[med-svn] [Git][med-team/libpsortb][master] 3 commits: gcc14.patch: new: fix multiple issues caught by gcc14.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sun Aug 25 14:13:17 BST 2024
Étienne Mollier pushed to branch master at Debian Med / libpsortb
Commits:
3f8bda35 by Étienne Mollier at 2024-08-25T15:10:45+02:00
gcc14.patch: new: fix multiple issues caught by gcc14.
Closes: #1075198
- - - - -
9436dc50 by Étienne Mollier at 2024-08-25T15:11:28+02:00
d/control: add myself to uploaders.
- - - - -
956a218b by Étienne Mollier at 2024-08-25T15:12:15+02:00
Ready for upload to unstable.
- - - - -
4 changed files:
- debian/changelog
- debian/control
- + debian/patches/gcc14.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+libpsortb (1.0+dfsg-7) unstable; urgency=medium
+
+ * gcc14.patch: new: fix multiple issues caught by gcc14. (Closes: #1075198)
+ * d/control: add myself to uploaders.
+
+ -- Étienne Mollier <emollier at debian.org> Sun, 25 Aug 2024 15:12:08 +0200
+
libpsortb (1.0+dfsg-6) unstable; urgency=medium
* Drop unused debug functions
=====================================
debian/control
=====================================
@@ -1,6 +1,7 @@
Source: libpsortb
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>,
+ Étienne Mollier <emollier at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
=====================================
debian/patches/gcc14.patch
=====================================
@@ -0,0 +1,372 @@
+Description: fix numerous issues caught by gcc 14.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1075198
+Forwarded: no
+Last-Update: 2024-08-25
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- libpsortb.orig/modhmm0.92b/core_algorithms_multialpha.c
++++ libpsortb/modhmm0.92b/core_algorithms_multialpha.c
+@@ -1187,14 +1187,14 @@
+
+ if(hmmp->alphabet_type == DISCRETE) {
+
+- a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size);
++ a_index = get_alphabet_index((struct letter_s*)(msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size);
+ if(a_index < 0) {
+ a_index = hmmp->a_size; /* if letter is wild card, use default column in subst matrix */
+ }
+ }
+ if(hmmp->nr_alphabets > 1) {
+ if(hmmp->alphabet_type_2 == DISCRETE) {
+- a_index_2 = get_alphabet_index((msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter,
++ a_index_2 = get_alphabet_index((struct letter_s*)(msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter,
+ hmmp->alphabet_2, hmmp->a_size_2);
+ if(a_index_2 < 0) {
+ a_index_2 = hmmp->a_size_2; /* if letter is wild card, use default column in subst matrix */
+@@ -1203,7 +1203,7 @@
+ }
+ if(hmmp->nr_alphabets > 2) {
+ if(hmmp->alphabet_type_3 == DISCRETE) {
+- a_index_3 = get_alphabet_index((msa_seq_infop->msa_seq_3 + (c * (hmmp->a_size_3+1)))->query_letter,
++ a_index_3 = get_alphabet_index((struct letter_s*)(msa_seq_infop->msa_seq_3 + (c * (hmmp->a_size_3+1)))->query_letter,
+ hmmp->alphabet_3, hmmp->a_size_3);
+ if(a_index_3 < 0) {
+ a_index_3 = hmmp->a_size_3; /* if letter is wild card, use default column in subst matrix */
+@@ -1212,7 +1212,7 @@
+ }
+ if(hmmp->nr_alphabets > 3) {
+ if(hmmp->alphabet_type_4 == DISCRETE) {
+- a_index_4 = get_alphabet_index((msa_seq_infop->msa_seq_4 + (c * (hmmp->a_size_4+1)))->query_letter,
++ a_index_4 = get_alphabet_index((struct letter_s*)(msa_seq_infop->msa_seq_4 + (c * (hmmp->a_size_4+1)))->query_letter,
+ hmmp->alphabet_4, hmmp->a_size_4);
+ if(a_index_4 < 0) {
+ a_index_4 = hmmp->a_size_4; /* if letter is wild card, use default column in subst matrix */
+@@ -1414,14 +1414,14 @@
+ a_index_3 = -1;
+ a_index_4 = -1;
+ if(hmmp->alphabet_type == DISCRETE) {
+- a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size);
++ a_index = get_alphabet_index((struct letter_s*)(msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size);
+ if(a_index < 0) {
+ a_index = hmmp->a_size; /* if letter is wild card, use default column in subst matrix */
+ }
+ }
+ if(hmmp->nr_alphabets > 1) {
+ if(hmmp->alphabet_type_2 == DISCRETE) {
+- a_index_2 = get_alphabet_index((msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter,
++ a_index_2 = get_alphabet_index((struct letter_s*)(msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter,
+ hmmp->alphabet_2, hmmp->a_size_2);
+ if(a_index_2 < 0) {
+ a_index_2 = hmmp->a_size_2; /* if letter is wild card, use default column in subst matrix */
+@@ -1430,7 +1430,7 @@
+ }
+ if(hmmp->nr_alphabets > 2) {
+ if(hmmp->alphabet_type_3 == DISCRETE) {
+- a_index_3 = get_alphabet_index((msa_seq_infop->msa_seq_3 + (c * (hmmp->a_size_3+1)))->query_letter,
++ a_index_3 = get_alphabet_index((struct letter_s*)(msa_seq_infop->msa_seq_3 + (c * (hmmp->a_size_3+1)))->query_letter,
+ hmmp->alphabet_3, hmmp->a_size_3);
+ if(a_index_3 < 0) {
+ a_index_3 = hmmp->a_size_3; /* if letter is wild card, use default column in subst matrix */
+@@ -1439,7 +1439,7 @@
+ }
+ if(hmmp->nr_alphabets > 3) {
+ if(hmmp->alphabet_type_4 == DISCRETE) {
+- a_index_4 = get_alphabet_index((msa_seq_infop->msa_seq_4 + (c * (hmmp->a_size_4+1)))->query_letter,
++ a_index_4 = get_alphabet_index((struct letter_s*)(msa_seq_infop->msa_seq_4 + (c * (hmmp->a_size_4+1)))->query_letter,
+ hmmp->alphabet_4, hmmp->a_size_4);
+ if(a_index_4 < 0) {
+ a_index_4 = hmmp->a_size_4; /* if letter is wild card, use default column in subst matrix */
+@@ -1603,14 +1603,14 @@
+ a_index_3 = -1;
+ a_index_4 = -1;
+ if(hmmp->alphabet_type == DISCRETE) {
+- a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size);
++ a_index = get_alphabet_index((struct letter_s*)(msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size);
+ if(a_index < 0) {
+ a_index = hmmp->a_size; /* if letter is wild card, use default column in subst matrix */
+ }
+ }
+ if(hmmp->nr_alphabets > 1) {
+ if(hmmp->alphabet_type_2 == DISCRETE) {
+- a_index_2 = get_alphabet_index((msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter,
++ a_index_2 = get_alphabet_index((struct letter_s*)(msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter,
+ hmmp->alphabet_2, hmmp->a_size_2);
+ if(a_index_2 < 0) {
+ a_index_2 = hmmp->a_size_2; /* if letter is wild card, use default column in subst matrix */
+@@ -1619,7 +1619,7 @@
+ }
+ if(hmmp->nr_alphabets > 2) {
+ if(hmmp->alphabet_type_3 == DISCRETE) {
+- a_index_3 = get_alphabet_index((msa_seq_infop->msa_seq_3 + (c * (hmmp->a_size_3+1)))->query_letter,
++ a_index_3 = get_alphabet_index((struct letter_s*)(msa_seq_infop->msa_seq_3 + (c * (hmmp->a_size_3+1)))->query_letter,
+ hmmp->alphabet_3, hmmp->a_size_3);
+ if(a_index_3 < 0) {
+ a_index_3 = hmmp->a_size_3; /* if letter is wild card, use default column in subst matrix */
+@@ -1628,7 +1628,7 @@
+ }
+ if(hmmp->nr_alphabets > 3) {
+ if(hmmp->alphabet_type_4 == DISCRETE) {
+- a_index_4 = get_alphabet_index((msa_seq_infop->msa_seq_4 + (c * (hmmp->a_size_4+1)))->query_letter,
++ a_index_4 = get_alphabet_index((struct letter_s*)(msa_seq_infop->msa_seq_4 + (c * (hmmp->a_size_4+1)))->query_letter,
+ hmmp->alphabet_4, hmmp->a_size_4);
+ if(a_index_4 < 0) {
+ a_index_4 = hmmp->a_size_4; /* if letter is wild card, use default column in subst matrix */
+@@ -1887,14 +1887,14 @@
+ a_index_3 = -1;
+ a_index_4 = -1;
+ if(hmmp->alphabet_type == DISCRETE) {
+- a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size);
++ a_index = get_alphabet_index((struct letter_s*)(msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size);
+ if(a_index < 0) {
+ a_index = hmmp->a_size; /* if letter is wild card, use default column in subst matrix */
+ }
+ }
+ if(hmmp->nr_alphabets > 1) {
+ if(hmmp->alphabet_type_2 == DISCRETE) {
+- a_index_2 = get_alphabet_index((msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter,
++ a_index_2 = get_alphabet_index((struct letter_s*)(msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter,
+ hmmp->alphabet_2, hmmp->a_size_2);
+ if(a_index_2 < 0) {
+ a_index_2 = hmmp->a_size_2; /* if letter is wild card, use default column in subst matrix */
+@@ -1903,7 +1903,7 @@
+ }
+ if(hmmp->nr_alphabets > 2) {
+ if(hmmp->alphabet_type_3 == DISCRETE) {
+- a_index_3 = get_alphabet_index((msa_seq_infop->msa_seq_3 + (c * (hmmp->a_size_3+1)))->query_letter,
++ a_index_3 = get_alphabet_index((struct letter_s*)(msa_seq_infop->msa_seq_3 + (c * (hmmp->a_size_3+1)))->query_letter,
+ hmmp->alphabet_3, hmmp->a_size_3);
+ if(a_index_3 < 0) {
+ a_index_3 = hmmp->a_size_3; /* if letter is wild card, use default column in subst matrix */
+@@ -1912,7 +1912,7 @@
+ }
+ if(hmmp->nr_alphabets > 3) {
+ if(hmmp->alphabet_type_4 == DISCRETE) {
+- a_index_4 = get_alphabet_index((msa_seq_infop->msa_seq_4 + (c * (hmmp->a_size_4+1)))->query_letter,
++ a_index_4 = get_alphabet_index((struct letter_s*)(msa_seq_infop->msa_seq_4 + (c * (hmmp->a_size_4+1)))->query_letter,
+ hmmp->alphabet_4, hmmp->a_size_4);
+ if(a_index_4 < 0) {
+ a_index_4 = hmmp->a_size_4; /* if letter is wild card, use default column in subst matrix */
+--- libpsortb.orig/modhmm0.92b/hmmsearch.c
++++ libpsortb/modhmm0.92b/hmmsearch.c
+@@ -532,7 +532,7 @@
+ through and record their locations */
+
+ if(hSites) {
+- hSites->helix = (helix_sites *) malloc(sizeof (helix_sites) * helices);
++ hSites->helix = (struct helix_site *) malloc(sizeof (helix_sites) * helices);
+ helixSite = hSites->helix;
+
+ hSites->helix_count = helices;
+--- libpsortb.orig/modhmm0.92b/readhmm.c
++++ libpsortb/modhmm0.92b/readhmm.c
+@@ -118,7 +118,7 @@
+ /* nr of trans tie groups */
+ if(fgets(s, MAX_LINE, file) != NULL) {
+ hmmp->nr_ttg = atoi(&s[29]);
+- hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s)));
++ hmmp->trans_tie_groups = (struct transition_s*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s)));
+ }
+ /* nr of emission priorfiles */
+ if(fgets(s, MAX_LINE, file) != NULL) {
+@@ -391,7 +391,7 @@
+ /* nr of trans tie groups */
+ if(fgets(s, MAX_LINE, file) != NULL) {
+ hmmp->nr_ttg = atoi(&s[29]);
+- hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s)));
++ hmmp->trans_tie_groups = (struct transition_s*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s)));
+ }
+ /* nr of emission priorfiles */
+ if(fgets(s, MAX_LINE, file) != NULL) {
+--- libpsortb.orig/modhmm0.92b/readseqs_multialpha.c
++++ libpsortb/modhmm0.92b/readseqs_multialpha.c
+@@ -80,7 +80,7 @@
+ inside_seq = NO;
+
+ /* read sequence name */
+- (seq_infop->seqs + seq_nr)->name[0] = "s";
++ (seq_infop->seqs + seq_nr)->name[0] = 's';
+
+ i = 0;
+ while((i <= nr_letters) && (seq[i] != '\0')) {
+--- libpsortb.orig/modhmm0.92b/readhmm_multialpha.c
++++ libpsortb/modhmm0.92b/readhmm_multialpha.c
+@@ -270,7 +270,7 @@
+ retrain_hmmp->distrib_groups = (int*)(malloc_or_die((hmmp->nr_d + hmmp->nr_v) * sizeof(int)));
+ memcpy(retrain_hmmp->distrib_groups, hmmp->distrib_groups,(hmmp->nr_d + hmmp->nr_v) * sizeof(int));
+
+- retrain_hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s)));
++ retrain_hmmp->trans_tie_groups = (struct transition_s*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s)));
+ memcpy(retrain_hmmp->trans_tie_groups, hmmp->trans_tie_groups,(hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s));
+
+
+@@ -466,7 +466,7 @@
+ /* nr of trans tie groups */
+ if(fgets(s, MAX_LINE, file) != NULL) {
+ hmmp->nr_ttg = atoi(&s[29]);
+- hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s)));
++ hmmp->trans_tie_groups = (struct transition_s*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s)));
+ }
+
+ /* nr of emission priorfiles */
+--- libpsortb.orig/modhmm0.92b/std_funcs.c
++++ libpsortb/modhmm0.92b/std_funcs.c
+@@ -2068,7 +2068,7 @@
+
+ /* get gap data (not implemented) */
+ for(i = 0; i < msa_seq_infop->msa_seq_length; i++) {
+- *(reverse_msa_seq_infop->gaps + (msa_seq_infop->msa_seq_length + i)) = END;
++ *(reverse_msa_seq_infop->gaps + (msa_seq_infop->msa_seq_length + i)) = (int*)END;
+ }
+ for(i = 0; i < msa_seq_infop->msa_seq_length; i++) {
+ *(reverse_msa_seq_infop->gaps + i) = (int*)(reverse_msa_seq_infop->gaps + (msa_seq_infop->msa_seq_length + i));
+@@ -2176,7 +2176,7 @@
+
+ /* get gap data (not implemented) */
+ for(i = 0; i < msa_seq_infop->msa_seq_length; i++) {
+- *(reverse_msa_seq_infop->gaps + (msa_seq_infop->msa_seq_length + i)) = END;
++ *(reverse_msa_seq_infop->gaps + (msa_seq_infop->msa_seq_length + i)) = (int*)END;
+ }
+ for(i = 0; i < msa_seq_infop->msa_seq_length; i++) {
+ *(reverse_msa_seq_infop->gaps + i) = (int*)(reverse_msa_seq_infop->gaps + (msa_seq_infop->msa_seq_length + i));
+@@ -2463,7 +2463,7 @@
+ if(em_di->nr_components <= 0) {
+ //printf("em_di nr comps = %d\n",em_di->nr_components);
+ //printf("alphabet = %d\n", alphabet);
+- return;
++ return YES; // Initially void, so YES, but actual intention is unclear.
+ }
+
+ /* set a_size and msa_seq according to alphabet */
+--- libpsortb.orig/modhmm0.92b/training_algorithms_multialpha.c
++++ libpsortb/modhmm0.92b/training_algorithms_multialpha.c
+@@ -698,7 +698,7 @@
+ /* loop over the alphabets */
+ for(alphabet_nr = 1; alphabet_nr <= hmmp->nr_alphabets; alphabet_nr++) {
+ if(alphabet_nr == 1) {
+- alphabet = hmmp->alphabet;
++ alphabet = (int)hmmp->alphabet;
+ subst_mtx = hmmp->subst_mtx;
+ a_size = hmmp->a_size;
+ E_cur = E;
+@@ -707,7 +707,7 @@
+ tmp_emissions = hmmp->emissions;
+ }
+ else if(alphabet_nr == 2) {
+- alphabet = hmmp->alphabet_2;
++ alphabet = (int)hmmp->alphabet_2;
+ subst_mtx = hmmp->subst_mtx_2;
+ a_size = hmmp->a_size_2;
+ E_cur = E_2;
+@@ -716,7 +716,7 @@
+ tmp_emissions = hmmp->emissions_2;
+ }
+ else if(alphabet_nr == 3) {
+- alphabet = hmmp->alphabet_3;
++ alphabet = (int)hmmp->alphabet_3;
+ subst_mtx = hmmp->subst_mtx_3;
+ a_size = hmmp->a_size_3;
+ E_cur = E_3;
+@@ -725,7 +725,7 @@
+ tmp_emissions = hmmp->emissions_3;
+ }
+ else if(alphabet_nr == 4) {
+- alphabet = hmmp->alphabet_4;
++ alphabet = (int)hmmp->alphabet_4;
+ subst_mtx = hmmp->subst_mtx_4;
+ a_size = hmmp->a_size_4;
+ E_cur = E_4;
+@@ -1636,28 +1636,28 @@
+ /* loop over the alphabets */
+ for(alphabet_nr = 1; alphabet_nr <= hmmp->nr_alphabets; alphabet_nr++) {
+ if(alphabet_nr == 1) {
+- alphabet = hmmp->alphabet;
++ alphabet = (int)hmmp->alphabet;
+ subst_mtx = hmmp->subst_mtx;
+ a_size = hmmp->a_size;
+ E_cur = E_ulab;
+ msa_seq = msa_seq_infop->msa_seq_1;
+ }
+ else if(alphabet_nr == 2) {
+- alphabet = hmmp->alphabet_2;
++ alphabet = (int)hmmp->alphabet_2;
+ subst_mtx = hmmp->subst_mtx_2;
+ a_size = hmmp->a_size_2;
+ E_cur = E_ulab_2;
+ msa_seq = msa_seq_infop->msa_seq_2;
+ }
+ else if(alphabet_nr == 3) {
+- alphabet = hmmp->alphabet_3;
++ alphabet = (int)hmmp->alphabet_3;
+ subst_mtx = hmmp->subst_mtx_3;
+ a_size = hmmp->a_size_3;
+ E_cur = E_ulab_3;
+ msa_seq = msa_seq_infop->msa_seq_3;
+ }
+ else if(alphabet_nr == 4) {
+- alphabet = hmmp->alphabet_4;
++ alphabet = (int)hmmp->alphabet_4;
+ subst_mtx = hmmp->subst_mtx_4;
+ a_size = hmmp->a_size_4;
+ E_cur = E_ulab_4;
+@@ -1781,28 +1781,28 @@
+ /* loop over the alphabets */
+ for(alphabet_nr = 1; alphabet_nr <= hmmp->nr_alphabets; alphabet_nr++) {
+ if(alphabet_nr == 1) {
+- alphabet = hmmp->alphabet;
++ alphabet = (int)hmmp->alphabet;
+ subst_mtx = hmmp->subst_mtx;
+ a_size = hmmp->a_size;
+ E_cur = E_lab;
+ msa_seq = msa_seq_infop->msa_seq_1;
+ }
+ else if(alphabet_nr == 2) {
+- alphabet = hmmp->alphabet_2;
++ alphabet = (int)hmmp->alphabet_2;
+ subst_mtx = hmmp->subst_mtx_2;
+ a_size = hmmp->a_size_2;
+ E_cur = E_lab_2;
+ msa_seq = msa_seq_infop->msa_seq_2;
+ }
+ else if(alphabet_nr == 3) {
+- alphabet = hmmp->alphabet_3;
++ alphabet = (int)hmmp->alphabet_3;
+ subst_mtx = hmmp->subst_mtx_3;
+ a_size = hmmp->a_size_3;
+ E_cur = E_lab_3;
+ msa_seq = msa_seq_infop->msa_seq_3;
+ }
+ else if(alphabet_nr == 4) {
+- alphabet = hmmp->alphabet_4;
++ alphabet = (int)hmmp->alphabet_4;
+ subst_mtx = hmmp->subst_mtx_4;
+ a_size = hmmp->a_size_4;
+ E_cur = E_lab_4;
+@@ -3586,11 +3586,11 @@
+ }
+ else if(scoring_method == SUBST_MTX_DOT_PRODUCT && use_nr_occ == YES) {
+ add_to_E_subst_mtx_dot_product_nr_occ(E, Eka_base, msa_seq, p, k, a_size, normalize, subst_mtx,
+- alphabet);
++ (char*)alphabet);
+ }
+ else if(scoring_method == SUBST_MTX_DOT_PRODUCT_PRIOR && use_nr_occ == YES) {
+ add_to_E_subst_mtx_dot_product_prior_nr_occ(E, Eka_base, msa_seq, p, k, a_size, normalize, subst_mtx,
+- alphabet);
++ (char*)alphabet);
+ }
+ else if(scoring_method == DOT_PRODUCT) {
+ add_to_E_dot_product(E, Eka_base, msa_seq, p, k, a_size, normalize);
+@@ -3615,11 +3615,11 @@
+ }
+ else if(scoring_method == SUBST_MTX_DOT_PRODUCT) {
+ add_to_E_subst_mtx_dot_product(E, Eka_base, msa_seq, p, k, a_size, normalize, subst_mtx,
+- alphabet);
++ (char*)alphabet);
+ }
+ else if(scoring_method == SUBST_MTX_DOT_PRODUCT_PRIOR) {
+ add_to_E_subst_mtx_dot_product_prior(E, Eka_base, msa_seq, p, k, a_size, normalize, subst_mtx,
+- alphabet);
++ (char*)alphabet);
+ }
+ else {
+ printf("Error: Unrecognized scoring method\n");
=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@ use_debian_packaged_libs.patch
use_debian_packaged_libsvm.patch
remove_unused_debug_functions.patch
fix-implicit-declaration.patch
+gcc14.patch
View it on GitLab: https://salsa.debian.org/med-team/libpsortb/-/compare/e012d8d5064d68dce0d9c37283097e13bc72569a...956a218bcb42f355dbc86b75a1d90ac450fd32e3
--
View it on GitLab: https://salsa.debian.org/med-team/libpsortb/-/compare/e012d8d5064d68dce0d9c37283097e13bc72569a...956a218bcb42f355dbc86b75a1d90ac450fd32e3
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