From ba3d6ddada23eaa04f85228bee3438ab479b4442 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Sun, 23 Oct 2022 21:50:52 +0100 Subject: gentoo auto-resync : 23:10:2022 - 21:50:51 --- sci-biology/Manifest.gz | Bin 19999 -> 20002 bytes sci-biology/eugene/Manifest | 3 +- sci-biology/eugene/eugene-4.1d-r1.ebuild | 1 + sci-biology/eugene/files/eugene-4.1d-clang16.patch | 22 + sci-biology/poa/Manifest | 3 +- sci-biology/poa/files/poa-2-clang16.patch | 74 ++ sci-biology/poa/poa-2-r1.ebuild | 3 +- sci-biology/unafold/Manifest | 4 +- .../unafold/files/unafold-3.8-autotools.patch | 41 ++ .../unafold/files/unafold-3.8-clang16.patch | 775 +++++++++++++++++++++ sci-biology/unafold/unafold-3.8-r1.ebuild | 24 +- 11 files changed, 937 insertions(+), 13 deletions(-) create mode 100644 sci-biology/eugene/files/eugene-4.1d-clang16.patch create mode 100644 sci-biology/poa/files/poa-2-clang16.patch create mode 100644 sci-biology/unafold/files/unafold-3.8-autotools.patch create mode 100644 sci-biology/unafold/files/unafold-3.8-clang16.patch (limited to 'sci-biology') diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz index bc1599b5acc3..997e93a3aa25 100644 Binary files a/sci-biology/Manifest.gz and b/sci-biology/Manifest.gz differ 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 T TabChaine :: 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 } -- cgit v1.2.3