[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
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20240825/91d1f1d4/attachment-0001.htm>


More information about the debian-med-commit mailing list