sci-biology:t-coffee-11.00-r3:20230223-070421.log

sci-biology:t-coffee-11.00-r3:20230223-070421.log (text/plain), 34.34 KB, created by Toralf Förster on 2023-02-23 17:59:04 UTC

 * Package:    sci-biology/t-coffee-11.00-r3:0
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_musl kernel_linux userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox

>>> Unpacking source...
>>> Unpacking T-COFFEE_distribution_Version_11.00.4466924.tar.gz to /var/tmp/portage/sci-biology/t-coffee-11.00-r3/work
>>> Source unpacked in /var/tmp/portage/sci-biology/t-coffee-11.00-r3/work
>>> Preparing source in /var/tmp/portage/sci-biology/t-coffee-11.00-r3/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 ]
 * Applying t-coffee-11.00-makefile.patch ...
 [ ok ]
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/t-coffee-11.00-r3/work/T-COFFEE_distribution_Version_11.00.4466924 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/t-coffee-11.00-r3/work/T-COFFEE_distribution_Version_11.00.4466924 ...
make -j5 -C t_coffee_source t_coffee 
make: Entering directory '/var/tmp/portage/sci-biology/t-coffee-11.00-r3/work/T-COFFEE_distribution_Version_11.00.4466924/t_coffee_source'
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wno-write-strings -Wno-unused-result  -I. -MD -MF t_coffee_lib/t_coffee.deps -c -o t_coffee_lib/t_coffee.o t_coffee_lib/t_coffee.c
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wno-write-strings -Wno-unused-result  -I. -MD -MF km_coffee/km_coffee.deps -c -o km_coffee/km_coffee.o km_coffee/km_coffee.c
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wno-write-strings -Wno-unused-result  -I. -MD -MF km_coffee/kmeans.deps -c -o km_coffee/kmeans.o km_coffee/kmeans.c
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wno-write-strings -Wno-unused-result  -I. -MD -MF km_coffee/km_util.deps -c -o km_coffee/km_util.o km_coffee/km_util.c
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wno-write-strings -Wno-unused-result  -I. -MD -MF km_coffee/classes.deps -c -o km_coffee/classes.o km_coffee/classes.c
km_coffee/km_util.c: In function 'char* my_make_temp_dir(char*, char*)':
km_coffee/km_util.c:96:69: warning: format '%s' expects a matching 'char*' argument [-Wformat=]
   96 |         fprintf(stderr, "This error was caused by '%s' in '%s'\n", function);
      |                                                            ~^
      |                                                             |
      |                                                             char*

x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wno-write-strings -Wno-unused-result  -I. -MD -MF km_coffee/Vector.deps -c -o km_coffee/Vector.o km_coffee/Vector.c
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wno-write-strings -Wno-unused-result  -I. -MD -MF km_coffee/Stack.deps -c -o km_coffee/Stack.o km_coffee/Stack.c
t_coffee_lib/t_coffee.c: In function 'char** km_coffee(int, char**)':
t_coffee_lib/t_coffee.c:6527:1: warning: no return statement in function returning non-void [-Wreturn-type]
 6527 | }
      | ^
t_coffee_lib/t_coffee.c: In function 'Alignment* km_align_seq_slow(char*, Alignment*, int, char**, int, int)':
t_coffee_lib/t_coffee.c:6766:1: warning: control reaches end of non-void function [-Wreturn-type]
 6766 | }
      | ^
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wno-write-strings -Wno-unused-result  -I. -MD -MF fastal/iteration.deps -c -o fastal/iteration.o fastal/iteration.c
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wno-write-strings -Wno-unused-result  -I. -MD -MF fastal/scoring.deps -c -o fastal/scoring.o fastal/scoring.c
km_coffee/Vector.c: In function 'void print_vecs(VectorSet*, char*)':
km_coffee/Vector.c:869:34: warning: format '%i' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=]
  869 |                 fprintf(out_F, "%i ", i);
      |                                 ~^    ~
      |                                  |    |
      |                                  int  size_t {aka long unsigned int}
      |                                 %li
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wno-write-strings -Wno-unused-result  -I. -MD -MF fastal/fastal_opt_parsing.deps -c -o fastal/fastal_opt_parsing.o fastal/fastal_opt_parsing.c
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wno-write-strings -Wno-unused-result  -I. -MD -MF fastal/diagonal.deps -c -o fastal/diagonal.o fastal/diagonal.c
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wno-write-strings -Wno-unused-result  -I. -MD -MF fastal/tree.deps -c -o fastal/tree.o fastal/tree.c
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wno-write-strings -Wno-unused-result  -I. -MD -MF fastal/parttree.deps -c -o fastal/parttree.o fastal/parttree.c
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wno-write-strings -Wno-unused-result  -I. -MD -MF fastal/fastal.deps -c -o fastal/fastal.o fastal/fastal.c
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wno-write-strings -Wno-unused-result  -I. -MD -MF dev_lib/dev1.deps -c -o dev_lib/dev1.o dev_lib/dev1.c
fastal/parttree.c: In function 'void makepointtable_fast(int*, int, int, int)':
fastal/parttree.c:757:23: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  757 |         register int *p;
      |                       ^
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wno-write-strings -Wno-unused-result  -I. -MD -MF dp_lib/showpair.deps -c -o dp_lib/showpair.o dp_lib/showpair.c
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wno-write-strings -Wno-unused-result  -I. -MD -MF dp_lib/evaluate.deps -c -o dp_lib/evaluate.o dp_lib/evaluate.c
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
dp_lib/evaluate.c: In function 'Alignment* msa2distances(Alignment*, Constraint_list*, float, float, int)':
dp_lib/evaluate.c:2909:67: warning: format '%f' expects argument of type 'double', but argument 4 has type 'int' [-Wformat=]
 2909 |             fprintf (stdout, "##Groups s1: %20s std_th: %3.2f min_size: %3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min, min_aa, gsize);
      |                                                         ~~~~^                                                                                ~~~
      |                                                             |                                                                                 |
      |                                                             double                                                                            int
      |                                                         %3.2d
dp_lib/evaluate.c:2909:81: warning: format '%d' expects argument of type 'int', but argument 5 has type 'double' [-Wformat=]
 2909 | rintf (stdout, "##Groups s1: %20s std_th: %3.2f min_size: %3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min, min_aa, gsize);
      |                                                           ~~^                                                                      ~~~~~~~
      |                                                             |                                                                      |
      |                                                             int                                                                    double
      |                                                           %3f
dp_lib/evaluate.c:2909:93: warning: format '%f' expects argument of type 'double', but argument 6 has type 'int' [-Wformat=]
 2909 | t, "##Groups s1: %20s std_th: %3.2f min_size: %3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min, min_aa, gsize);
      |                                                          ~~~^                                                                   ~~~~~~~~
      |                                                             |                                                                   |
      |                                                             double                                                              int
      |                                                          %.3d
dp_lib/evaluate.c:2909:109: warning: format '%d' expects argument of type 'int', but argument 7 has type 'double' [-Wformat=]
 2909 |  %20s std_th: %3.2f min_size: %3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min, min_aa, gsize);
      |                                                           ~~^                                                             ~~~~~~
      |                                                             |                                                             |
      |                                                             int                                                           double
      |                                                           %3f
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wno-write-strings -Wno-unused-result  -I. -MD -MF dp_lib/evaluate_for_struc.deps -c -o dp_lib/evaluate_for_struc.o dp_lib/evaluate_for_struc.c
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wno-write-strings -Wno-unused-result  -I. -MD -MF dp_lib/CUSTOM_evaluate_for_struc.deps -c -o dp_lib/CUSTOM_evaluate_for_struc.o dp_lib/CUSTOM_evaluate_for_struc.c
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
dp_lib/util_dp_drivers.c: In function 'Constraint_list* sap_pair(char*, char*, Constraint_list*)':
dp_lib/util_dp_drivers.c:2051:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
 2051 |             register int a;
      |                          ^
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wno-write-strings -Wno-unused-result  -I. -MD -MF dp_lib/util_dp_est.deps -c -o dp_lib/util_dp_est.o dp_lib/util_dp_est.c
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wno-write-strings -Wno-unused-result  -I. -MD -MF dp_lib/util_dp_fasta_sw.deps -c -o dp_lib/util_dp_fasta_sw.o dp_lib/util_dp_fasta_sw.c
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wno-write-strings -Wno-unused-result  -I. -MD -MF dp_lib/util_dp_fasta_nw.deps -c -o dp_lib/util_dp_fasta_nw.o dp_lib/util_dp_fasta_nw.c
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
dp_lib/util_dp_fasta_nw.c: In function 'int* makepointtable(int*, int*, int)':
dp_lib/util_dp_fasta_nw.c:157:17: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  157 |   register int *p;
      |                 ^
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wno-write-strings -Wno-unused-result  -I. -MD -MF dp_lib/util_dp_gotoh_nw.deps -c -o dp_lib/util_dp_gotoh_nw.o dp_lib/util_dp_gotoh_nw.c
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
dp_lib/util_dp_sim.c: In function 'int addnode(int, int, int, int, int, int, int)':
dp_lib/util_dp_sim.c:173:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  173 |   register int d;
      |                ^
dp_lib/util_dp_sim.c: In function 'int sim_pair_wise_lalign(Alignment*, int*, int**, Constraint_list*)':
dp_lib/util_dp_sim.c:248:20: warning: empty parentheses were disambiguated as a function declaration [-Wvexing-parse]
  248 |   vertexptr findmax();                  /* return the largest score node */
      |                    ^~
dp_lib/util_dp_sim.c:248:20: note: remove parentheses to default-initialize a variable
  248 |   vertexptr findmax();                  /* return the largest score node */
      |                    ^~
      |                    --
dp_lib/util_dp_sim.c:248:20: note: or replace parentheses with braces to value-initialize a variable
dp_lib/util_dp_sim.c: In function 'int big_pass(int*, int*, int, int, int, int)':
dp_lib/util_dp_sim.c:481:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  481 | { register  int  i, j;                  /* row and column indices */
      |                  ^
dp_lib/util_dp_sim.c:481:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  481 | { register  int  i, j;                  /* row and column indices */
      |                     ^
dp_lib/util_dp_sim.c:482:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  482 |   register  int  c;                     /* best score at current point */
      |                  ^
dp_lib/util_dp_sim.c:483:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  483 |   register  int  f;                     /* best score ending with insertion */
      |                  ^
dp_lib/util_dp_sim.c:484:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  484 |   register  int  d;                     /* best score ending with deletion */
      |                  ^
dp_lib/util_dp_sim.c:485:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  485 |   register  int  p;                     /* best score at (i-1, j-1) */
      |                  ^
dp_lib/util_dp_sim.c:486:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  486 |   register  int  ci, cj;                /* end-point associated with c */
      |                  ^~
dp_lib/util_dp_sim.c:486:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  486 |   register  int  ci, cj;                /* end-point associated with c */
      |                      ^~
dp_lib/util_dp_sim.c:487:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  487 |   register  int  di, dj;                /* end-point associated with d */
      |                  ^~
dp_lib/util_dp_sim.c:487:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  487 |   register  int  di, dj;                /* end-point associated with d */
      |                      ^~
dp_lib/util_dp_sim.c:488:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  488 |   register  int  fi, fj;                /* end-point associated with f */
      |                  ^~
dp_lib/util_dp_sim.c:488:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  488 |   register  int  fi, fj;                /* end-point associated with f */
      |                      ^~
dp_lib/util_dp_sim.c:489:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  489 |   register  int  pi, pj;                /* end-point associated with p */
      |                  ^~
dp_lib/util_dp_sim.c:489:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  489 |   register  int  pi, pj;                /* end-point associated with p */
      |                      ^~
dp_lib/util_dp_sim.c: In function 'int locate(int*, int*, int)':
dp_lib/util_dp_sim.c:562:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  562 | { register  int  i, j;                  /* row and column indices */
      |                  ^
dp_lib/util_dp_sim.c:562:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  562 | { register  int  i, j;                  /* row and column indices */
      |                     ^
dp_lib/util_dp_sim.c:563:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  563 |   register  int  c;                     /* best score at current point */
      |                  ^
dp_lib/util_dp_sim.c:564:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  564 |   register  int  f;                     /* best score ending with insertion */
      |                  ^
dp_lib/util_dp_sim.c:565:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  565 |   register  int  d;                     /* best score ending with deletion */
      |                  ^
dp_lib/util_dp_sim.c:566:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  566 |   register  int  p;                     /* best score at (i-1, j-1) */
      |                  ^
dp_lib/util_dp_sim.c:567:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  567 |   register  int  ci, cj;                /* end-point associated with c */
      |                  ^~
dp_lib/util_dp_sim.c:567:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  567 |   register  int  ci, cj;                /* end-point associated with c */
      |                      ^~
dp_lib/util_dp_sim.c:568:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  568 |   register  int  di=0, dj=0;            /* end-point associated with d */
      |                  ^~
dp_lib/util_dp_sim.c:568:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  568 |   register  int  di=0, dj=0;            /* end-point associated with d */
      |                        ^~
dp_lib/util_dp_sim.c:569:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  569 |   register  int  fi, fj;                /* end-point associated with f */
      |                  ^~
dp_lib/util_dp_sim.c:569:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  569 |   register  int  fi, fj;                /* end-point associated with f */
      |                      ^~
dp_lib/util_dp_sim.c:570:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  570 |   register  int  pi, pj;                /* end-point associated with p */
      |                  ^~
dp_lib/util_dp_sim.c:570:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  570 |   register  int  pi, pj;                /* end-point associated with p */
      |                      ^~
dp_lib/util_dp_sim.c:572:16: warning: empty parentheses were disambiguated as a function declaration [-Wvexing-parse]
  572 |   int   addnode();                      /* function for inserting a node */
      |                ^~
dp_lib/util_dp_sim.c:572:16: note: remove parentheses to default-initialize a variable
  572 |   int   addnode();                      /* function for inserting a node */
      |                ^~
      |                --
dp_lib/util_dp_sim.c:572:16: note: or replace parentheses with braces to value-initialize a variable
dp_lib/util_dp_sim.c: In function 'int small_pass(int*, int*, int, int)':
dp_lib/util_dp_sim.c:786:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  786 | { register  int  i, j;                  /* row and column indices */
      |                  ^
dp_lib/util_dp_sim.c:786:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  786 | { register  int  i, j;                  /* row and column indices */
      |                     ^
dp_lib/util_dp_sim.c:787:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  787 |   register  int  c;                     /* best score at current point */
      |                  ^
dp_lib/util_dp_sim.c:788:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  788 |   register  int  f;                     /* best score ending with insertion */
      |                  ^
dp_lib/util_dp_sim.c:789:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  789 |   register  int  d;                     /* best score ending with deletion */
      |                  ^
dp_lib/util_dp_sim.c:790:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  790 |   register  int  p;                     /* best score at (i-1, j-1) */
      |                  ^
dp_lib/util_dp_sim.c:791:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  791 |   register  int  ci, cj;                /* end-point associated with c */
      |                  ^~
dp_lib/util_dp_sim.c:791:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  791 |   register  int  ci, cj;                /* end-point associated with c */
      |                      ^~
dp_lib/util_dp_sim.c:792:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  792 |   register  int  di, dj;                /* end-point associated with d */
      |                  ^~
dp_lib/util_dp_sim.c:792:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  792 |   register  int  di, dj;                /* end-point associated with d */
      |                      ^~
dp_lib/util_dp_sim.c:793:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  793 |   register  int  fi, fj;                /* end-point associated with f */
      |                  ^~
dp_lib/util_dp_sim.c:793:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  793 |   register  int  fi, fj;                /* end-point associated with f */
      |                      ^~
dp_lib/util_dp_sim.c:794:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  794 |   register  int  pi, pj;                /* end-point associated with p */
      |                  ^~
dp_lib/util_dp_sim.c:794:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  794 |   register  int  pi, pj;                /* end-point associated with p */
      |                      ^~
dp_lib/util_dp_sim.c: In function 'SIM_NODE* findmax()':
dp_lib/util_dp_sim.c:864:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  864 |   register int i, j;
      |                ^
dp_lib/util_dp_sim.c:864:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  864 |   register int i, j;
      |                   ^
dp_lib/util_dp_sim.c: In function 'int no_cross()':
dp_lib/util_dp_sim.c:883:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  883 |   register int i;
      |                ^
dp_lib/util_dp_sim.c: In function 'int diff_sim(int*, int*, int, int, int, int)':
dp_lib/util_dp_sim.c:911:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  911 |     register int   i, j;
      |                    ^
dp_lib/util_dp_sim.c:911:23: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  911 |     register int   i, j;
      |                       ^
dp_lib/util_dp_sim.c:912:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  912 |     register int c, e, d, s;
      |                  ^
dp_lib/util_dp_sim.c:912:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  912 |     register int c, e, d, s;
      |                     ^
dp_lib/util_dp_sim.c:912:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  912 |     register int c, e, d, s;
      |                        ^
dp_lib/util_dp_sim.c:912:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  912 |     register int c, e, d, s;
      |                           ^
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wno-write-strings -Wno-unused-result  -I. -MD -MF dp_lib/util_dp_ssec_pwaln.deps -c -o dp_lib/util_dp_ssec_pwaln.o dp_lib/util_dp_ssec_pwaln.c
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wno-write-strings -Wno-unused-result  -I. -MD -MF dp_lib/util_dp_clean_maln.deps -c -o dp_lib/util_dp_clean_maln.o dp_lib/util_dp_clean_maln.c
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -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
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wno-write-strings -Wno-unused-result  -I. -MD -MF io_lib/tree_util.deps -c -o io_lib/tree_util.o io_lib/tree_util.c
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wno-write-strings -Wno-unused-result  -I. -MD -MF io_lib/pb_util_read_seq_util.deps -c -o io_lib/pb_util_read_seq_util.o io_lib/pb_util_read_seq_util.c
io_lib/pb_util_read_seq_util.c: In function 'void* ckalloc(size_t)':
io_lib/pb_util_read_seq_util.c:68:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
   68 |         register void *ret;
      |                        ^~~
io_lib/pb_util_read_seq_util.c: In function 'void* ckvrealloc(void*, size_t)':
io_lib/pb_util_read_seq_util.c:91:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
   91 |         register void *ret;
      |                        ^~~
io_lib/pb_util_read_seq_util.c: In function 'char* rtrim(char*)':
io_lib/pb_util_read_seq_util.c:191:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  191 |         register int p;
      |                      ^
io_lib/pb_util_read_seq_util.c: In function 'char* upstr(char*)':
io_lib/pb_util_read_seq_util.c:240:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  240 |         register char *s = str;
      |                        ^
io_lib/pb_util_read_seq_util.c: In function 'char* lowstr(char*)':
io_lib/pb_util_read_seq_util.c:258:24: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  258 |         register char *s = str;
      |                        ^
io_lib/pb_util_read_seq_util.c: In function 'void get_path(char*, char*)':
io_lib/pb_util_read_seq_util.c:356:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  356 |         register int i;
      |                      ^
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wno-write-strings -Wno-unused-result  -I. -MD -MF io_lib/pb_util_read_sequence.deps -c -o io_lib/pb_util_read_sequence.o io_lib/pb_util_read_sequence.c
io_lib/tree_util.c: In function 'Alignment* phylotrim(Alignment*, NT_node, char*, char*, char*)':
io_lib/tree_util.c:1299:1: warning: no return statement in function returning non-void [-Wreturn-type]
 1299 | }
      | ^
io_lib/tree_util.c: In function 'tnode* no_rec_free_tree(NT_node)':
io_lib/tree_util.c:2317:1: warning: no return statement in function returning non-void [-Wreturn-type]
 2317 | }
      | ^
x86_64-gentoo-linux-musl-g++ -pipe -march=native -fno-diagnostics-color -O2 -Wno-write-strings -Wno-unused-result  -I. -MD -MF io_lib/io_func.deps -c -o io_lib/io_func.o io_lib/io_func.c
io_lib/pb_util_read_sequence.c: In function 'void fill_chartab()':
io_lib/pb_util_read_sequence.c:79:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
   79 |         register int i;
      |                      ^
io_lib/pb_util_read_sequence.c:80:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
   80 |         register int c;
      |                      ^
io_lib/tree_util.c: In function 'int node_sort(char*, NT_node)':
io_lib/tree_util.c:6067:1: warning: no return statement in function returning non-void [-Wreturn-type]
 6067 | }
      | ^
io_lib/tree_util.c: In function 'int treelist2leafgroup(Sequence*, Sequence*, char*)':
io_lib/tree_util.c:6321:1: warning: no return statement in function returning non-void [-Wreturn-type]
 6321 | }
      | ^
io_lib/tree_util.c: In function 'int count_tree_groups(Sequence*, char*)':
io_lib/tree_util.c:6424:1: warning: no return statement in function returning non-void [-Wreturn-type]
 6424 | }
      | ^
io_lib/tree_util.c: In function 'int treelist2splits(Sequence*, Sequence*)':
io_lib/tree_util.c:6802:1: warning: no return statement in function returning non-void [-Wreturn-type]
 6802 | }
      | ^
io_lib/tree_util.c: In function 'int treelist2splits_old(Sequence*, Sequence*)':
io_lib/tree_util.c:6886:1: warning: no return statement in function returning non-void [-Wreturn-type]
 6886 | }
      | ^
io_lib/tree_util.c: In function 'int treelist2frame(Sequence*, Sequence*)':
io_lib/tree_util.c:6959:1: warning: no return statement in function returning non-void [-Wreturn-type]
 6959 | }
      | ^
io_lib/tree_util.c: In function 'char* graph2cons_d(long unsigned int, int)':
io_lib/tree_util.c:9328:25: error: invalid operands of types 'long unsigned int' and 'std::nullptr_t' to binary 'operator!='
 9328 |       while ((c=rn_c(s))!=NULL)
      |                         ^
In file included from ./util_lib/util.h:34,
                 from ./util_lib_header.h:30,
                 from io_lib/tree_util.c:34:
io_lib/tree_util.c: In function 'long unsigned int insert_gap_in_graph_d(long unsigned int)':
io_lib/tree_util.c:9346:20: error: cannot convert 'std::nullptr_t' to 'long unsigned int' in initialization
 9346 |   unsigned long pn=NULL;
      |                    ^~~~
io_lib/tree_util.c:9348:22: error: cannot convert 'std::nullptr_t' to 'long unsigned int' in return
 9348 |   if (!start) return NULL;
      |                      ^~~~
io_lib/tree_util.c:9361:14: error: cannot convert 'std::nullptr_t' to 'long unsigned int'
 9361 |       wn_c(n,NULL);
      |              ^~~~
      |              |
      |              std::nullptr_t
io_lib/tree_util.c:9112:46: note:   initializing argument 2 of 'void wn_c(long unsigned int, long unsigned int)'
 9112 | void wn_c    (unsigned long n, unsigned long t);
      |                                ~~~~~~~~~~~~~~^
In file included from ./util_lib/util.h:34,
                 from ./util_lib_header.h:30,
                 from io_lib/io_func.c:34:
io_lib/io_func.c: In function 'int output_raw_score(Alignment*, Alignment*, char*)':
io_lib/io_func.c:1235:17: error: cannot convert 'std::nullptr_t' to 'int' in return
 1235 |   if (!A)return NULL;
      |                 ^~~~
io_lib/io_func.c: In function 'int aln2compressed_ps(Alignment*, char*)':
io_lib/io_func.c:2076:1: warning: no return statement in function returning non-void [-Wreturn-type]
 2076 | }
      | ^
make: *** [makefile:9: io_lib/io_func.o] Error 1
make: *** Waiting for unfinished jobs....
io_lib/tree_util.c: In function 'int check_node(ALN_node, char*)':
io_lib/tree_util.c:8937:1: warning: control reaches end of non-void function [-Wreturn-type]
 8937 | }
      | ^
make: *** [makefile:9: io_lib/tree_util.o] Error 1
make: Leaving directory '/var/tmp/portage/sci-biology/t-coffee-11.00-r3/work/T-COFFEE_distribution_Version_11.00.4466924/t_coffee_source'
 * ERROR: sci-biology/t-coffee-11.00-r3::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/t-coffee-11.00-r3::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/t-coffee-11.00-r3::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:t-coffee-11.00-r3:20230223-070421.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/t-coffee-11.00-r3/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/t-coffee-11.00-r3/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/t-coffee-11.00-r3/work/T-COFFEE_distribution_Version_11.00.4466924'
 * S: '/var/tmp/portage/sci-biology/t-coffee-11.00-r3/work/T-COFFEE_distribution_Version_11.00.4466924'