--- Begin Message ---
Source: libpsortb
Version: 1.0+dfsg-5
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lu...@debian.org
Usertags: ftbfs-20240313 ftbfs-trixie ftbfs-impfuncdef
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
This is most likely caused by a change in dpkg 1.22.6, that enabled
-Werror=implicit-function-declaration. For more information, see
https://wiki.debian.org/qa.debian.org/FTBFS#A2024-03-13_-Werror.3Dimplicit-function-declaration
Relevant part (hopefully):
> /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I..
> -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
> -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
> -fstack-protector-strong -fstack-clash-protection -Wformat
> -Werror=format-security -fcf-protection -c -o std_funcs.lo std_funcs.c
> libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time
> -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c
> debug_funcs.c -fPIC -DPIC -o .libs/debug_funcs.o
> libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time
> -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c
> readseqs_multialpha.c -fPIC -DPIC -o .libs/readseqs_multialpha.o
> libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time
> -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c
> readhmm.c -fPIC -DPIC -o .libs/readhmm.o
> libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time
> -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c
> hmmsearch.c -fPIC -DPIC -o .libs/hmmsearch.o
> libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time
> -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c
> std_calculation_funcs.c -fPIC -DPIC -o .libs/std_calculation_funcs.o
> libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time
> -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c
> readhmm_multialpha.c -fPIC -DPIC -o .libs/readhmm_multialpha.o
> libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time
> -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c
> core_algorithms_multialpha.c -fPIC -DPIC -o
> .libs/core_algorithms_multialpha.o
> libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time
> -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c
> std_funcs.c -fPIC -DPIC -o .libs/std_funcs.o
> debug_funcs.c: In function ‘dump_viterbi_path’:
> debug_funcs.c:320:38: error: implicit declaration of function ‘get_mtx_index’
> [-Werror=implicit-function-declaration]
> 320 | dump_viterbi_path(viterbi_mtxp + get_mtx_index(row-1, cur->prev,
> row_size), hmmp,
> | ^~~~~~~~~~~~~
> debug_funcs.c: In function ‘dump_replacement_letters’:
> debug_funcs.c:861:14: warning: format ‘%c’ expects argument of type ‘int’,
> but argument 2 has type ‘struct letter_s’ [-Wformat=]
> 861 | printf("%c ", (*(replacement_letters->letters + i)));
> | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> | | |
> | int struct letter_s
> debug_funcs.c: In function ‘dump_replacement_letters_multi’:
> debug_funcs.c:915:16: warning: format ‘%c’ expects argument of type ‘int’,
> but argument 2 has type ‘struct letter_s’ [-Wformat=]
> 915 | printf("%c ", (*(replacement_letters->letters_1 + i)));
> | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> | | |
> | int struct letter_s
> debug_funcs.c:918:16: warning: format ‘%c’ expects argument of type ‘int’,
> but argument 2 has type ‘struct letter_s’ [-Wformat=]
> 918 | printf("%c ", (*(replacement_letters->letters_2 + i)));
> | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> | | |
> | int struct letter_s
> debug_funcs.c:921:16: warning: format ‘%c’ expects argument of type ‘int’,
> but argument 2 has type ‘struct letter_s’ [-Wformat=]
> 921 | printf("%c ", (*(replacement_letters->letters_3 + i)));
> | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> | | |
> | int struct letter_s
> debug_funcs.c:924:16: warning: format ‘%c’ expects argument of type ‘int’,
> but argument 2 has type ‘struct letter_s’ [-Wformat=]
> 924 | printf("%c ", (*(replacement_letters->letters_4 + i)));
> | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> | | |
> | int struct letter_s
> readhmm_multialpha.c: In function ‘copy_hmm_struct’:
> readhmm_multialpha.c:273:34: warning: assignment to ‘struct transition_s *’
> from incompatible pointer type ‘int *’ [-Wincompatible-pointer-types]
> 273 | retrain_hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t +
> hmmp->nr_ttg) * sizeof(struct transition_s)));
> | ^
> readhmm_multialpha.c: In function ‘readhmm_multialpha’:
> readhmm_multialpha.c:469:28: warning: assignment to ‘struct transition_s *’
> from incompatible pointer type ‘int *’ [-Wincompatible-pointer-types]
> 469 | hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t +
> hmmp->nr_ttg) * sizeof(struct transition_s)));
> | ^
> hmmsearch.c: In function ‘get_scores’:
> hmmsearch.c:535:19: warning: assignment to ‘struct helix_site *’ from
> incompatible pointer type ‘helix_sites *’ [-Wincompatible-pointer-types]
> 535 | hSites->helix = (helix_sites *) malloc(sizeof (helix_sites) *
> helices);
> | ^
> hmmsearch.c: In function ‘get_nullmodel_score_multi’:
> hmmsearch.c:656:42: warning: format ‘%s’ expects argument of type ‘char *’,
> but argument 2 has type ‘struct letter_s *’ [-Wformat=]
> 656 | printf("Could not find letter %s when scoring null
> model\n", &seq[l]);
> | ~^
> ~~~~~~~
> | |
> |
> | char *
> struct letter_s *
> hmmsearch.c:674:44: warning: format ‘%s’ expects argument of type ‘char *’,
> but argument 2 has type ‘struct letter_s *’ [-Wformat=]
> 674 | printf("Could not find letter %s when scoring null
> model\n", &seq_2[l]);
> | ~^
> ~~~~~~~~~
> | |
> |
> | char *
> struct letter_s *
> hmmsearch.c:693:44: warning: format ‘%s’ expects argument of type ‘char *’,
> but argument 2 has type ‘struct letter_s *’ [-Wformat=]
> 693 | printf("Could not find letter %s when scoring null
> model\n", &seq_3[l]);
> | ~^
> ~~~~~~~~~
> | |
> |
> | char *
> struct letter_s *
> std_calculation_funcs.c: In function ‘update_labelings’:
> hmmsearch.c:712:44: warning: format ‘%s’ expects argument of type ‘char *’,
> but argument 2 has type ‘struct letter_s *’ [-Wformat=]
> 712 | printf("Could not find letter %s when scoring null
> model\n", &seq[l]);
> | ~^
> ~~~~~~~
> | |
> |
> | char *
> struct letter_s *
> std_calculation_funcs.c:1295:21: warning: cast from pointer to integer of
> different size [-Wpointer-to-int-cast]
> 1295 | cur_address = (int)((cur_rowp+v)->labeling);
> | ^
> std_calculation_funcs.c:1309:12: warning: cast from pointer to integer of
> different size [-Wpointer-to-int-cast]
> 1309 | if((int)((cur_rowp+w)->labeling) == cur_address && (cur_rowp
> + w)->is_updated == NO) {
> | ^
> readseqs_multialpha.c: In function ‘get_sequence_fasta_multi’:
> readseqs_multialpha.c:83:39: warning: assignment to ‘char’ from ‘char *’
> makes integer from pointer without a cast [-Wint-conversion]
> 83 | (seq_infop->seqs + seq_nr)->name[0] = "s";
> | ^
> std_calculation_funcs.c: In function ‘deallocate_row_labelings’:
> std_calculation_funcs.c:1425:21: warning: cast from pointer to integer of
> different size [-Wpointer-to-int-cast]
> 1425 | cur_address = (int)((prev_rowp+v)->labeling);
> | ^
> readseqs_multialpha.c: In function ‘get_sequence_std_multi’:
> readseqs_multialpha.c:121:55: warning: unknown escape sequence: '\s'
> 121 | if(line[0] == '<' || line[0] == '#' || line[0] == '\s' || line[0]
> == '\n' || line[0] == '/') {
> | ^~~~
> std_calculation_funcs.c:1430:12: warning: cast from pointer to integer of
> different size [-Wpointer-to-int-cast]
> 1430 | if((int)((prev_rowp+w)->labeling) == cur_address) {
> | ^
> readseqs_multialpha.c: In function ‘get_sequences_msa_std_multi’:
> readseqs_multialpha.c:372:18: warning: unknown escape sequence: '\s'
> 372 | else if(i == '\s' && i == '\n') {
> | ^~~~
> readseqs_multialpha.c:389:22: error: implicit declaration of function
> ‘read_multi_prior_file_multi’; did you mean ‘read_prior_file_multi’?
> [-Werror=implicit-function-declaration]
> 389 | read_priorfile = read_multi_prior_file_multi(&em_di_1, hmmp,
> priorfile_a1, 1);
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~
> | read_prior_file_multi
> readhmm.c: In function ‘readhmm’:
> readhmm.c:121:28: warning: assignment to ‘struct transition_s *’ from
> incompatible pointer type ‘int *’ [-Wincompatible-pointer-types]
> 121 | hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t +
> hmmp->nr_ttg) * sizeof(struct transition_s)));
> | ^
> readhmm_multialpha.c:326:3: warning: ignoring return value of ‘fgets’
> declared with attribute ‘warn_unused_result’ [-Wunused-result]
> 326 | fgets(s, MAX_LINE, file);
> | ^~~~~~~~~~~~~~~~~~~~~~~~
> readhmm.c: In function ‘readanhmm’:
> readhmm.c:397:28: warning: assignment to ‘struct transition_s *’ from
> incompatible pointer type ‘int *’ [-Wincompatible-pointer-types]
> 397 | hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t +
> hmmp->nr_ttg) * sizeof(struct transition_s)));
> | ^
> readhmm_multialpha.c: In function ‘read_module_multi’:
> readhmm_multialpha.c:1042:5: warning: ignoring return value of ‘fgets’
> declared with attribute ‘warn_unused_result’ [-Wunused-result]
> 1042 | fgets(s, MAX_LINE, file);
> | ^~~~~~~~~~~~~~~~~~~~~~~~
> readhmm_multialpha.c:1077:5: warning: ignoring return value of ‘fgets’
> declared with attribute ‘warn_unused_result’ [-Wunused-result]
> 1077 | fgets(s, MAX_LINE, file);
> | ^~~~~~~~~~~~~~~~~~~~~~~~
> readhmm_multialpha.c:1111:5: warning: ignoring return value of ‘fgets’
> declared with attribute ‘warn_unused_result’ [-Wunused-result]
> 1111 | fgets(s, MAX_LINE, file);
> | ^~~~~~~~~~~~~~~~~~~~~~~~
> readhmm_multialpha.c:1140:5: warning: ignoring return value of ‘fgets’
> declared with attribute ‘warn_unused_result’ [-Wunused-result]
> 1140 | fgets(s, MAX_LINE, file);
> | ^~~~~~~~~~~~~~~~~~~~~~~~
> readhmm_multialpha.c:1143:7: warning: ignoring return value of ‘fgets’
> declared with attribute ‘warn_unused_result’ [-Wunused-result]
> 1143 | fgets(s, MAX_LINE, file);
> | ^~~~~~~~~~~~~~~~~~~~~~~~
> readhmm_multialpha.c:1169:7: warning: ignoring return value of ‘fgets’
> declared with attribute ‘warn_unused_result’ [-Wunused-result]
> 1169 | fgets(s, MAX_LINE, file);
> | ^~~~~~~~~~~~~~~~~~~~~~~~
> readhmm_multialpha.c:1172:7: warning: ignoring return value of ‘fgets’
> declared with attribute ‘warn_unused_result’ [-Wunused-result]
> 1172 | fgets(s, MAX_LINE, file);
> | ^~~~~~~~~~~~~~~~~~~~~~~~
> readhmm_multialpha.c:1198:7: warning: ignoring return value of ‘fgets’
> declared with attribute ‘warn_unused_result’ [-Wunused-result]
> 1198 | fgets(s, MAX_LINE, file);
> | ^~~~~~~~~~~~~~~~~~~~~~~~
> readhmm_multialpha.c:1202:7: warning: ignoring return value of ‘fgets’
> declared with attribute ‘warn_unused_result’ [-Wunused-result]
> 1202 | fgets(s, MAX_LINE, file);
> | ^~~~~~~~~~~~~~~~~~~~~~~~
> readhmm_multialpha.c:1229:7: warning: ignoring return value of ‘fgets’
> declared with attribute ‘warn_unused_result’ [-Wunused-result]
> 1229 | fgets(s, MAX_LINE, file);
> | ^~~~~~~~~~~~~~~~~~~~~~~~
> readhmm_multialpha.c:1236:3: warning: ignoring return value of ‘fgets’
> declared with attribute ‘warn_unused_result’ [-Wunused-result]
> 1236 | fgets(s, MAX_LINE, file);
> | ^~~~~~~~~~~~~~~~~~~~~~~~
> readhmm.c: In function ‘readhmm’:
> readhmm.c:69:3: warning: ignoring return value of ‘fgets’ declared with
> attribute ‘warn_unused_result’ [-Wunused-result]
> 69 | fgets(s, MAX_LINE, file);
> | ^~~~~~~~~~~~~~~~~~~~~~~~
> readseqs_multialpha.c: In function ‘get_sequence_std_multi’:
> readseqs_multialpha.c:286:7: warning: ignoring return value of ‘fgets’
> declared with attribute ‘warn_unused_result’ [-Wunused-result]
> 286 | fgets(line, MAX_LINE, seqfile);
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> readhmm.c: In function ‘readanhmm’:
> readhmm.c:345:3: warning: ignoring return value of ‘fgets’ declared with
> attribute ‘warn_unused_result’ [-Wunused-result]
> 345 | fgets(s, MAX_LINE, file);
> | ^~~~~~~~~~~~~~~~~~~~~~~~
> core_algorithms_multialpha.c: In function ‘msa_forward_multi’:
> core_algorithms_multialpha.c:1192:87: warning: passing argument 1 of
> ‘get_alphabet_index’ from incompatible pointer type
> [-Wincompatible-pointer-types]
> 1192 | a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c *
> (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size);
> |
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
> |
> |
> |
> char *
> In file included from core_algorithms_multialpha.c:7:
> funcs.h:136:24: note: expected ‘struct letter_s *’ but argument is of type
> ‘char *’
> 136 | int get_alphabet_index(struct letter_s*, char*, int);
> | ^~~~~~~~~~~~~~~~
> readhmm.c: In function ‘read_module’:
> core_algorithms_multialpha.c:1199:93: warning: passing argument 1 of
> ‘get_alphabet_index’ from incompatible pointer type
> [-Wincompatible-pointer-types]
> 1199 | a_index_2 = get_alphabet_index((msa_seq_infop->msa_seq_2 + (c
> * (hmmp->a_size_2+1)))->query_letter,
> |
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
> |
> |
> |
> char *
> funcs.h:136:24: note: expected ‘struct letter_s *’ but argument is of type
> ‘char *’
> 136 | int get_alphabet_index(struct letter_s*, char*, int);
> | ^~~~~~~~~~~~~~~~
> core_algorithms_multialpha.c:1208:93: warning: passing argument 1 of
> ‘get_alphabet_index’ from incompatible pointer type
> [-Wincompatible-pointer-types]
> 1208 | a_index_3 = get_alphabet_index((msa_seq_infop->msa_seq_3 + (c
> * (hmmp->a_size_3+1)))->query_letter,
> |
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
> |
> |
> |
> char *
> readhmm.c:751:5: warning: ignoring return value of ‘fgets’ declared with
> attribute ‘warn_unused_result’ [-Wunused-result]
> 751 | fgets(s, MAX_LINE, file);
> | ^~~~~~~~~~~~~~~~~~~~~~~~
> funcs.h:136:24: note: expected ‘struct letter_s *’ but argument is of type
> ‘char *’
> 136 | int get_alphabet_index(struct letter_s*, char*, int);
> | ^~~~~~~~~~~~~~~~
> core_algorithms_multialpha.c:1217:93: warning: passing argument 1 of
> ‘get_alphabet_index’ from incompatible pointer type
> [-Wincompatible-pointer-types]
> 1217 | a_index_4 = get_alphabet_index((msa_seq_infop->msa_seq_4 + (c
> * (hmmp->a_size_4+1)))->query_letter,
> |
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
> |
> |
> |
> char *
> readseqs_multialpha.c: In function ‘get_sequences_msa_std_multi’:
> funcs.h:136:24: note: expected ‘struct letter_s *’ but argument is of type
> ‘char *’
> 136 | int get_alphabet_index(struct letter_s*, char*, int);
> | ^~~~~~~~~~~~~~~~
> readhmm.c:786:5: warning: ignoring return value of ‘fgets’ declared with
> attribute ‘warn_unused_result’ [-Wunused-result]
> 786 | fgets(s, MAX_LINE, file);
> | ^~~~~~~~~~~~~~~~~~~~~~~~
> readseqs_multialpha.c:625:7: warning: ignoring return value of ‘fgets’
> declared with attribute ‘warn_unused_result’ [-Wunused-result]
> 625 | fgets(line, MAX_LINE, seqfile);
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> readhmm.c:821:5: warning: ignoring return value of ‘fgets’ declared with
> attribute ‘warn_unused_result’ [-Wunused-result]
> 821 | fgets(s, MAX_LINE, file);
> | ^~~~~~~~~~~~~~~~~~~~~~~~
> readseqs_multialpha.c:754:9: warning: ignoring return value of ‘fgets’
> declared with attribute ‘warn_unused_result’ [-Wunused-result]
> 754 | fgets(line, MAX_LINE, seqfile);
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> readhmm.c:850:5: warning: ignoring return value of ‘fgets’ declared with
> attribute ‘warn_unused_result’ [-Wunused-result]
> 850 | fgets(s, MAX_LINE, file);
> | ^~~~~~~~~~~~~~~~~~~~~~~~
> readseqs_multialpha.c:874:9: warning: ignoring return value of ‘fgets’
> declared with attribute ‘warn_unused_result’ [-Wunused-result]
> 874 | fgets(line, MAX_LINE, seqfile);
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> readhmm.c:854:3: warning: ignoring return value of ‘fgets’ declared with
> attribute ‘warn_unused_result’ [-Wunused-result]
> 854 | fgets(s, MAX_LINE, file);
> | ^~~~~~~~~~~~~~~~~~~~~~~~
> readseqs_multialpha.c:995:9: warning: ignoring return value of ‘fgets’
> declared with attribute ‘warn_unused_result’ [-Wunused-result]
> 995 | fgets(line, MAX_LINE, seqfile);
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> core_algorithms_multialpha.c: In function ‘msa_backward_multi’:
> core_algorithms_multialpha.c:1419:87: warning: passing argument 1 of
> ‘get_alphabet_index’ from incompatible pointer type
> [-Wincompatible-pointer-types]
> 1419 | a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c *
> (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size);
> |
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
> |
> |
> |
> char *
> funcs.h:136:24: note: expected ‘struct letter_s *’ but argument is of type
> ‘char *’
> 136 | int get_alphabet_index(struct letter_s*, char*, int);
> | ^~~~~~~~~~~~~~~~
> core_algorithms_multialpha.c:1426:93: warning: passing argument 1 of
> ‘get_alphabet_index’ from incompatible pointer type
> [-Wincompatible-pointer-types]
> 1426 | a_index_2 = get_alphabet_index((msa_seq_infop->msa_seq_2 + (c
> * (hmmp->a_size_2+1)))->query_letter,
> |
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
> |
> |
> |
> char *
> funcs.h:136:24: note: expected ‘struct letter_s *’ but argument is of type
> ‘char *’
> 136 | int get_alphabet_index(struct letter_s*, char*, int);
> | ^~~~~~~~~~~~~~~~
> core_algorithms_multialpha.c:1435:93: warning: passing argument 1 of
> ‘get_alphabet_index’ from incompatible pointer type
> [-Wincompatible-pointer-types]
> 1435 | a_index_3 = get_alphabet_index((msa_seq_infop->msa_seq_3 + (c
> * (hmmp->a_size_3+1)))->query_letter,
> |
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
> |
> |
> |
> char *
> funcs.h:136:24: note: expected ‘struct letter_s *’ but argument is of type
> ‘char *’
> 136 | int get_alphabet_index(struct letter_s*, char*, int);
> | ^~~~~~~~~~~~~~~~
> readhmm.c: In function ‘read_prior_files’:
> core_algorithms_multialpha.c:1444:93: warning: passing argument 1 of
> ‘get_alphabet_index’ from incompatible pointer type
> [-Wincompatible-pointer-types]
> 1444 | a_index_4 = get_alphabet_index((msa_seq_infop->msa_seq_4 + (c
> * (hmmp->a_size_4+1)))->query_letter,
> |
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
> |
> |
> |
> char *
> funcs.h:136:24: note: expected ‘struct letter_s *’ but argument is of type
> ‘char *’
> 136 | int get_alphabet_index(struct letter_s*, char*, int);
> | ^~~~~~~~~~~~~~~~
> readhmm.c:1231:5: warning: ignoring return value of ‘fgets’ declared with
> attribute ‘warn_unused_result’ [-Wunused-result]
> 1231 | fgets(ps, 2048, priorfile);
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~
> core_algorithms_multialpha.c: In function ‘msa_viterbi_multi’:
> core_algorithms_multialpha.c:1608:87: warning: passing argument 1 of
> ‘get_alphabet_index’ from incompatible pointer type
> [-Wincompatible-pointer-types]
> 1608 | a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c *
> (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size);
> |
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
> |
> |
> |
> char *
> funcs.h:136:24: note: expected ‘struct letter_s *’ but argument is of type
> ‘char *’
> 136 | int get_alphabet_index(struct letter_s*, char*, int);
> | ^~~~~~~~~~~~~~~~
> core_algorithms_multialpha.c:1615:93: warning: passing argument 1 of
> ‘get_alphabet_index’ from incompatible pointer type
> [-Wincompatible-pointer-types]
> 1615 | a_index_2 = get_alphabet_index((msa_seq_infop->msa_seq_2 + (c
> * (hmmp->a_size_2+1)))->query_letter,
> |
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
> |
> |
> |
> char *
> funcs.h:136:24: note: expected ‘struct letter_s *’ but argument is of type
> ‘char *’
> 136 | int get_alphabet_index(struct letter_s*, char*, int);
> | ^~~~~~~~~~~~~~~~
> core_algorithms_multialpha.c:1624:93: warning: passing argument 1 of
> ‘get_alphabet_index’ from incompatible pointer type
> [-Wincompatible-pointer-types]
> 1624 | a_index_3 = get_alphabet_index((msa_seq_infop->msa_seq_3 + (c
> * (hmmp->a_size_3+1)))->query_letter,
> |
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
> |
> |
> |
> char *
> funcs.h:136:24: note: expected ‘struct letter_s *’ but argument is of type
> ‘char *’
> 136 | int get_alphabet_index(struct letter_s*, char*, int);
> | ^~~~~~~~~~~~~~~~
> core_algorithms_multialpha.c:1633:93: warning: passing argument 1 of
> ‘get_alphabet_index’ from incompatible pointer type
> [-Wincompatible-pointer-types]
> 1633 | a_index_4 = get_alphabet_index((msa_seq_infop->msa_seq_4 + (c
> * (hmmp->a_size_4+1)))->query_letter,
> |
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
> |
> |
> |
> char *
> funcs.h:136:24: note: expected ‘struct letter_s *’ but argument is of type
> ‘char *’
> 136 | int get_alphabet_index(struct letter_s*, char*, int);
> | ^~~~~~~~~~~~~~~~
> std_funcs.c: In function ‘get_replacement_letter_index_single’:
> core_algorithms_multialpha.c: In function ‘msa_one_best_multi’:
> core_algorithms_multialpha.c:1892:87: warning: passing argument 1 of
> ‘get_alphabet_index’ from incompatible pointer type
> [-Wincompatible-pointer-types]
> 1892 | a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c *
> (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size);
> |
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
> |
> |
> |
> char *
> funcs.h:136:24: note: expected ‘struct letter_s *’ but argument is of type
> ‘char *’
> 136 | int get_alphabet_index(struct letter_s*, char*, int);
> | ^~~~~~~~~~~~~~~~
> std_funcs.c:683:62: warning: comparison between pointer and integer
> 683 | if(((replacement_letters->letters + a_index)->letter)[0] == c) {
> | ^~
> core_algorithms_multialpha.c:1899:93: warning: passing argument 1 of
> ‘get_alphabet_index’ from incompatible pointer type
> [-Wincompatible-pointer-types]
> 1899 | a_index_2 = get_alphabet_index((msa_seq_infop->msa_seq_2 + (c
> * (hmmp->a_size_2+1)))->query_letter,
> |
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
> |
> |
> |
> char *
> funcs.h:136:24: note: expected ‘struct letter_s *’ but argument is of type
> ‘char *’
> 136 | int get_alphabet_index(struct letter_s*, char*, int);
> | ^~~~~~~~~~~~~~~~
> core_algorithms_multialpha.c:1908:93: warning: passing argument 1 of
> ‘get_alphabet_index’ from incompatible pointer type
> [-Wincompatible-pointer-types]
> 1908 | a_index_3 = get_alphabet_index((msa_seq_infop->msa_seq_3 + (c
> * (hmmp->a_size_3+1)))->query_letter,
> |
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
> |
> |
> |
> char *
> funcs.h:136:24: note: expected ‘struct letter_s *’ but argument is of type
> ‘char *’
> 136 | int get_alphabet_index(struct letter_s*, char*, int);
> | ^~~~~~~~~~~~~~~~
> core_algorithms_multialpha.c:1917:93: warning: passing argument 1 of
> ‘get_alphabet_index’ from incompatible pointer type
> [-Wincompatible-pointer-types]
> 1917 | a_index_4 = get_alphabet_index((msa_seq_infop->msa_seq_4 + (c
> * (hmmp->a_size_4+1)))->query_letter,
> |
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
> |
> |
> |
> char *
> funcs.h:136:24: note: expected ‘struct letter_s *’ but argument is of type
> ‘char *’
> 136 | int get_alphabet_index(struct letter_s*, char*, int);
> | ^~~~~~~~~~~~~~~~
> std_funcs.c: In function ‘get_reverse_msa_seq’:
> std_funcs.c:2076:74: warning: assignment to ‘int *’ from ‘int’ makes pointer
> from integer without a cast [-Wint-conversion]
> 2076 | *(reverse_msa_seq_infop->gaps + (msa_seq_infop->msa_seq_length +
> i)) = END;
> |
> ^
> std_funcs.c: In function ‘get_reverse_msa_seq_multi’:
> std_funcs.c:2184:74: warning: assignment to ‘int *’ from ‘int’ makes pointer
> from integer without a cast [-Wint-conversion]
> 2184 | *(reverse_msa_seq_infop->gaps + (msa_seq_infop->msa_seq_length +
> i)) = END;
> |
> ^
> std_funcs.c: In function ‘update_shares_prior_multi’:
> std_funcs.c:2471:5: warning: ‘return’ with no value, in function returning
> non-void
> 2471 | return;
> | ^~~~~~
> std_funcs.c:2457:5: note: declared here
> 2457 | int update_shares_prior_multi(struct emission_dirichlet_s *em_di,
> struct hmm_multi_s *hmmp,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~
> std_funcs.c: In function ‘get_nr_alphabets’:
> std_funcs.c:2731:10: warning: ‘fgets’ writing 4000 bytes into a region of
> size 1000 overflows the destination [-Wstringop-overflow=]
> 2731 | if(fgets(s, MAX_LINE, hmmfile) != NULL) {
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~
> std_funcs.c:2724:8: note: destination object ‘s’ of size 1000
> 2724 | char s[1000];
> | ^
> In file included from /usr/include/stdio.h:906,
> from std_funcs.c:1:
> /usr/include/x86_64-linux-gnu/bits/stdio2.h:209:1: note: in a call to
> function ‘fgets’ declared with attribute ‘access (write_only, 1, 2)’
> 209 | fgets (char *__restrict __s, int __n, FILE *__restrict __stream)
> | ^~~~~
> std_funcs.c:2738:8: warning: ‘fgets’ writing 4000 bytes into a region of size
> 1000 overflows the destination [-Wstringop-overflow=]
> 2738 | if(fgets(s, MAX_LINE, hmmfile) != NULL) {
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~
> std_funcs.c:2724:8: note: destination object ‘s’ of size 1000
> 2724 | char s[1000];
> | ^
> /usr/include/x86_64-linux-gnu/bits/stdio2.h:209:1: note: in a call to
> function ‘fgets’ declared with attribute ‘access (write_only, 1, 2)’
> 209 | fgets (char *__restrict __s, int __n, FILE *__restrict __stream)
> | ^~~~~
> libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time
> -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c
> hmmsearch.c -o hmmsearch.o >/dev/null 2>&1
> libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time
> -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c
> readhmm.c -o readhmm.o >/dev/null 2>&1
> /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I..
> -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
> -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
> -fstack-protector-strong -fstack-clash-protection -Wformat
> -Werror=format-security -fcf-protection -c -o
> training_algorithms_multialpha.lo training_algorithms_multialpha.c
> cc1: some warnings being treated as errors
> libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time
> -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c
> training_algorithms_multialpha.c -fPIC -DPIC -o
> .libs/training_algorithms_multialpha.o
> make[3]: *** [Makefile:479: debug_funcs.lo] Error 1
The full build log is available from:
http://qa-logs.debian.net/2024/03/13/libpsortb_1.0+dfsg-5_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20240313;users=lu...@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240313&fusertaguser=lu...@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
--- End Message ---
pgp2OcZwyCVaP.pgp
