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-rw-r--r--sci-biology/poa/files/poa-2-clang16.patch74
-rw-r--r--sci-biology/poa/poa-2-r1.ebuild3
2 files changed, 76 insertions, 1 deletions
diff --git a/sci-biology/poa/files/poa-2-clang16.patch b/sci-biology/poa/files/poa-2-clang16.patch
new file mode 100644
index 000000000000..5399dd631f48
--- /dev/null
+++ b/sci-biology/poa/files/poa-2-clang16.patch
@@ -0,0 +1,74 @@
+--- a/black_flag.c
++++ b/black_flag.c
+@@ -82,7 +82,7 @@
+
+
+
+-int handle_crash_init(void (*crash_fun)())
++int handle_crash_init(void (*crash_fun)(int))
+ {
+ #define HANDLE_CRASH_MAX 5
+ int i,signal_type[HANDLE_CRASH_MAX]
+--- a/black_flag.h
++++ b/black_flag.h
+@@ -230,7 +230,7 @@
+ ((INDEX)<(MINIMUM_BOUND) || (INDEX)>=(MAXIMUM_BOUND))
+
+ void handle_crash(int sigcode);
+-int handle_crash_init(void (*crash_fun)());
++int handle_crash_init(void (*crash_fun)(int));
+ int black_flag(int bug_level,
+ char sourcefile[],
+ int sourceline,
+--- a/default.h
++++ b/default.h
+@@ -19,7 +19,6 @@
+
+ typedef void *voidptr; /* ~~e: should be moved out to generic typing header
+ --- */
+-typedef int (*funptr)();
+
+ #define LOOPB(i,size) for ((i)=(size);(i)-- >0;)
+ #define LOOP(i,size) for ((i)=(size);(i)-- >0;)
+@@ -152,7 +151,7 @@
+ else if (NULL == ((memptr)=(ATYPE *)calloc((size_t)(N),sizeof(ATYPE)))) { \
+ fprintf(stderr,"%s, line %d: *** out of memory \n",__FILE__,__LINE__); \
+ fprintf(stderr,"Unable to meet request: %s[%d]\n",STRINGIFY(memptr),(N)); \
+- fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \
++ fprintf(stderr,"requested %d x %zu bytes \n",(N),sizeof(ATYPE)); \
+ MALLOC_FAILURE_ACTION; \
+ }
+
+@@ -193,7 +192,7 @@
+ else { \
+ fprintf(stderr,"%s, line %d: *** out of memory \n",__FILE__,__LINE__); \
+ fprintf(stderr,"Unable to meet request: %s\n",STRINGIFY(memptr)); \
+- fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \
++ fprintf(stderr,"requested %d x %zu bytes \n",(NUM),sizeof(ATYPE)); \
+ REALLOC_FAILURE_ACTION; \
+ } \
+ }
+--- a/fasta_format.c
++++ b/fasta_format.c
+@@ -2,6 +2,7 @@
+ #include "default.h"
+ #include "seq_util.h"
+
++char *stringptr_cat_pos(stringptr *s1,const char s2[],int *pos);
+
+
+ /** reads FASTA formatted sequence file, and saves the sequences to
+--- a/msa_format.c
++++ b/msa_format.c
+@@ -16,6 +16,11 @@
+
+ #include "msa_format.h"
+
++void fuse_ring_identities(int len_x,LPOLetter_T seq_x[],
++ int len_y,LPOLetter_T seq_y[],
++ LPOLetterRef_T al_x[],
++ LPOLetterRef_T al_y[]);
++void build_seq_to_po_index(LPOSequence_T *seq);
+
+ /** is `ch' an allowed residue? (a-z OR A-Z OR ? OR [ OR ]) */
+ static int is_residue_char (char ch);
diff --git a/sci-biology/poa/poa-2-r1.ebuild b/sci-biology/poa/poa-2-r1.ebuild
index d87f2a638117..f6d9b756f3d5 100644
--- a/sci-biology/poa/poa-2-r1.ebuild
+++ b/sci-biology/poa/poa-2-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -21,6 +21,7 @@ S="${WORKDIR}/${MY_P}"
PATCHES=(
"${FILESDIR}"/${P}-respect-flags.patch
"${FILESDIR}"/${P}-fno-common.patch
+ "${FILESDIR}"/${P}-clang16.patch
)
src_configure() {