gentoo auto-resync : 23:10:2022 - 21:50:51

11 files changed, 937 insertions, 13 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index bc1599b5acc3..997e93a3aa25 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/eugene/Manifest b/sci-biology/eugene/Manifest
index 78dd82270c34..21120d84e544 100644
--- a/sci-biology/eugene/Manifest
+++ b/sci-biology/eugene/Manifest
@@ -2,8 +2,9 @@ AUX eugene-3.6-overflow.patch 252 BLAKE2B 83b82992d734996b2878028329642ec015a53f
 AUX eugene-3.6-plugins.patch 1843 BLAKE2B 8bf8f09a43ec35838058094188973f985f69992e7f273b5c40f71abf39b498ec9bad1f8c8db9f0b1f5ec77796abefbf150afa9dc3a6764d33d16c3bdc175f87d SHA512 66d9191656821ec958804462aec83885560dfa35f075e1b012401d9ee4b86368b83005353d0093af0b95dc313b1fee6995f981504737242820125c5ead20ae9c
 AUX eugene-4.1-format-security.patch 609 BLAKE2B 1571c5c3af87e5ea49fa1f5b5ce19487c1493aa85e8f7782645874abf62c9e5d09e2e8c4c6aa2c5f44aedba257859d0245fcbbd28ae57d24dae118c562561a3a SHA512 f4eedd5b70309d4b8eedce8f3a4f79b65e595d407e88fd79e7f4f2f8c98880432366124b7f0a34c9032c9a498a1db607b0cac20304e84ec01f736589924ff362
 AUX eugene-4.1d-Wformat.patch 2719 BLAKE2B 6dbdcb4e9946d0245eeeca1ff23b5d52ff3b37a64cbd88838229836323959325c7f54c9b00dec0abc02c218c4761ddef00def7f111c41df628af6d06f2147a6e SHA512 b235c11791caea63109009b858cde7ec179166640f009bf58caf33a8502345360efb71208a330572d7f870c468810bb9ab54db3e2af187a0d2baba7e12c6ff96
+AUX eugene-4.1d-clang16.patch 638 BLAKE2B 31ba74851ef79712e2583775c1cefc80035d4dc02b1f81992b3f341f53d7e0685ac550c8f26200734bb1492b600e4a1cd76ed7737688d3a161f2524ab316233c SHA512 0e94106908d97d568aae6575ad7e49408ed46b489cd5ed29eb1a646f6af8f450d9d7b79355b7335b0db97783bc26059fdbf6fb690ef37214ff6ce5590a86c728
 AUX eugene-4.1d-fix-c++14.patch 635 BLAKE2B d6e72bd7e4b80f21ebbc78cfc5f791fa23b0c22cd3414a5ecaaf50c54e1789625901bd0f9a5357f523de5dbca02d75229557d8a032f2e7cdd345e7dae3dbe19d SHA512 8ff6a8a2ee4b70b14d0fa9984c057307fe5b7d22e8a26969d82fb1ab7ee30a90cb3520ea8d3e16a59f09dfc46a3310cb43c621fabb31a39216209a4c3523e718
 AUX eugene-4.1d-portable-getopt.patch 1433 BLAKE2B 8de256a490936a6c893c055917919a7cfc6a510675b4c12021d7cedb8a6cdf4aa73fb60d6ae4186b1df7abb784da09a9dc440464d8cbd90ac5d9ea758262391e SHA512 6a365eed393a27c080ec6f0eaa288a88e7909daa657637cb819aeb3e908934f8f228bd1026205402bc180e54c4ffe56be5ff5eedc95d3817b65da08774c9496c
 DIST eugene-4.1d.tar.gz 7473965 BLAKE2B 537ba871b701a5c199791809f76ea883ff77fe768e27a69b95186ef82ab32cab9b5761405a9fadfeea9f58fe88cadce83bba4b1fa6cba5f4ede2347a516d1df0 SHA512 dab37930e211b3783954f6e4a762450760201b77e0b4214f16724516d9be583d0a7ec44a2f510e73f4370e9c2dc67a425456a057fdba8f51cb72386e16a26ef5
-EBUILD eugene-4.1d-r1.ebuild 950 BLAKE2B 33eeae7972f006763a905f06542482714564d8b46d05485886f9441520a3ec9e39620a583ec66d097bc2a26b62ccf953fcc2699075426b8b855541c0af26fd48 SHA512 95ef458f3af2b1ab478d239ebb83cf64105c3b9128e06e72642d0e559ef405beb7e6b2b494320a7a866a108498715408ee693111a0b3ebd5e02297c156811cd0
+EBUILD eugene-4.1d-r1.ebuild 990 BLAKE2B 3c00ecefa82adfd64bc57cc9f8ad89e09cb29a2bec5a4552b64bd7477173f56a4bdca24f2dc2001385bf45800f4c865ea7095f8b7e181c528fa4dbee26e11e40 SHA512 a6ba26dd315a52f65a2e7a501ad515caa6fa499ef560d4c5b2b94586a146c6b84852fdbe8f6fc662088b2a72597a9b45e7a7a20cbeca0ccc742033d25f181e7d
 MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de
diff --git a/sci-biology/eugene/eugene-4.1d-r1.ebuild b/sci-biology/eugene/eugene-4.1d-r1.ebuild
index b1d9f409c096..40fb83ffc058 100644
--- a/sci-biology/eugene/eugene-4.1d-r1.ebuild
+++ b/sci-biology/eugene/eugene-4.1d-r1.ebuild
@@ -27,6 +27,7 @@ PATCHES=(
 	"${FILESDIR}"/${PN}-4.1d-fix-c++14.patch
 	"${FILESDIR}"/${PN}-4.1d-Wformat.patch
 	"${FILESDIR}"/${PN}-4.1d-portable-getopt.patch
+	"${FILESDIR}"/${PN}-4.1d-clang16.patch
 )
 
 src_prepare() {
diff --git a/sci-biology/eugene/files/eugene-4.1d-clang16.patch b/sci-biology/eugene/files/eugene-4.1d-clang16.patch
new file mode 100644
index 000000000000..21a3ec0a8b62
--- /dev/null
+++ b/sci-biology/eugene/files/eugene-4.1d-clang16.patch
@@ -0,0 +1,22 @@
+--- a/src/GDIF/gdIF.c
++++ b/src/GDIF/gdIF.c
+@@ -228,7 +228,7 @@
+ 		    ToY(phase, pos), (unsigned char *)st, Col[col]);
+ }
+ 
+-void ClosePNG()
++void ClosePNG(void)
+ {
+   int i;
+ 
+--- a/src/SensorPlugins/0_SensorTk/markov.cc
++++ b/src/SensorPlugins/0_SensorTk/markov.cc
+@@ -790,7 +790,7 @@
+ // cumule les valeurs des cases des codons synonymes et renvoie le total.
+ template<class CHAINE, typename T> T TabChaine<CHAINE,T> :: cumuleVAL (int indice) const
+ {
+-  char* codegenetique=CODEGENETIQUE;
++  const char* codegenetique=CODEGENETIQUE;
+   T cumul=0;
+   for (int i=0 ; i<64 ; i++) {
+     if ( codegenetique[i] == codegenetique[indice] )
diff --git a/sci-biology/poa/Manifest b/sci-biology/poa/Manifest
index b9b4d77ee43b..b867b628de1e 100644
--- a/sci-biology/poa/Manifest
+++ b/sci-biology/poa/Manifest
@@ -1,5 +1,6 @@
+AUX poa-2-clang16.patch 2406 BLAKE2B 24a49f9b9c3acc33541f7143250d871584c9bab2ec28a46cbaa7100377b9fcc3906490a4903b36d3f51e1fbcfd88f8182c477b3491a94dd3bdee3016be4e833d SHA512 dd2fd8e3e0f644648f93beea89784ee0008eeaae5231fd7c50f1cba2eb7327857c0be4cbc435d2dfd6834cf09b2f9d97d954a856142e06bfe44344ac80947477
 AUX poa-2-fno-common.patch 357 BLAKE2B 5d239201e987f1fc45e82019a27b2c8e81015cd2b6b5b35f90838a8fff16bb08b51da5e6e9e1ac163bd6591341ba96a870fce4949a79e9ca558ce8c765d15ba4 SHA512 9d8f6552fd43a0f40da9cb7a5316e0e434df793fb9f7522b60e067061d14a7b27299feb02a8603cb4f6039b205723f562ea5c54c15ab3bd6582f2e6e7c223c43
 AUX poa-2-respect-flags.patch 874 BLAKE2B ee278cdbc6ec0603bc28087bd008caa70fe39668360a1473891ed997bde93f31ef7586acc9137a23a4d3123047ce5b600c3d6418a89e1e62ca70545b99a3112b SHA512 95e2e7c43ba18f9238b379ea13d3a6004cf580c75d484dbe43f01c823484f84eb93c3d2fe1ae3c98583c51c660ab24e6dc580d132649adedbf30d8675d8107b0
 DIST poaV2.tar.gz 62612 BLAKE2B 92f7b2926dd7fc93745411fc04c8dd3380c32e3e87cf89afa81aefe787a1aa0e7a416d08809cce531a21d5118398a9474a751a742ee1fca47e83bd907444e9c0 SHA512 2a54b025f0a74ff4c01828f3e4b9e8e135bffe26d08f651f981bc95a64196173b5d887ef988a25c1f5fbf89333b4771622d5dc93946d66e7ec9abacb6167595c
-EBUILD poa-2-r1.ebuild 857 BLAKE2B 436c6a4db2fa826ebb3f0a3d59df5d88f746a6c025f227be6b4916f7b6b34dde51013ae48355ea080dc19ba763972e62d3b1a87b17c19349ba0f3ed2df50409c SHA512 7fadf68dd86ac01c83eb65ef6e8512428b7c5fa84b1071f538458e46ff3116d02ff4f18a7d8e2bc32c360caee2bac2ca998a3a824442f662613a8808e893e7b7
+EBUILD poa-2-r1.ebuild 891 BLAKE2B 4c0e42af595a527f95ce4248146774a322fe7d1e2d309664c6dcd37c588511f0bfc33a1274dd96d89fd4780f69fc61641e6c1a7cdd4d03c6d445fb12dd7d58f0 SHA512 d89e34e9733879d1bce07d4d2f357cf1fa7b10461c407ba89640c674d4557d5e3ec34fc2537e1e31ce484bbe6ec898ce248b9de3243eca0c91e123d9969f8cc0
 MISC metadata.xml 348 BLAKE2B a159034e493b50e7390db0516a4f478d14877323a256152eb9e596251cc71b161a38f9b740313f015ed2ef1757d0110d7e368eabf37b0e295d063d3770708ec7 SHA512 6452fa4eda03932e1ddfb7ac88b5b5dd4ea5429767ea06d1ac4db1df87e88159333a7c817f101b34975d20cb35d0b62f8947d658eba47ab917c0ecfa106f29d1
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() {
diff --git a/sci-biology/unafold/Manifest b/sci-biology/unafold/Manifest
index 4a2a02fb5201..0baa8116410e 100644
--- a/sci-biology/unafold/Manifest
+++ b/sci-biology/unafold/Manifest
@@ -1,4 +1,6 @@
+AUX unafold-3.8-autotools.patch 1278 BLAKE2B a21de292b1deeb7292f009e9ec8814d89dcb6fd1df761814d0972be4455f0b54cca8f82c0d6a374e31be8128a64677007e433cf0570fb947334a6f033b3e8e3b SHA512 8b9c838d24f0d538e83f7879031611c7c664f57dcb615fa8a5d372604cf5477c33031543fe62f62fc075f955434a8e20cac5ade2b3ccf40c113ffffd2a816a29
+AUX unafold-3.8-clang16.patch 14214 BLAKE2B de04583f894c16c6f83b8ab3e8780f04e8095c39fe8bb28e66844c198e0cc4f5fe2bde739c468f21280a14367e0ab85c39db11231c2fb7e647db507d51974f79 SHA512 35fa92f981855db18f8b8b420d659740e589f309d8830393727ddb576867aecb1e9b336259bb345f984d4456c24d7062d86189411a83227b481619c59c35ad1d
 AUX unafold-3.8-doc-version.patch 308 BLAKE2B 6fba108c6338f9b974fc20e328f9af7d4ffc735889a32b74e36573ed68453af11922c15c626c48b997784378ad9cec79fe928ef184a224bcca570c7d59158851 SHA512 53a7ad53704830ac50fa463fb340cd8823e57af83b97ee40a969a338af62bce11934bc54b37a43b4f5bdd4faea919b2e3b4d8532926a8c185f53dcb5ce3c5afd
 DIST unafold-3.8.tar.bz2 282418 BLAKE2B 0dddff9dc440362ce3b24d18f42aa47d2dc817de93eba900de76dc73393feabb09ac57cb77af6c8db0ab8c0958f0fd459911fd813fa004b616fedffe9aebd069 SHA512 4c83cf0122e4d4ec2b713833adb11eb608b0f880f5b68114aefd8c7fa980c8d02f9a6cfc0c88cd640b4457e65954b05189118e8ac5ed207b2f9910738ca71a6c
-EBUILD unafold-3.8-r1.ebuild 609 BLAKE2B 4f6e5867e63d272781eb88b6cfef00e41a067b7e97a8c61ee0e5c380369e155452afa6c35f153a3b3c39ea54cd02c2ed039ea793fb0f52b7afc91bf45e2c8ca4 SHA512 3ffe39a79f0162a645237cc5c4763abd0b41775f09546d2cf792ed9dcfe30219ba9540feac3ae8758616c5f0f48de3b7643b17d6682cf426a8f9f799e509b9e1
+EBUILD unafold-3.8-r1.ebuild 686 BLAKE2B e4e4a071fd3f40b47ab5fcd12b43c570ec0763a155475b212097aea3204a36054aa35f9dec17ca3844cbdb781d0f558a77375276b84a0a311ce9867e0ed45f4a SHA512 fa059582b7bf49731b61985a288c91c37a002b2950c87647568dc0de6fff0f2078633a70ce42508999cdd61b4b1867ad7a8498485a7675e2b90d6a2711fd25b5
 MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de
diff --git a/sci-biology/unafold/files/unafold-3.8-autotools.patch b/sci-biology/unafold/files/unafold-3.8-autotools.patch
new file mode 100644
index 000000000000..ecf29b470c2c
--- /dev/null
+++ b/sci-biology/unafold/files/unafold-3.8-autotools.patch
@@ -0,0 +1,41 @@
+--- a/configure.ac
++++ b/configure.ac
+@@ -2,7 +2,7 @@
+ AC_INIT(UNAFold, 3.8, markhn@rpi.edu)
+ AC_CONFIG_SRCDIR(src/hybrid.c)
+ AC_CONFIG_AUX_DIR(config)
+-AM_CONFIG_HEADER(config.h:config.in)
++AC_CONFIG_HEADERS(config.h:config.in)
+ AM_INIT_AUTOMAKE
+ AC_CANONICAL_BUILD
+ AC_PROG_CC
+@@ -12,7 +12,6 @@
+ if test -z "$PERL"; then
+    AC_MSG_ERROR(Perl not found)
+ fi
+-AC_PROG_PERL_VERSION(5.6.1, , AC_MSG_ERROR(Perl 5.6.1 or better is required))
+ AC_CHECK_PROG(GNUPLOT, gnuplot, [system('gnuplot', \"\$prefix.gp\") == 0 or die $!;])
+ 
+ AC_MSG_CHECKING(whether compiler needs -mieee)
+@@ -28,6 +27,7 @@
+ 
+ 
+ # Checks for libraries.
++AX_CHECK_GL
+ AX_CHECK_GLUT
+ AM_CONDITIONAL(GLUT, test -n "$GLUT_LIBS")
+ AX_CHECK_GD
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -33,9 +33,9 @@
+ endif GLUT
+ 
+ hybrid_plot_ng_SOURCES = hybrid-plot-ng.c getopt.h util.h xmalloc.h
+-hybrid_plot_ng_CFLAGS = @GD_CFLAGS@
++hybrid_plot_ng_CFLAGS = @GD_CFLAGS@ $(GL_CFLAGS)
+ hybrid_plot_ng_LDFLAGS = @GD_LDFLAGS@
+-hybrid_plot_ng_LDADD = getopt.$(OBJEXT) getopt1.$(OBJEXT) xmalloc.$(OBJEXT) @GD_LIBS@ -lm
++hybrid_plot_ng_LDADD = getopt.$(OBJEXT) getopt1.$(OBJEXT) xmalloc.$(OBJEXT) @GD_LIBS@ $(GL_LIBS) -lm
+ 
+ sbs_SOURCES = getopt.c getopt1.c energy.c xmalloc.c sbs.c energy.h getopt.h xmalloc.h
+ sbs_LDADD = -lm
diff --git a/sci-biology/unafold/files/unafold-3.8-clang16.patch b/sci-biology/unafold/files/unafold-3.8-clang16.patch
new file mode 100644
index 000000000000..fabc28e1fd88
--- /dev/null
+++ b/sci-biology/unafold/files/unafold-3.8-clang16.patch
@@ -0,0 +1,775 @@
+--- a/src/ct-energy.c
++++ b/src/ct-energy.c
+@@ -24,8 +24,8 @@
+ double auPenalty(int, int);
+ double chooseDangle(int, int);
+ double tstackOrDangle(int, int, int);
+-int isHomodimer();
+-int isCircular();
++int isHomodimer(void);
++int isCircular(void);
+ 
+ int readStructure(FILE* file);
+ 
+@@ -87,7 +87,7 @@
+   {NULL, 0, NULL, 0}
+ };
+ 
+-void usage()
++void usage(void)
+ {
+   puts("Usage: ct-energy [OPTION] [FILE]...");
+   puts("");
+@@ -1247,7 +1247,7 @@
+   return 1;
+ }
+ 
+-int isHomodimer()
++int isHomodimer(void)
+ {
+   int i;
+ 
+@@ -1272,7 +1272,7 @@
+   return 1;
+ }
+ 
+-int isCircular()
++int isCircular(void)
+ {
+   return g_prev[0] == g_len && g_next[g_len - 1] % g_len == 1;
+ }
+--- a/src/energy.c
++++ b/src/energy.c
+@@ -15,6 +15,7 @@
+ #endif
+ 
+ #include "energy.h"
++#include "util.h"
+ #include "xmalloc.h"
+ 
+ #ifndef isinf
+--- a/src/hybrid.c
++++ b/src/hybrid.c
+@@ -39,10 +39,10 @@
+ #endif
+ 
+ void initializeMatrix(double**, int, double);
+-void limitBasePairs();
+-void prohibit();
+-void force();
+-void prefilter();
++void limitBasePairs(void);
++void prohibit(void);
++void force(void);
++void prefilter(void);
+ void fillMatrix(double**, int, double);
+ void fillMatrix_noI(double**, int, double);
+ void calculateProb(double**, double*, double*, double**, double**, double, double, int, double);
+@@ -706,7 +706,7 @@
+       matrix[i - 1][n - 1] = (reverse ? R0(n, i) : L0(i, n));
+ }
+ 
+-void limitBasePairs()
++void limitBasePairs(void)
+ {
+   if (g_bpFile)
+     {
+@@ -740,7 +740,7 @@
+     }
+ }
+ 
+-void prohibit()
++void prohibit(void)
+ {
+   int i, j, k;
+   struct constraintListNode *top, *newTop;
+@@ -788,7 +788,7 @@
+ }
+ 
+ #if ENABLE_FORCE
+-void force()
++void force(void)
+ {
+   int i, j, k;
+   struct constraintListNode *top, *newTop;
+@@ -880,7 +880,7 @@
+ 	}
+ } */
+ 
+-void prefilter()
++void prefilter(void)
+ {
+   char** in;
+   int i, j, k, count;
+--- a/src/hybrid-min.c
++++ b/src/hybrid-min.c
+@@ -53,10 +53,10 @@
+ } *pairList;
+ 
+ void initializeMatrices(double);
+-void limitBasePairs();
+-void prohibit();
+-void force();
+-void prefilter();
++void limitBasePairs(void);
++void prohibit(void);
++void force(void);
++void prefilter(void);
+ void fillMatrixL(double);
+ void fillMatrixR(double);
+ void fillMatrixL_noI(double);
+@@ -88,7 +88,7 @@
+ #define min2(a, b) ((a) < (b) ? (a) : (b))
+ ENERGY min4(ENERGY, ENERGY, ENERGY, ENERGY);
+ void pushPairList(int, int, int, ENERGY);
+-void sortPairList();
++void sortPairList(void);
+ 
+ ENERGY *lprime, *rprime;
+ 
+@@ -885,7 +885,7 @@
+ 	}
+ }
+ 
+-void limitBasePairs()
++void limitBasePairs(void)
+ {
+   if (g_bpFile)
+     {
+@@ -919,7 +919,7 @@
+     }
+ }
+ 
+-void prohibit()
++void prohibit(void)
+ {
+   int i, j, k;
+   struct constraintListNode* top;
+@@ -965,7 +965,7 @@
+ }
+ 
+ #if ENABLE_FORCE
+-void force()
++void force(void)
+ {
+   int i, j, k;
+   struct constraintListNode* top;
+@@ -1041,7 +1041,7 @@
+   return length;
+ }
+ 
+-void prefilter()
++void prefilter(void)
+ {
+   int i, j;
+ 
+@@ -1055,7 +1055,7 @@
+ 	}
+ } */
+ 
+-void prefilter()
++void prefilter(void)
+ {
+   char** in;
+   int i, j, k, count;
+@@ -2235,7 +2235,7 @@
+   pairList = node;
+ }
+ 
+-void sortPairList()
++void sortPairList(void)
+ {
+   struct pairListNode *a, *b;
+ 
+--- a/src/hybrid-plot.c
++++ b/src/hybrid-plot.c
+@@ -70,13 +70,13 @@
+ void displayCallbackInput(void);
+ void keyboardCallbackInput(unsigned char, int, int);
+ 
+-void fixLength();
+-void fixGrid();
+-void fixLabels();
+-void fixZoomGrid();
+-void fixZoomLabels();
++void fixLength(void);
++void fixGrid(void);
++void fixLabels(void);
++void fixZoomGrid(void);
++void fixZoomLabels(void);
+ void readFiles(char*);
+-void sortTemps();
++void sortTemps(void);
+ double* inputRecords(FILE*);
+ int filter(int, int);
+ 
+@@ -1157,7 +1157,7 @@
+     }
+ }
+ 
+-void fixLength()
++void fixLength(void)
+ {
+   int m, n;
+ 
+@@ -1177,7 +1177,7 @@
+     }
+ }
+ 
+-void fixGrid()
++void fixGrid(void)
+ {
+   int m;
+ 
+@@ -1193,7 +1193,7 @@
+     g_grid = pow(10, m + 1);
+ }
+ 
+-void fixLabels()
++void fixLabels(void)
+ {
+   int longestNum;
+ 
+@@ -1202,7 +1202,7 @@
+     g_labels += g_grid;
+ }
+ 
+-void fixZoomGrid()
++void fixZoomGrid(void)
+ {
+   int m;
+ 
+@@ -1221,7 +1221,7 @@
+     g_zoomGrid = pow(10, m + 1);
+ }
+ 
+-void fixZoomLabels()
++void fixZoomLabels(void)
+ {
+   int longestNum;
+ 
+@@ -1310,7 +1310,7 @@
+   return scores;
+ }
+ 
+-void sortTemps()
++void sortTemps(void)
+ {
+   int i, j;
+   char* tempC;
+--- a/src/hybrid-plot-ng.c
++++ b/src/hybrid-plot-ng.c
+@@ -24,28 +24,28 @@
+  */
+ 
+ #if HAVE_GD
+-void initPNG();
++void initPNG(void);
+ void titlePNG(char*);
+-void borderPNG();
+-void gridPNG();
++void borderPNG(void);
++void gridPNG(void);
+ void plotDotPNG(int, int, double);
+ void vertCenterPNG(char*, int);
+ void horzCenterPNG(char*, int);
+ void selectionPNG(char*, int);
+ #endif
+ 
+-void initPS();
++void initPS(void);
+ void titlePS(char*);
+-void borderPS();
+-void gridPS();
++void borderPS(void);
++void gridPS(void);
+ void plotDotPS(int, int, double);
+ void vertCenterPS(char*, int);
+ void horzCenterPS(char*, int);
+ void selectionPS(char*, int);
+ 
+-void fixSize();
+-void fixGrid();
+-void fixLabels();
++void fixSize(void);
++void fixGrid(void);
++void fixLabels(void);
+ double* inputRecords(FILE*);
+ int filter(int, int);
+ int (*getColor)(double);
+@@ -114,10 +114,10 @@
+   char* plotFile;
+ 
+   /* functions to call - either PS or PNG */
+-  void (*init)();
++  void (*init)(void);
+   void (*title)(char*);
+-  void (*border)();
+-  void (*grid)();
++  void (*border)(void);
++  void (*grid)(void);
+   void (*plotDot)(int, int, double);
+   void (*vertCenter)(char*, int);
+   void (*horzCenter)(char*, int);
+@@ -474,7 +474,7 @@
+   return 0;
+ }
+ 
+-void initPS()
++void initPS(void)
+ {
+   int i;
+ 
+@@ -517,7 +517,7 @@
+   fprintf(g_file, "(%s) showCenter\n", wordString);
+ }
+ 
+-void borderPS()
++void borderPS(void)
+ {
+   fputs("92 126 moveto\n", g_file);
+   fputs("576 126 lineto\n", g_file);
+@@ -527,7 +527,7 @@
+   fputs("stroke\n", g_file);
+ }
+ 
+-void gridPS()
++void gridPS(void)
+ {
+   double x1, y1;
+   int i, j;
+@@ -639,7 +639,7 @@
+ 
+ #if HAVE_GD
+ 
+-void initPNG()
++void initPNG(void)
+ {
+   int i;
+ 
+@@ -671,12 +671,12 @@
+   gdImageString(g_image, gdFontMediumBold, 306 - 7 * strlen(wordString) / 2, 51, (unsigned char*) wordString, g_black);
+ }
+ 
+-void borderPNG()
++void borderPNG(void)
+ {
+   gdImageRectangle(g_image, 92, 92, 576, 576, g_black);
+ }
+ 
+-void gridPNG()
++void gridPNG(void)
+ {
+   int i, j;
+   char buffer[8];
+@@ -776,7 +776,7 @@
+ 
+ #endif
+ 
+-void fixSize()
++void fixSize(void)
+ {
+   int m, n;
+ 
+@@ -796,7 +796,7 @@
+     }
+ }
+ 
+-void fixGrid()
++void fixGrid(void)
+ {
+   int m;
+ 
+@@ -812,7 +812,7 @@
+     g_grid = pow(10, m + 1);
+ }
+ 
+-void fixLabels()
++void fixLabels(void)
+ {
+   int longestNum;
+ 
+--- a/src/hybrid-ss.c
++++ b/src/hybrid-ss.c
+@@ -47,10 +47,10 @@
+ #define ssOK(i, j) 1
+ #endif
+ 
+-void initializeMatrices();
+-void fillMatrices1();
++void initializeMatrices(void);
++void fillMatrices1(void);
+ void fillMatrices2(double*, double*);
+-void fillMatrices1_noI();
++void fillMatrices1_noI(void);
+ void fillMatrices2_noI(double*, double*);
+ void calculateProb(double*, double*, double*, double*, double*, double);
+ void calculateProb_noI(double*, double*, double*, double*, double*);
+@@ -713,7 +713,7 @@
+ 
+ #include "hybrid-ss_init.h"
+ 
+-void fillMatrices1()
++void fillMatrices1(void)
+ {
+   int i, j, k;
+   FILE* file;
+@@ -783,7 +783,7 @@
+     }
+ }
+ 
+-void fillMatrices1_noI()
++void fillMatrices1_noI(void)
+ {
+   int i, j, k;
+   FILE* file;
+--- a/src/hybrid-ss_init.h
++++ b/src/hybrid-ss_init.h
+@@ -14,7 +14,7 @@
+   return length;
+ } */
+ 
+-void prefilter()
++void prefilter(void)
+ {
+   char** in;
+   int i, j, k, count;
+@@ -45,7 +45,7 @@
+   free(in);
+ }
+ 
+-void initializeMatrices()
++void initializeMatrices(void)
+ {
+   int i, j, k;
+   struct constraintListNode *top, *newTop;
+--- a/src/hybrid-ss-min.c
++++ b/src/hybrid-ss-min.c
+@@ -57,10 +57,10 @@
+   struct pairListNode* next;
+ } *pairList;
+ 
+-void initializeMatrices();
+-void fillMatrices1();
+-void fillMatrices2();
+-void computeQ53();
++void initializeMatrices(void);
++void fillMatrices1(void);
++void fillMatrices2(void);
++void computeQ53(void);
+ void traceback(int, int, int, int*, int*, int*);
+ void traceback_noI(int, int, int, int*, int*, int*);
+ void setStack(int, int, int*, int*);
+@@ -108,7 +108,7 @@
+ int equal(ENERGY, ENERGY);
+ void push(struct stackNode**, int, int, int);
+ void pushPairList(int, int, int, ENERGY);
+-void sortPairList();
++void sortPairList(void);
+ 
+ int g_len;
+ ENERGY *q, *qprime, *qm, *q5, *q3;
+@@ -887,7 +887,7 @@
+   return length;
+ }
+ 
+-void prefilter()
++void prefilter(void)
+ {
+   char** in;
+   int i, j, k, count;
+@@ -918,7 +918,7 @@
+   free(in);
+ }
+ 
+-void initializeMatrices()
++void initializeMatrices(void)
+ {
+   int i, j, k;
+   struct constraintListNode* top;
+@@ -1072,7 +1072,7 @@
+     }
+ }
+ 
+-void fillMatrices1()
++void fillMatrices1(void)
+ {
+   int i, j, k;
+   FILE* file;
+@@ -1181,7 +1181,7 @@
+     }
+ }
+ 
+-void fillMatrices2()
++void fillMatrices2(void)
+ {
+   int i, j, k;
+   FILE* file;
+@@ -1283,7 +1283,7 @@
+     }
+ }
+ 
+-void computeQ53()
++void computeQ53(void)
+ {
+   int i, j;
+ 
+@@ -3137,7 +3137,7 @@
+   pairList = node;
+ }
+ 
+-void sortPairList()
++void sortPairList(void)
+ {
+   struct pairListNode *a, *b;
+ 
+--- a/src/hybrid-ss-noml.c
++++ b/src/hybrid-ss-noml.c
+@@ -45,11 +45,11 @@
+ #define ssOK(i, j) 1
+ #endif
+ 
+-void initializeMatrices();
+-void fillMatrices1();
+-void fillMatrices2();
+-void fillMatrices1_noI();
+-void fillMatrices2_noI();
++void initializeMatrices(void);
++void fillMatrices1(void);
++void fillMatrices2(void);
++void fillMatrices1_noI(void);
++void fillMatrices2_noI(void);
+ void calculateProb(double*, double*, double*, double);
+ void calculateProb_noI(double*, double*, double*, double);
+ void traceback(int*, int*, int*);
+@@ -652,7 +652,7 @@
+   return length;
+ } */
+ 
+-void prefilter()
++void prefilter(void)
+ {
+   char** in;
+   int i, j, k, count;
+@@ -683,7 +683,7 @@
+   free(in);
+ }
+ 
+-void initializeMatrices()
++void initializeMatrices(void)
+ {
+   int i, j, k;
+   struct constraintListNode *top, *newTop;
+@@ -826,7 +826,7 @@
+ 	}
+ }
+ 
+-void fillMatrices1()
++void fillMatrices1(void)
+ {
+   int i, j, k;
+   FILE* file;
+@@ -885,7 +885,7 @@
+     }
+ }
+ 
+-void fillMatrices1_noI()
++void fillMatrices1_noI(void)
+ {
+   int i, j, k;
+   FILE* file;
+@@ -944,7 +944,7 @@
+     }
+ }
+ 
+-void fillMatrices2()
++void fillMatrices2(void)
+ {
+   int i, j;
+   FILE* file;
+@@ -986,7 +986,7 @@
+     }
+ }
+ 
+-void fillMatrices2_noI()
++void fillMatrices2_noI(void)
+ {
+   int i, j;
+   FILE* file;
+--- a/src/hybrid-ss-simple.c
++++ b/src/hybrid-ss-simple.c
+@@ -47,11 +47,11 @@
+ #define ssOK(i, j) 1
+ #endif
+ 
+-void initializeMatrices();
+-void fillMatrices1();
+-void fillMatrices2();
+-void fillMatrices1_noI();
+-void fillMatrices2_noI();
++void initializeMatrices(void);
++void fillMatrices1(void);
++void fillMatrices2(void);
++void fillMatrices1_noI(void);
++void fillMatrices2_noI(void);
+ void calculateProb(double*, double*, double*, double);
+ void calculateProb_noI(double*, double*, double*);
+ void traceback(int*, int*, int*);
+@@ -598,7 +598,7 @@
+ 
+ #include "hybrid-ss_init.h"
+ 
+-void fillMatrices1()
++void fillMatrices1(void)
+ {
+   int i, j, k;
+   FILE* file;
+@@ -658,7 +658,7 @@
+     }
+ }
+ 
+-void fillMatrices1_noI()
++void fillMatrices1_noI(void)
+ {
+   int i, j, k;
+   FILE* file;
+@@ -718,7 +718,7 @@
+     }
+ }
+ 
+-void fillMatrices2()
++void fillMatrices2(void)
+ {
+   int i, j, k;
+   FILE* file;
+@@ -789,7 +789,7 @@
+     }
+ }
+ 
+-void fillMatrices2_noI()
++void fillMatrices2_noI(void)
+ {
+   int i, j, k;
+   FILE* file;
+--- a/src/util.h
++++ b/src/util.h
+@@ -24,18 +24,18 @@
+ 
+ /* #define NO_GU_BASEPAIRS */
+ 
+-int roundInt(double d)
++static int roundInt(double d)
+ {
+   return (int) (d + .5);
+ }
+ 
+-void strcatc(char* str, char c)
++static void strcatc(char* str, char c)
+ {
+   str[strlen(str) + 1] = 0;
+   str[strlen(str)] = c;
+ }
+ 
+-char* filename(char* file)
++static char* filename(char* file)
+ {
+   char* name;
+ 
+@@ -46,7 +46,7 @@
+   return name;
+ }
+ 
+-void checkArray(char** array, unsigned int* available, unsigned int used, unsigned int increment)
++static void checkArray(char** array, unsigned int* available, unsigned int used, unsigned int increment)
+ {
+   if (used == *available)
+     {
+@@ -55,7 +55,7 @@
+     }
+ }
+ 
+-int input(FILE* file, char** name, char** sequence)
++static int input(FILE* file, char** name, char** sequence)
+ {
+   /* read string from file */
+   int current, last, state;
+@@ -120,7 +120,7 @@
+   return 1;
+ }
+ 
+-unsigned char toNum(char c)
++static unsigned char toNum(char c)
+ {
+   c = toupper(c);
+   switch (c)
+@@ -137,7 +137,7 @@
+   return 4;
+ }
+ 
+-int seqcmp(unsigned char* seq1, unsigned char* seq2, int length)
++static int seqcmp(unsigned char* seq1, unsigned char* seq2, int length)
+ {
+   int i;
+ 
+@@ -149,7 +149,7 @@
+   return 0;
+ }
+ 
+-void readSequence(char* file, char** name, char** string, unsigned char** seq, int* len)
++static void readSequence(char* file, char** name, char** string, unsigned char** seq, int* len)
+ {
+   int i;
+   FILE* f;
+@@ -171,14 +171,14 @@
+ }
+ 
+ #ifdef NO_GU_BASEPAIRS
+-const int BPI[6][6] = {{6, 6, 6, 0, 6, 6},
++static const int BPI[6][6] = {{6, 6, 6, 0, 6, 6},
+ 		       {6, 6, 1, 6, 6, 6},
+ 		       {6, 2, 6, 6, 6, 6},
+ 		       {3, 6, 6, 6, 6, 6},
+ 		       {6, 6, 6, 6, 6, 6},
+ 		       {6, 6, 6, 6, 6, 6}};
+ #else
+-const int BPI[6][6] = {{6, 6, 6, 0, 6, 6},
++static const int BPI[6][6] = {{6, 6, 6, 0, 6, 6},
+ 		       {6, 6, 1, 6, 6, 6},
+ 		       {6, 2, 6, 4, 6, 6},
+ 		       {3, 6, 5, 6, 6, 6},
+@@ -187,7 +187,7 @@
+ #endif
+ #define basePairIndex(a, b) BPI[a][b]
+ 
+-int min3(int a, int b, int c)
++static int min3(int a, int b, int c)
+ {
+   if (a <= b && a <= c)
+     return a;
+@@ -196,7 +196,7 @@
+   return c;
+ }
+ 
+-int same(unsigned char* a, unsigned char* b, int len)
++static int same(unsigned char* a, unsigned char* b, int len)
+ {
+   int i;
+ 
+@@ -206,7 +206,7 @@
+   return 1;
+ }
+ 
+-void version(const char* prog)
++static void version(const char* prog)
+ {
+   printf("%s (%s) %s\n", prog, PACKAGE_NAME, PACKAGE_VERSION);
+   puts("By Nicholas R. Markham and Michael Zuker");
+@@ -216,7 +216,7 @@
+   exit(EXIT_SUCCESS);
+ }
+ 
+-void readOrDie(unsigned int num, const char* name, FILE* file, const char* format, ...)
++static void readOrDie(unsigned int num, const char* name, FILE* file, const char* format, ...)
+ {
+   va_list arg;
+   va_start(arg, format);
diff --git a/sci-biology/unafold/unafold-3.8-r1.ebuild b/sci-biology/unafold/unafold-3.8-r1.ebuild
index 6aec75f0336d..51bbe5dfd325 100644
--- a/sci-biology/unafold/unafold-3.8-r1.ebuild
+++ b/sci-biology/unafold/unafold-3.8-r1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
-inherit flag-o-matic
+inherit autotools
 
 DESCRIPTION="Unified Nucleic Acid Folding and hybridization package"
 HOMEPAGE="http://mfold.rna.albany.edu/"
@@ -12,19 +12,25 @@ SRC_URI="http://dinamelt.bioinfo.rpi.edu/download/${P}.tar.bz2"
 LICENSE="unafold"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE="custom-cflags"
 
 RDEPEND="
 	media-libs/freeglut
 	media-libs/gd
 	virtual/opengl"
 DEPEND="${RDEPEND}"
+BDEPEND="sys-devel/autoconf-archive"
 
-PATCHES=( "${FILESDIR}"/${P}-doc-version.patch )
-
-src_configure() {
-	# recommended in README
-	use custom-cflags || append-flags -O3
+PATCHES=(
+	"${FILESDIR}"/${P}-doc-version.patch
+	"${FILESDIR}"/${P}-autotools.patch
+	"${FILESDIR}"/${P}-clang16.patch
+)
 
+src_prepare() {
 	default
+	eautoreconf
+}
+
+src_configure() {
+	econf --disable-coverage
 }