[med-svn] [Git][med-team/fasta3][master] * Fix build with gcc-15
Andreas Tille (@tille)
gitlab at salsa.debian.org
Tue Sep 23 20:01:29 BST 2025
Andreas Tille pushed to branch master at Debian Med / fasta3
Commits:
7e5e5c62 by Andreas Tille at 2025-09-23T21:01:15+02:00
* Fix build with gcc-15
Closes: #1096607
- - - - -
3 changed files:
- debian/changelog
- + debian/patches/gcc-15.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+fasta3 (36.3.8i.14-Nov-2020-4) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * Fix build with gcc-15
+ Closes: #1096607
+
+ -- Andreas Tille <tille at debian.org> Tue, 23 Sep 2025 20:39:27 +0200
+
fasta3 (36.3.8i.14-Nov-2020-3) unstable; urgency=medium
* Team upload.
=====================================
debian/patches/gcc-15.patch
=====================================
@@ -0,0 +1,136 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: 2025-09-23
+Bug-Debian: https://bugs.debian.org/1096607
+Description: Fix gcc-15 build issues
+
+--- a/src/mmgetaa.c
++++ b/src/mmgetaa.c
+@@ -81,17 +81,22 @@ aranlib_mb(char *str, int cnt, fseek_t s
+
+ /* mmap()ed functions */
+ #ifdef USE_MMAP
+-int agetlibm(); void aranlibm();
+-int lgetlibm(); void lranlibm();
+-void vranlibm();
+-int gcg_getlibm();
++int agetlibm(unsigned char *seq, int maxs, char *libstr, int n_libstr, fseek_t *libpos, int *lcont, struct lmf_str *m_fd, long *l_off);
++void aranlibm(char *str, int cnt, fseek_t libpos, char *libstr, struct lmf_str *m_fd);
++int lgetlibm(unsigned char *seq, int maxs, char *libstr, int n_libstr, fseek_t *libpos, int *lcont, struct lmf_str *m_fd, long *l_off);
++void lranlibm(char *str, int cnt, fseek_t seek, char *libstr, struct lmf_str *m_fd);
++void vranlibm(char *str, int cnt, fseek_t libpos, char *libstr, struct lmf_str *m_fd);
++int gcg_getlibm(unsigned char *seq, int maxs, char *libstr, int n_libstr, fseek_t *libpos, int *lcont, struct lmf_str *m_fd, long *l_off);
+
+-int (*getlibam[])()={
+- agetlibm,lgetlibm, NULL, NULL,NULL,agetlibm,gcg_getlibm
++typedef int (*getlib_func_t)(unsigned char *, int, char *, int, fseek_t *, int *, struct lmf_str *, long *);
++typedef void (*ranlib_func_t)(char *, int, fseek_t, char *, struct lmf_str *);
++
++getlib_func_t getlibam[] = {
++ agetlibm, lgetlibm, NULL, NULL, NULL, agetlibm, gcg_getlibm
+ };
+
+-void (*ranlibam[])()={
+- aranlibm,lranlibm,NULL,NULL,NULL,vranlibm,vranlibm
++ranlib_func_t ranlibam[] = {
++ aranlibm, lranlibm, NULL, NULL, NULL, vranlibm, vranlibm
+ };
+ #endif
+
+--- a/src/altlib.h
++++ b/src/altlib.h
+@@ -85,7 +85,7 @@ void qranlib(char *, int, fseek_t, char
+ extern int ncbl2_getliba(unsigned char *, int, char *, int, fseek_t *, int *,
+ struct lmf_str *, long *);
+ extern void ncbl2_ranlib(char *, int, fseek_t, char *, struct lmf_str *);
+-void ncbl2_closelib();
++void ncbl2_closelib(struct lmf_str *m_fptr);
+ #endif
+
+ #ifdef MYSQL_DB
+--- a/src/mm_file.h
++++ b/src/mm_file.h
+@@ -58,7 +58,7 @@ typedef int64_t MM_OFF;
+ #include "defs.h"
+ #endif
+
+-extern unsigned long adler32();
++extern unsigned long adler32(unsigned long, const unsigned char *, unsigned int);
+
+ struct lmf_str {
+ FILE *libf; /* sequence file being read */
+--- a/src/ncbl2_mlib.c
++++ b/src/ncbl2_mlib.c
+@@ -851,7 +851,7 @@ struct lmf_str
+ if (date_str!=NULL) free(date_str);
+
+ #ifdef DEBUG
+- fprintf(stderr,"*** INFO [%s:%d] - %s format: BL2 (%s) max_cnt: %d, totlen: %lld, maxlen %ld\n",
++ fprintf(stderr,"*** INFO [%s:%d] - %s format: BL2 (%s) max_cnt: %d, totlen: %ld, maxlen %ld\n",
+ __FILE__,__LINE__,
+ m_fptr->lb_name,m_fptr->mm_flg ? "mmap" : "fopen",
+ m_fptr->max_cnt,m_fptr->tot_len,m_fptr->max_len);
+@@ -1102,7 +1102,7 @@ ncbl2_getliba(unsigned char *seq,
+ if (m_fd->mm_flg) sptr = (unsigned char *)m_fd->mmap_addr;
+ else {
+ if ((tmp=fread(seq,(size_t)1,(size_t)seq_len,m_fd->libf))!=(size_t)seq_len) {
+- fprintf(stderr,"*** ERROR [%s:%d] - could not read sequence record: %lld %ld != %ld\n",
++ fprintf(stderr,"*** ERROR [%s:%d] - could not read sequence record: %ld %ld != %ld\n",
+ __FILE__,__LINE__, *libpos,tmp,seq_len);
+ goto error;
+ }
+@@ -1147,7 +1147,7 @@ ncbl2_getliba(unsigned char *seq,
+ seq[seqcnt]= EOSEQ;
+ return (seqcnt);
+
+-error: fprintf(stderr,"*** ERROR [%s:%d] - error reading %s at %lld\n",__FILE__,__LINE__,libstr,*libpos);
++error: fprintf(stderr,"*** ERROR [%s:%d] - error reading %s at %ld\n",__FILE__,__LINE__,libstr,*libpos);
+ fflush(stderr);
+ return (-1);
+ }
+@@ -1431,7 +1431,7 @@ ncbl2_getlibn(unsigned char *seq,
+ if (!m_fd->mm_flg) {
+ if ((tmp=fread(seq,(size_t)1,(size_t)seqcnt,m_fd->libf))!=(size_t)seqcnt) {
+ fprintf(stderr,
+- "*** ERROR [%s:%d] - could not read sequence record: %s %lld %ld != %ld: %d\n",
++ "*** ERROR [%s:%d] - could not read sequence record: %s %ld %ld != %ld: %d\n",
+ __FILE__,__LINE__,libstr, *libpos,tmp,seqcnt,*seq);
+ goto error;
+ }
+@@ -1451,7 +1451,7 @@ ncbl2_getlibn(unsigned char *seq,
+ seqcnt = ((maxs+3)/4)-1;
+ if (!m_fd->mm_flg) {
+ if ((tmp=fread(seq,(size_t)1,(size_t)(seqcnt),m_fd->libf))!=(size_t)(seqcnt)) {
+- fprintf(stderr,"*** ERROR [%s:%d] - could not read sequence record: %lld %ld/%ld\n",
++ fprintf(stderr,"*** ERROR [%s:%d] - could not read sequence record: %ld %ld/%ld\n",
+ __FILE__,__LINE__, *libpos,tmp,seqcnt);
+ goto error;
+ }
+@@ -1675,7 +1675,7 @@ ncbl2_getlibn(unsigned char *seq,
+ return (4*seqcnt);
+ }
+
+-error: fprintf(stderr,"*** ERROR [%s:%d] - reading %s at %lld\n",__FILE__,__LINE__,libstr,*libpos);
++error: fprintf(stderr,"*** ERROR [%s:%d] - reading %s at %ld\n",__FILE__,__LINE__,libstr,*libpos);
+ fflush(stderr);
+ return (-1);
+ }
+--- a/src/pssm_asn_subs.c
++++ b/src/pssm_asn_subs.c
+@@ -656,7 +656,7 @@ unsigned char *
+ get_astr_userfld_data(struct asn_bstruct *asnp) {
+ double real;
+ long ival;
+- int bool;
++ int bool_val;
+
+ ABPP = chk_asn_buf(asnp, 32);
+
+@@ -675,7 +675,7 @@ get_astr_userfld_data(struct asn_bstruct
+ break;
+ case ASN_USERFLD_D_BOOL :
+ ABP_INC2;
+- ABPP = get_astr_bool(asnp, &bool) + 2;
++ ABPP = get_astr_bool(asnp, &bool_val) + 2;
+ break;
+ case ASN_USERFLD_D_OS :
+ ABP_INC2;
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
Makefile.patch
local_tests
adjust-scripts
+gcc-15.patch
View it on GitLab: https://salsa.debian.org/med-team/fasta3/-/commit/7e5e5c62d1f0889b988644f91127b2094be3f731
--
View it on GitLab: https://salsa.debian.org/med-team/fasta3/-/commit/7e5e5c62d1f0889b988644f91127b2094be3f731
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