diff --git a/.gitignore b/.gitignore index c642a29..6e3e817 100644 --- a/.gitignore +++ b/.gitignore @@ -9,4 +9,3 @@ seaview_4.2.6.tar.gz /seaview_4.6.tar.gz /seaview_4.6.2.1.tar.gz /seaview_5.0.tar.gz -/seaview_5.1.tar.gz diff --git a/seaview-chris.patch b/seaview-chris.patch index 9809f5a..27e51dc 100644 --- a/seaview-chris.patch +++ b/seaview-chris.patch @@ -1,3 +1,160 @@ +diff -drup seaview.0/csrc/dnapars.c seaview.1/csrc/dnapars.c +--- seaview.0/csrc/dnapars.c 2019-12-05 14:33:14.000000000 +0100 ++++ seaview.1/csrc/dnapars.c 2020-02-22 00:13:57.435533320 +0100 +@@ -77,41 +77,41 @@ void load_tree(long treei); + /* function prototypes */ + + +-Char infilename[FNMLNGTH], outfilename[FNMLNGTH], intreename[FNMLNGTH], *outtreename, ++static Char infilename[FNMLNGTH], outfilename[FNMLNGTH], intreename[FNMLNGTH], *outtreename, + weightfilename[FNMLNGTH]; + char basechar[32]="ACMGRSVTWYHKDBNO???????????????"; +-node *root; +-long chars, col, msets, ith, njumble, jumb, maxtrees; ++static node *root; ++static long chars, col, msets, ith, njumble, jumb, maxtrees; + /* chars = number of sites in actual sequences */ +-long inseed, inseed0; +-double threshold; +-boolean jumble, usertree, thresh, weights, thorough, rearrfirst, ++//long inseed, inseed0; ++static double threshold; ++static boolean jumble, usertree, thresh, weights, thorough, rearrfirst, + trout, progress, stepbox, ancseq, mulsets, justwts, firstset, mulf, + multf; +-steptr oldweight; +-longer seed; +-pointarray treenode; /* pointers to all nodes in tree */ +-long *enterorder; +-long *zeros; ++static steptr oldweight; ++static longer seed; ++static pointarray treenode; /* pointers to all nodes in tree */ ++static long *enterorder; ++static long *zeros; + + /* local variables for Pascal maketree, propagated globally for C version: */ + +-long minwhich; ++static long minwhich; + static double like, minsteps, bestyet, bestlike, bstlike2; +-boolean lastrearr, recompute; +-double nsteps[maxuser]; +-long **fsteps; +-node *there, *oldnufork; +-long *place; +-bestelm *bestrees; +-long *threshwt; +-baseptr nothing; +-gbases *garbage; +-node *temp, *temp1, *temp2, *tempsum, *temprm, *tempadd, *tempf, *tmp, *tmp1, ++static boolean lastrearr, recompute; ++static double nsteps[maxuser]; ++static long **fsteps; ++static node *there, *oldnufork; ++static long *place; ++static bestelm *bestrees; ++static long *threshwt; ++static baseptr nothing; ++static gbases *garbage; ++static node *temp, *temp1, *temp2, *tempsum, *temprm, *tempadd, *tempf, *tmp, *tmp1, + *tmp2, *tmp3, *tmprm, *tmpadd; +-boolean *names; +-node *grbg; +-char *progname; ++static boolean *names; ++static node *grbg; ++static char *progname; + + + static void getoptions(int arg_maxtrees, dnapars_S_option s_option) +diff -drup seaview.0/csrc/phylip.c seaview.1/csrc/phylip.c +--- seaview.0/csrc/phylip.c 2019-12-05 14:33:14.000000000 +0100 ++++ seaview.1/csrc/phylip.c 2020-02-21 23:56:39.801177617 +0100 +@@ -143,7 +143,7 @@ void init(int argc, char** argv) + /* Set default terminal characteristics */ + ibmpc = IBMCRT; + ansi = ANSICRT; +- javarun = false; ++ //javarun = false; + + /* Clear the screen */ + cleerhome(); +diff -drup seaview.0/csrc/phylip.h seaview.1/csrc/phylip.h +--- seaview.0/csrc/phylip.h 2019-12-05 14:33:14.000000000 +0100 ++++ seaview.1/csrc/phylip.h 2020-02-21 23:57:42.782897666 +0100 +@@ -342,7 +342,7 @@ MALLOCRETURN *mymalloc(long); + /* Lower-triangular format. */ + #define MAT_LOWERTRI (MAT_LOWER | MAT_MACHINE) + +-boolean javarun; ++//boolean javarun; + + typedef long *steptr; + typedef long longer[6]; +@@ -363,7 +363,7 @@ extern long spp, words, bits; + extern boolean ibmpc, ansi, tranvsp; + //extern naym *nayme; /* names of species */ + extern char* *nayme; /* names of species */ +-boolean firstplotblock; // for debugging BMP output ++//boolean firstplotblock; // for debugging BMP output + + #define ebcdic EBCDIC + +diff -drup seaview.0/csrc/protpars.c seaview.1/csrc/protpars.c +--- seaview.0/csrc/protpars.c 2019-12-05 14:33:14.000000000 +0100 ++++ seaview.1/csrc/protpars.c 2020-02-22 00:13:49.931328198 +0100 +@@ -104,30 +104,30 @@ extern void awake_from_C(void); + + + +-Char infilename[FNMLNGTH], outfilename[FNMLNGTH], intreename[FNMLNGTH], *outtreename, weightfilename[FNMLNGTH]; +-node *root; +-long chars, col, msets, ith, njumble, jumb; ++static Char infilename[FNMLNGTH], outfilename[FNMLNGTH], intreename[FNMLNGTH], *outtreename, weightfilename[FNMLNGTH]; ++static node *root; ++static long chars, col, msets, ith, njumble, jumb; + /* chars = number of sites in actual sequences */ +-long inseed, inseed0; +-boolean jumble, usertree, weights, thresh, trout, progress, stepbox, ++static long inseed, inseed0; ++static boolean jumble, usertree, weights, thresh, trout, progress, stepbox, + justwts, ancseq, mulsets, firstset; +-codetype whichcode; +-long fullset, fulldel; +-pointarray treenode; /* pointers to all nodes in tree */ +-double threshold; +-steptr threshwt; +-longer seed; +-long *enterorder; ++static codetype whichcode; ++static long fullset, fulldel; ++static pointarray treenode; /* pointers to all nodes in tree */ ++static double threshold; ++static steptr threshwt; ++static longer seed; ++static long *enterorder; + sitearray translate[(long)quest - (long)ala + 1]; + aas trans[4][4][4]; +-long **fsteps; +-bestelm *bestrees; +-boolean dummy; +-gseq *garbage; +-node *temp, *temp1; +-Char ch; +-aas tmpa; +-char *progname; ++static long **fsteps; ++static bestelm *bestrees; ++static boolean dummy; ++static gseq *garbage; ++static node *temp, *temp1; ++static Char ch; ++static aas tmpa; ++static char *progname; + + /* Local variables for maketree, propagated globally for c version: */ + long minwhich; diff -drup seaview.0/Makefile seaview.1/Makefile --- seaview.0/Makefile 2019-12-28 18:12:13.000000000 +0100 +++ seaview.1/Makefile 2020-02-21 23:42:03.294287605 +0100 @@ -9,13 +166,13 @@ diff -drup seaview.0/Makefile seaview.1/Makefile +PHYMLNAME= -DPHYMLNAME=\"phyml\" - #to use your own, uninstalled FLTK library, -@@ -21,7 +21,7 @@ CSRC = csrc + #to compile with PDF (through PDFlib Lite) rather than PostScript output, +@@ -30,7 +30,7 @@ CSRC = csrc #DEBUG = -g #OPT = -O0 -OPT ?= -O3 +OPT ?= $(RPM_OPT_FLAGS) - SVFLAGS = $(CPPFLAGS) $(CFLAGS) -Dunix $(OPT) -I. $(IFLTK) -I$(CSRC) $(DEBUG) $(HELPFILE) $(PHYMLNAME) + SVFLAGS = $(CPPFLAGS) $(CFLAGS) -Dunix $(OPT) -I. $(IFLTK) -I$(CSRC) $(DEBUG) $(HELPFILE) $(PHYMLNAME) $(PDF_PS_FLAGS) diff --git a/seaview.spec b/seaview.spec index 73d871e..063435a 100644 --- a/seaview.spec +++ b/seaview.spec @@ -1,13 +1,14 @@ Name: seaview -Version: 5.1 +Version: 5.0 Release: 5%{?dist} Summary: Graphical multiple sequence alignment editor -License: GPL-3.0-or-later + +License: GPLv2+ URL: http://doua.prabi.fr/software/seaview -Source0: ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_5.1.tar.gz +Source0: ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_5.0.tar.gz Source1: seaview.desktop Patch0: seaview-chris.patch -BuildRequires: make +BuildRequires: make BuildRequires: gcc-c++ BuildRequires: fltk-devel BuildRequires: desktop-file-utils @@ -23,7 +24,7 @@ alignment. %prep %setup -q -n seaview -%patch -P0 -p 1 -b .chris +%patch0 -p 1 -b .chris %build @@ -66,47 +67,6 @@ install -m 644 seaview.1 $RPM_BUILD_ROOT/%{_mandir}/man1 %changelog -* Fri Jul 17 2026 Fedora Release Engineering - 5.1-5 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_45_Mass_Rebuild - -* Sat Jan 24 2026 Richard Shaw - 5.1-4 -- Rebuild with fltk 1.4. - -* Sat Jan 17 2026 Fedora Release Engineering - 5.1-3 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_44_Mass_Rebuild - -* Tue Aug 05 2025 Christian Iseli - 5.1-2 -- Fix license denomination - as specified in the source code - -* Thu Jul 31 2025 Christian Iseli - 5.1-1 -- New upstream version -- Fix FTBFS bugzilla 2385624 -- Update license definition according to upstream - -* Fri Jul 25 2025 Fedora Release Engineering - 5.0-13 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_43_Mass_Rebuild - -* Sun Jan 19 2025 Fedora Release Engineering - 5.0-12 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_42_Mass_Rebuild - -* Fri Jul 26 2024 Miroslav Suchý - 5.0-11 -- convert license to SPDX - -* Sat Jul 20 2024 Fedora Release Engineering - 5.0-10 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild - -* Sat Jan 27 2024 Fedora Release Engineering - 5.0-9 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild - -* Sat Jul 22 2023 Fedora Release Engineering - 5.0-8 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild - -* Sat Jan 21 2023 Fedora Release Engineering - 5.0-7 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild - -* Sat Jul 23 2022 Fedora Release Engineering - 5.0-6 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild - * Sat Jan 22 2022 Fedora Release Engineering - 5.0-5 - Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild diff --git a/sources b/sources index a3e10e6..2ec44a4 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (seaview_5.1.tar.gz) = 1f9e76325be35cc5597b79cb658397784f09b24d9ef9b462623afba50ed00a20dd1e9c0094d36ee1a738f7122ed42c57e3fd154fab08dc31a85bd6e5f392119c +SHA512 (seaview_5.0.tar.gz) = e5a3b1465f1dcf3ca39e6ff81a5197427932ccf13bb249540c6c29fad5a57ede64b08df019dec0468727515c2baacda34c257832f40b9e73bdde55add4a5a518