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| author |   David Seifert <soap@gentoo.org> | 2022-10-23 20:18:06 +0100 |
|---|---|---|
| committer | David Seifert <soap@gentoo.org> | 2022-10-23 20:18:06 +0100 |
| commit | fa0ac988b12a27a62fa356dd2db95528534bea20 (patch) | |
| tree | 67ee507998448576ec6638658306e0d50f80a49a /sci-biology | |
| parent | sci-biology/eugene: fix clang 16 build (diff) | |
| download | gentoo-fa0ac988b12a27a62fa356dd2db95528534bea20.tar.gz gentoo-fa0ac988b12a27a62fa356dd2db95528534bea20.tar.bz2 gentoo-fa0ac988b12a27a62fa356dd2db95528534bea20.zip | |
sci-biology/poa: fix clang 16 build
Closes: https://bugs.gentoo.org/875038
Signed-off-by: David Seifert <soap@gentoo.org>
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/poa/files/poa-2-clang16.patch | 74 | ||||
| -rw-r--r-- | sci-biology/poa/poa-2-r1.ebuild | 3 |
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() { |