diff options
Diffstat (limited to 'sci-biology/dialign2')
| -rw-r--r-- | sci-biology/dialign2/Manifest | 5 | ||||
| -rw-r--r-- | sci-biology/dialign2/dialign2-2.2.1-r1.ebuild (renamed from sci-biology/dialign2/dialign2-2.2.1.ebuild) | 24 | ||||
| -rw-r--r-- | sci-biology/dialign2/files/dialign2-2.2.1-Wimplicit.patch | 205 | ||||
| -rw-r--r-- | sci-biology/dialign2/files/dialign2-2.2.1-fix-build-system.patch | 6 |
4 files changed, 225 insertions, 15 deletions
diff --git a/sci-biology/dialign2/Manifest b/sci-biology/dialign2/Manifest index 137467c1ad2b..4e0d01571cdf 100644 --- a/sci-biology/dialign2/Manifest +++ b/sci-biology/dialign2/Manifest @@ -1,4 +1,5 @@ -AUX dialign2-2.2.1-fix-build-system.patch 819 BLAKE2B c639532a8bc95744c91f07f0e672255110b31e2964bb8bfbacaa6b401dcee6a10e29199d9a19614f690a610109c2a5f0ab785b66c144373ceb4724112182cab2 SHA512 8a85911d1743c186f3dea402333e502cfd4f7807065277a2657d790ab9cf1c8d535fbb25abf994f83cdab9849d4ec203d8db8198cf10fa91996d61b63d98f807 +AUX dialign2-2.2.1-Wimplicit.patch 5674 BLAKE2B e6af3beda47e2c0e3c73434c6aac27fc8c4ce3ca3a3f1b09f2719672270717235274886afd2c0e8b2f1eb76ae1f9ddf6f9cd66e6cc5d4a3794190dce2b72d676 SHA512 c6fccdfa3c6a373dcee9ea734085b2c4f5e9ee4a0218b91500cdcc52b429b9e787a8cb9c25cf96b589b9f95c57ffa522a4a75cca5b17064b2bfc21827269b962 +AUX dialign2-2.2.1-fix-build-system.patch 845 BLAKE2B bbc4dbfcae56bd463253b61a437f9dce0101b5bc3b70504408df3a37ca74f3e95ce450d42c4c49ea92eedbcb400b39905fe8650b37e2e93c5cfc21ae36e560c5 SHA512 dee19a8c430b79bbfc6c89bc6fe4cd0b300c24f4351cadaffd17cfaad71c38944f28f805efb46d0d66ea512005e47b838ceb85189bd4b8bd107db070ff0d0cb9 DIST dialign-2.2.1-src.tar.gz 209015 BLAKE2B daf903b735e164879a8ceb998ca5ea0c5243927d9b88b4041633af06da7d1f608d58933ee098393e99093b7d11587a59277d9d0927214df0341a8a623b0d5608 SHA512 eb51fbc8d81e384ac19e9cc957be233287a1d81a7f020d77ab16ee6943382bd4e81099c0c9028fcff130def62cdf19de59e9a9c08ea4cb67b9d8f1939eb3bc45 -EBUILD dialign2-2.2.1.ebuild 836 BLAKE2B abb98cbbfcfe09ead711558bb07b41dcd79aa706793d1aadff9eb258daac8bd42ccbef2fbb74602b0e71bc99aa863a749b0239d63c23edc78982116e4febcf0e SHA512 6714a835544683e1b135ee65aa0728e1f2943349358b4d1505c583f1beba3b4210f3fdec01625ef8bf7a92605274f47233e7ce630cd9a2996e77a098d1990e51 +EBUILD dialign2-2.2.1-r1.ebuild 817 BLAKE2B 2e34fd2980597cf20ad1e4a37c3ae4fed42cc0b50f728d6a1e90d4343eed8ad36b8675fdf32af4c0d00ceb57173ca27f3112149290bf94a294b522e3c350a8fc SHA512 2bafe6011fc6835275f4a16dc3d11a3ad964bf032df5adfd56d2d37f58071543a05e7766a0915806802950735115a5a2c836874e62557936e690e9a57cf98f6c MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de diff --git a/sci-biology/dialign2/dialign2-2.2.1.ebuild b/sci-biology/dialign2/dialign2-2.2.1-r1.ebuild index db310e3fe8d3..13b56b66c37b 100644 --- a/sci-biology/dialign2/dialign2-2.2.1.ebuild +++ b/sci-biology/dialign2/dialign2-2.2.1-r1.ebuild @@ -1,24 +1,26 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 -inherit flag-o-matic toolchain-funcs +inherit toolchain-funcs DESCRIPTION="Multiple sequence alignment" HOMEPAGE="http://bibiserv.techfak.uni-bielefeld.de/dialign" SRC_URI="http://bibiserv.techfak.uni-bielefeld.de/applications/dialign/resources/downloads/dialign-${PV}-src.tar.gz" +S="${WORKDIR}/dialign_package" LICENSE="LGPL-2.1" SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -S=${WORKDIR}/dialign_package -PATCHES=( "${FILESDIR}"/${PN}-2.2.1-fix-build-system.patch ) +PATCHES=( + "${FILESDIR}"/${PN}-2.2.1-fix-build-system.patch + "${FILESDIR}"/${PN}-2.2.1-Wimplicit.patch +) src_configure() { tc-export CC - append-cppflags -I. -DCONS } src_compile() { @@ -26,12 +28,12 @@ src_compile() { } src_install() { - dobin src/${PN}-2 - insinto /usr/share/${PN} + dobin src/dialign2-2 + + insinto /usr/share/dialign2 doins -r dialign2_dir/. - cat >> "${T}"/80${PN} <<- EOF || die - DIALIGN2_DIR="${EPREFIX}/usr/share/${PN}" + newenvd - 80dialign2 <<- EOF + DIALIGN2_DIR="${EPREFIX}/usr/share/dialign2" EOF - doenvd "${T}"/80${PN} } diff --git a/sci-biology/dialign2/files/dialign2-2.2.1-Wimplicit.patch b/sci-biology/dialign2/files/dialign2-2.2.1-Wimplicit.patch new file mode 100644 index 000000000000..3f886171b070 --- /dev/null +++ b/sci-biology/dialign2/files/dialign2-2.2.1-Wimplicit.patch @@ -0,0 +1,205 @@ +--- a/src/alig_graph_closure.c ++++ b/src/alig_graph_closure.c +@@ -27,7 +27,7 @@ + void init_seq(CLOSURE *clos, int nbreseq, int *longseq); + void desinit_seq(CLOSURE *clos); + +-int print_aligSets(CLOSURE *clos, int nseq, int i); ++void print_aligSets(CLOSURE *clos, int nseq, int i); + + char DEBUG=0; + +@@ -309,7 +309,7 @@ + } + + +-int print_aligSets(CLOSURE *clos, int nseq, int i) ++void print_aligSets(CLOSURE *clos, int nseq, int i) + { + char nouveau_, terminer; + int n, ng, nd, nn, k; +@@ -395,7 +395,7 @@ + liberer(clos); + } + +-int addAlignedPositions(CLOSURE *clos, int seq1, int i, int seq2, int j) ++void addAlignedPositions(CLOSURE *clos, int seq1, int i, int seq2, int j) + { + char nouveau_, terminer; + int n, n1, n2, ng1, ng2, nd1, nd2, nn, k; +@@ -623,7 +623,7 @@ + return(!path(clos, y, j, x, i)); + } + +-int addAlignedSegments(CLOSURE *clos, int x, int i, int y, int j, int l) ++void addAlignedSegments(CLOSURE *clos, int x, int i, int y, int j, int l) + { + int k; + +--- a/src/alig_graph_closure.h ++++ b/src/alig_graph_closure.h +@@ -43,13 +43,13 @@ + + void freeAligGraphClosure(CLOSURE *clos); + +-int addAlignedPositions(CLOSURE *clos, int x, int i, int y, int j); ++void addAlignedPositions(CLOSURE *clos, int x, int i, int y, int j); + + int alignablePositions(CLOSURE *clos, int x, int i, int y, int j); + + int alignedPositions(CLOSURE *clos, int x, int i, int y, int j); + +-int addAlignedSegments(CLOSURE *clos, int x, int i, int y, int j, int l); ++void addAlignedSegments(CLOSURE *clos, int x, int i, int y, int j, int l); + + int alignableSegments(CLOSURE *clos, int x, int i, int y, int j, int l); + +--- a/src/anchor.c ++++ b/src/anchor.c +@@ -17,6 +17,7 @@ + #include "define.h" + #include "dialign.h" + #include "alig_graph_closure.h" ++#include "pratique.h" + + + extern int anc_num, *seqlen ; +@@ -24,6 +25,8 @@ + extern char *seq[MAX_SEQNUM]; + extern struct multi_frag *anchor_frg ; + ++extern int word_count( char *seq ); ++ + void anchor_check( int s1, int s2, int b1, int b2, int l , float scr ) { + + if( +@@ -101,7 +104,7 @@ + } + + +-int multi_anc_read( char *file_name ) { ++void multi_anc_read( char *file_name ) { + + char anc_file_name[ NAME_LEN ] ; + FILE *fp; +--- a/src/dialign.c ++++ b/src/dialign.c +@@ -218,7 +218,7 @@ + extern void subst_mat(char *file_name, int fragno , struct multi_frag *smp ); + extern int seq_read( char *in_file , char *sq[MAX_SEQNUM] , char **sqn , char **fsqn) ; + extern int anc_read( char *file_name ) ; +- extern int multi_anc_read( char *file_name ) ; ++ extern void multi_anc_read( char *file_name ) ; + extern void randomize( int r_numb , FILE *fp1 ); + extern int mini2(int a, int b); + extern int maxi2(int a, int b); +@@ -250,6 +250,9 @@ + extern void av_tree_print(); + extern void matrix_read( FILE *fp_mat ) ; + extern void mem_alloc( ) ; ++ extern void regex_parse( char *mot_regex ) ; ++ extern void seq_parse( char *mot_regex ) ; ++ extern void exclude_frg_read( char *file_name , int ***exclude_list) ; + + + /******************************/ +@@ -258,7 +261,7 @@ + + + +-main(int argc, char **argv) ++int main(int argc, char **argv) + { + int k, anc1, dia_counter, tmpi1, tmpi2 ; + +--- a/src/functions.c ++++ b/src/functions.c +@@ -853,7 +853,7 @@ + } + } + +-wgt_type_count( int num , int e_len, int *plus_cnt, int *minus_cnt, ++void wgt_type_count( int num , int e_len, int *plus_cnt, int *minus_cnt, + int *nuc_cnt , int *frg_inv, struct multi_frag *dia ) { + + int i, dc, pc, s1, pos; +@@ -882,7 +882,7 @@ + + + +-plot_calc( int num , int e_len, float *w_count, float *pl, ++void plot_calc( int num , int e_len, float *w_count, float *pl, + struct multi_frag *dia , FILE *fp_csc ) + { + int i, dc, pc, s1, pos; +--- a/src/input.c ++++ b/src/input.c +@@ -17,6 +17,7 @@ + #include "define.h" + #include "dialign.h" + #include "alig_graph_closure.h" ++#include "pratique.h" + + extern int max_dia , self_comparison ; + extern int sim_score[21][21]; +@@ -370,8 +371,11 @@ + } + + +- if ( fgets( line , MLINE , fp ) == NULL ) +- erreur("\n\n problem with file %s \n\n", file_name ); ++ if ( fgets( line , MLINE , fp ) == NULL ) { ++ char buffer [500]; ++ snprintf ( buffer, 500, "\n\n problem with file %s \n\n", file_name ); ++ erreur( buffer ); ++ } + else + if( w_type % 2 ) + av_sim_score_nuc = atof( line ); +--- a/src/output.c ++++ b/src/output.c +@@ -61,9 +61,9 @@ + extern void mini(int *a, int b); + extern void maxi(int *a, int b); + extern int int_test(float f); +- extern plot_calc( int num , int e_len, float *w_count, float *pl, ++ extern void plot_calc( int num , int e_len, float *w_count, float *pl, + struct multi_frag *dia , FILE *fp_csc ) ; +- extern wgt_type_count( int num , int e_len, int *plus_cnt, int *minus_cnt, ++ extern void wgt_type_count( int num , int e_len, int *plus_cnt, int *minus_cnt, + int *nuc_cnt , int *frg_inv, struct multi_frag *dia ) ; + + +--- a/src/pratique.c ++++ b/src/pratique.c +@@ -4,7 +4,7 @@ + + /* ------------------------------------------------------------*/ + +-void erreur(char *message) ++_Noreturn void erreur(char *message) + { + printf("%s\n", message); + exit(1); +--- a/src/pratique.h ++++ b/src/pratique.h +@@ -12,7 +12,7 @@ + + #define TAILLE_MAX_LIGNE_FICHIER 10000 + +-void erreur(char *message); ++_Noreturn void erreur(char *message); + + void *allouer(size_t taille); + void *reallouer(void *pointeur, size_t taille); +--- a/src/regex.c ++++ b/src/regex.c +@@ -151,7 +151,7 @@ + + } + +-seq_parse( char *mot_regex ) { ++void seq_parse( char *mot_regex ) { + int sn, ok , i ; + int sp, ap, rp, hv, match; + max_mot_offset = sqrt ( - log ( 0.1 ) * 10 / mot_factor ) * mot_offset_factor; diff --git a/sci-biology/dialign2/files/dialign2-2.2.1-fix-build-system.patch b/sci-biology/dialign2/files/dialign2-2.2.1-fix-build-system.patch index 45365c56e3a4..a4940ee867ee 100644 --- a/sci-biology/dialign2/files/dialign2-2.2.1-fix-build-system.patch +++ b/sci-biology/dialign2/files/dialign2-2.2.1-fix-build-system.patch @@ -1,14 +1,16 @@ --- a/src/makefile +++ b/src/makefile -@@ -10,8 +10,6 @@ +@@ -10,9 +10,7 @@ ############################### -CC = gcc -CFLAGS = -c -O -I$ -DCONS - #CFLAGS = -g -c -I$ -DCONS +-#CFLAGS = -g -c -I$ -DCONS ++CPPFLAGS += -I. -DCONS LIBS = -lm # + @@ -23,33 +21,4 @@ # |