dp_cdna_fasta_nw.o dp_lib/util_dp_cdna_fasta_nw.c
clang-10: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
clang-10: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
In file included from dp_lib/util_dp_cdna_fasta_nw.c:34:
In file included from ./util_lib_header.h:30:
./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment]
/*                                                                   */
^
In file included from dp_lib/util_dp_mm_nw.c:34:
In file included from ./util_lib_header.h:30:
./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment]
/*                                                                   */
^
dp_lib/util_dp_cdna_fasta_nw.c:288:132: warning: operator '?:' has lower
      precedence than '+'; '+' will be evaluated first [-Wparentheses]
  ...0+(M->F_TG_MODE==0)?M->f_gop:0;
     ~~~~~~~~~~~~~~~~~~~^
dp_lib/util_dp_cdna_fasta_nw.c:288:132: note: place parentheses around the '+'
      expression to silence this warning
  ...0+(M->F_TG_MODE==0)?M->f_gop:0;
                        ^
     (                  )
dp_lib/util_dp_cdna_fasta_nw.c:288:132: note: place parentheses around the '?:'
      expression to evaluate it first
  ...(M->F_TG_MODE==0)?M->f_gop:0;
                      ^
     (                           )
dp_lib/util_dp_cdna_fasta_nw.c:290:132: warning: operator '?:' has lower
      precedence than '+'; '+' will be evaluated first [-Wparentheses]
  ...0+(M->F_TG_MODE==0)?M->f_gop:0;
     ~~~~~~~~~~~~~~~~~~~^
dp_lib/util_dp_cdna_fasta_nw.c:290:132: note: place parentheses around the '+'
      expression to silence this warning
  ...0+(M->F_TG_MODE==0)?M->f_gop:0;
                        ^
     (                  )
dp_lib/util_dp_cdna_fasta_nw.c:290:132: note: place parentheses around the '?:'
      expression to evaluate it first
  ...(M->F_TG_MODE==0)?M->f_gop:0;
                      ^
     (                           )
1 warning generated.
x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_dp_drivers.deps -c -o dp_lib/util_dp_drivers.o dp_lib/util_dp_drivers.c
clang-10: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
In file included from dp_lib/util_dp_drivers.c:34:
In file included from ./util_lib_header.h:30:
./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment]
/*                                                                   */
^
dp_lib/util_dp_drivers.c:178:14: warning: address of array 'M->prfmode' will
      always evaluate to 'true' [-Wpointer-bool-conversion]
      if (M->prfmode && M->prfmode[0])mode=M->prfmode;
          ~~~^~~~~~~ ~~
dp_lib/util_dp_drivers.c:1080:6: warning: ignoring return value of function
      declared with pure attribute [-Wunused-value]
            atoi(strtok (seq,SEPARATORS));
            ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~
dp_lib/util_dp_drivers.c:1108:6: warning: ignoring return value of function
      declared with pure attribute [-Wunused-value]
            atoi(strtok (seq,SEPARATORS));
            ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~
dp_lib/util_dp_drivers.c:1149:4: warning: ignoring return value of function
      declared with pure attribute [-Wunused-value]
          atoi(strtok (seq,SEPARATORS));
          ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~
dp_lib/util_dp_drivers.c:1280:2: warning: ignoring return value of function
      declared with pure attribute [-Wunused-value]
        atoi(strtok (seq,SEPARATORS));
        ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~
dp_lib/util_dp_drivers.c:1328:10: warning: address of array 'M->param' will
      always evaluate to 'true' [-Wpointer-bool-conversion]
        if ( M->param)
        ~~   ~~~^~~~~
dp_lib/util_dp_drivers.c:1445:3: warning: ignoring return value of function
      declared with pure attribute [-Wunused-value]
  atoi(strtok (seq,SEPARATORS));
  ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~
dp_lib/util_dp_drivers.c:1451:11: warning: address of array 'M->param' will
      always evaluate to 'true' [-Wpointer-bool-conversion]
  if ( M->param)
  ~~   ~~~^~~~~
dp_lib/util_dp_drivers.c:1462:15: warning: using the result of an assignment as
      a condition without parentheses [-Wparentheses]
      if (A[a]=seq2R_template_profile(CL->S,s[a]))
          ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dp_lib/util_dp_drivers.c:1462:15: note: place parentheses around the assignment
      to silence this warning
      if (A[a]=seq2R_template_profile(CL->S,s[a]))
              ^
          (                                      )
dp_lib/util_dp_drivers.c:1462:15: note: use '==' to turn this assignment into an
      equality comparison
      if (A[a]=seq2R_template_profile(CL->S,s[a]))
              ^
              ==
dp_lib/util_dp_drivers.c:1581:3: warning: ignoring return value of function
      declared with pure attribute [-Wunused-value]
  atoi(strtok (seq,SEPARATORS));
  ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~
dp_lib/util_dp_drivers.c:1587:11: warning: address of array 'M->param' will
      always evaluate to 'true' [-Wpointer-bool-conversion]
  if ( M->param)
  ~~   ~~~^~~~~
dp_lib/util_dp_drivers.c:1717:4: warning: ignoring return value of function
      declared with pure attribute [-Wunused-value]
          atoi(strtok (seq,SEPARATORS));
          ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~
dp_lib/util_dp_drivers.c:1774:4: warning: ignoring return value of function
      declared with pure attribute [-Wunused-value]
          atoi(strtok (seq,SEPARATORS));
          ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~
dp_lib/util_dp_drivers.c:1906:4: warning: ignoring return value of function
      declared with pure attribute [-Wunused-value]
          atoi(strtok (seq,SEPARATORS));
          ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~
dp_lib/util_dp_drivers.c:1981:4: warning: ignoring return value of function
      declared with pure attribute [-Wunused-value]
          atoi(strtok (seq,SEPARATORS));
          ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~
dp_lib/util_dp_drivers.c:2051:13: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
            register int a;
            ^~~~~~~~~
dp_lib/util_dp_drivers.c:2073:6: warning: ignoring return value of function
      declared with pure attribute [-Wunused-value]
            atoi(strtok (seq,SEPARATORS));
            ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~
dp_lib/util_dp_drivers.c:2256:2: warning: ignoring return value of function
      declared with pure attribute [-Wunused-value]
        atoi(strtok (seq,SEPARATORS));
        ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~
dp_lib/util_dp_drivers.c:2950:19: warning: address of array 'CL->tree_mode' will
      always evaluate to 'true' [-Wpointer-bool-conversion]
        if ( !CL || !CL->tree_mode || !CL->tree_mode[0])
                    ~~~~~^~~~~~~~~
3 warnings generated.
x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_dp_suboptimal_nw.deps -c -o dp_lib/util_dp_suboptimal_nw.o dp_lib/util_dp_suboptimal_nw.c
dp_lib/util_dp_drivers.c:4295:22: warning: address of array 'CL->dp_mode' will
      always evaluate to 'true' [-Wpointer-bool-conversion]
      if ( CL && CL->dp_mode && strstr (CL->dp_mode, "collapse"))dump_co...
              ~~ ~~~~^~~~~~~
dp_lib/util_dp_drivers.c:4298:22: warning: address of array 'CL->dp_mode' will
      always evaluate to 'true' [-Wpointer-bool-conversion]
      if ( CL && CL->dp_mode && strstr (CL->dp_mode, "collapse"))
              ~~ ~~~~^~~~~~~
dp_lib/util_dp_drivers.c:4383:38: warning: logical not is only applied to the
      left hand side of this comparison [-Wlogical-not-parentheses]
  if ((!get_int_variable ("n_core")||!get_int_variable ("n_core")>1) && ...
                                     ^                           ~
dp_lib/util_dp_drivers.c:4383:38: note: add parentheses after the '!' to
      evaluate the comparison first
  if ((!get_int_variable ("n_core")||!get_int_variable ("n_core")>1) && ...
                                     ^
                                      (                            )
dp_lib/util_dp_drivers.c:4383:38: note: add parentheses around left hand side
      expression to silence this warning
  if ((!get_int_variable ("n_core")||!get_int_variable ("n_core")>1) && ...
                                     ^
                                     (                           )
dp_lib/util_dp_drivers.c:4383:66: warning: result of comparison of constant 1
      with expression of type 'bool' is always false
      [-Wtautological-constant-compare]
  if ((!get_int_variable ("n_core")||!get_int_variable ("n_core")>1) && ...
                                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
clang-10: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
In file included from dp_lib/util_dp_suboptimal_nw.c:34:
In file included from ./util_lib_header.h:30:
./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment]
/*                                                                   */
^
1 warning generated.
x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_dp_gotoh_sw.deps -c -o dp_lib/util_dp_gotoh_sw.o dp_lib/util_dp_gotoh_sw.c
clang-10: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
In file included from dp_lib/util_dp_gotoh_sw.c:34:
In file included from ./util_lib_header.h:30:
./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment]
/*                                                                   */
^
1 warning generated.
x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/evaluate.deps -c -o dp_lib/evaluate.o dp_lib/evaluate.c
clang-10: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
24 warnings generated.
x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_graph_maln.deps -c -o dp_lib/util_graph_maln.o dp_lib/util_graph_maln.c
clang-10: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
In file included from dp_lib/evaluate.c:35:
In file included from ./util_lib_header.h:30:
./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment]
/*                                                                   */
^
In file included from dp_lib/util_graph_maln.c:34:
In file included from ./util_lib_header.h:30:
./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment]
/*                                                                   */
^
dp_lib/evaluate.c:2909:134: warning: format specifies type 'double' but the
      argument has type 'int' [-Wformat]
  ...%3.2f min_size: %3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1...
     ~~~~~                                                                                ^~~
     %3.2d
dp_lib/evaluate.c:2909:138: warning: format specifies type 'int' but the
      argument has type 'float' [-Wformat]
  ...%3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th...
     ~~~                                                                      ^~~~~~~
     %3f
dp_lib/evaluate.c:2909:147: warning: format specifies type 'double' but the
      argument has type 'int' [-Wformat]
  ...%.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min...
     ~~~~                                                                   ^~~~~~~~
     %.3d
dp_lib/evaluate.c:2909:157: warning: format specifies type 'int' but the
      argument has type 'float' [-Wformat]
  ...%3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min, min_aa, ...
     ~~~                                                             ^~~~~~
     %3f
dp_lib/evaluate.c:3850:14: warning: self-comparison always evaluates to false
      [-Wtautological-compare]
  if (prf1[0]!=prf1[0]){fprintf ( stderr, "\nERROR: Inconsistent number ...
             ^
1 warning generated.
x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/evaluate_for_domain.deps -c -o dp_lib/evaluate_for_domain.o dp_lib/evaluate_for_domain.c
clang-10: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
In file included from dp_lib/evaluate_for_domain.c:34:
In file included from ./util_lib_header.h:30:
./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment]
/*                                                                   */
^
1 warning generated.
x86_64-pc-linux-gnu-clang++ -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/evaluate_dirichlet.deps -c -o dp_lib/evaluate_dirichlet.o dp_lib/evaluate_dirichlet.c
clang-10: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
In file included from dp_lib/evaluate_dirichlet.c:34:
In file included from ./util_lib_header.h:30:
./util_lib/util.h:54:1: warning: '/*' within block comment [-Wcomment]
/*                                                                   */
^
dp_lib/evaluate_dirichlet.c:543:8: error: 'lgamma_r' is missing exception
      specification 'throw()'
double lgamma_r(double x, int *signgamp)
       ^
                                         throw()
./dp_lib/evaluate_dirichlet.h:57:8: note: previous declaration is here
double lgamma_r(double x, int *signgamp);
       ^
1 warning and 1 error generated.
make: *** [makefile:11: dp_lib/evaluate_dirichlet.o] Error 1
make: *** Waiting for unfinished jobs....
6 warnings generated.
make: Leaving directory '/var/tmp/portage/sci-biology/t-coffee-11.00-r2/work/T-COFFEE_distribution_Version_11.00.4466924/t_coffee_source'
 * ERROR: sci-biology/t-coffee-11.00-r2::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/t-coffee-11.00-r2::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/t-coffee-11.00-r2::gentoo'`.
 * The complete build log is located at '/var/log/emerge-log/build/sci-biology/t-coffee-11.00-r2:20200708-182332.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/t-coffee-11.00-r2/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/t-coffee-11.00-r2/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/t-coffee-11.00-r2/work/T-COFFEE_distribution_Version_11.00.4466924'
 * S: '/var/tmp/portage/sci-biology/t-coffee-11.00-r2/work/T-COFFEE_distribution_Version_11.00.4466924'



emerge --info:
Portage 2.3.103 (python 3.7.8-final-0, default/linux/amd64/17.1, gcc-10.1.0, glibc-2.31-r5, 5.4.0-1015-aws x86_64)
=================================================================
System uname: Linux-5.4.0-1015-aws-x86_64-AMD_EPYC_7571-with-gentoo-2.7
KiB Mem:     7895548 total,   2137588 free
KiB Swap:          0 total,         0 free
Timestamp of repository gentoo: Thu, 09 Jul 2020 10:35:22 +0000
sh bash 5.0_p17
ld GNU ld (Gentoo 2.34 p4) 2.34.0
app-shells/bash:          5.0_p17::gentoo
dev-lang/perl:            5.30.3-r2::gentoo
dev-lang/python:          2.7.18::gentoo, 3.7.8-r1::gentoo, 3.8.3-r1::gentoo, 3.9.0_beta4::gentoo
dev-util/cmake:           3.18.0_rc3::gentoo
sys-apps/baselayout:      2.7::gentoo
sys-apps/openrc:          0.42.1::gentoo
sys-apps/sandbox:         2.20::gentoo
sys-devel/autoconf:       2.69-r5::gentoo
sys-devel/automake:       1.16.2::gentoo
sys-devel/binutils:       2.34-r1::gentoo
sys-devel/gcc:            10.1.0-r2::gentoo
sys-devel/gcc-config:     2.3.1::gentoo
sys-devel/libtool:        2.4.6-r6::gentoo
sys-devel/make:           4.3::gentoo
sys-kernel/linux-headers: 5.7::gentoo (virtual/os-headers)
sys-libs/glibc:           2.31-r5::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: -1000
    sync-rsync-verify-max-age: 24
    sync-rsync-verify-jobs: 1
    sync-rsync-verify-metamanifest: yes
    sync-rsync-extra-opts: 

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CC="x86_64-pc-linux-gnu-clang"
CFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXX="x86_64-pc-linux-gnu-clang++"
CXXFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS="--with-bdeps=y --binpkg-respect-use=y -1 -b -k"
ENV_UNSET="DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN GOPATH PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR"
FCFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg collision-protect config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign split-log strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="C.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -fuse-ld=lld -Wl,--defsym=__gentoo_check_ldflags__=0"
MAKEOPTS="-j2 V=1"
PKGDIR="/root/.packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git"
PORTAGE_TMPDIR="/var/tmp"
USE="acl amd64 berkdb bzip2 cli crypt dri fortran gdbm iconv ipv6 libtirpc multilib ncurses nls nptl openmp pam pcre readline seccomp split-usr ssl tcpd unicode xattr zlib" ABI_X86="64" ADA_TARGET="gnat_2018" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="karbon sheets words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext sse sse2" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="libinput" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-2" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_7" PYTHON_TARGETS="python2_7 python3_7" RUBY_TARGETS="ruby25" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa dummy v4l" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account"
Unset:  CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS