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.
