Date: Mon, 6 Dec 2021 01:03:03 GMT From: Muhammad Moinur Rahman <bofh@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 908f72ff107d - main - biology/seaview: Update version 5.0.4=>5.0.5 Message-ID: <202112060103.1B6133s5038661@gitrepo.freebsd.org>
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The branch main has been updated by bofh: URL: https://cgit.FreeBSD.org/ports/commit/?id=908f72ff107dea687ffd3bee46bb00028f34cdac commit 908f72ff107dea687ffd3bee46bb00028f34cdac Author: Muhammad Moinur Rahman <bofh@FreeBSD.org> AuthorDate: 2021-12-05 22:44:15 +0000 Commit: Muhammad Moinur Rahman <bofh@FreeBSD.org> CommitDate: 2021-12-06 01:02:42 +0000 biology/seaview: Update version 5.0.4=>5.0.5 Relnotes: http://doua.prabi.fr/software/seaview_data/CHANGES --- biology/seaview/Makefile | 5 +-- biology/seaview/distinfo | 6 +-- biology/seaview/files/patch-csrc_dnapars.c | 70 ------------------------------ 3 files changed, 4 insertions(+), 77 deletions(-) diff --git a/biology/seaview/Makefile b/biology/seaview/Makefile index 3508d87dfddc..f36b20cc0ccf 100644 --- a/biology/seaview/Makefile +++ b/biology/seaview/Makefile @@ -1,7 +1,7 @@ # Created by: frankch@waru.life.nthu.edu.tw PORTNAME= seaview -PORTVERSION= 5.0.4 +PORTVERSION= 5.0.5 PORTEPOCH= 1 CATEGORIES= biology MASTER_SITES= ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/ @@ -37,9 +37,6 @@ post-patch: ${REINPLACE_CMD} -e \ 's|^\(CC\) |#\1 | ; s|-ldl || ; \ s|^\(CXX\) |#\1 |' ${WRKSRC}/Makefile - ${REINPLACE_CMD} -E \ - '/firstplotblock|javarun|\*progname/s,^,extern ,' \ - ${WRKSRC}/csrc/phylip.h ${WRKSRC}/csrc/protpars.c ${ECHO_CMD} 'boolean javarun;' >> ${WRKSRC}/csrc/phylip.c do-install: diff --git a/biology/seaview/distinfo b/biology/seaview/distinfo index 808ce3214db5..7afee1b07658 100644 --- a/biology/seaview/distinfo +++ b/biology/seaview/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1592674569 -SHA256 (seaview_5.0.4.tar.gz) = e153e7fe1dd0b466ce7a00e8b78d5d232aa26063ab82f78eb43811780c41d727 -SIZE (seaview_5.0.4.tar.gz) = 472837 +TIMESTAMP = 1638663734 +SHA256 (seaview_5.0.5.tar.gz) = ce8f5e98ba47883bfa91e91bc79e4d3a26f158dd9983b5e78331a452a4b1f8f2 +SIZE (seaview_5.0.5.tar.gz) = 471739 diff --git a/biology/seaview/files/patch-csrc_dnapars.c b/biology/seaview/files/patch-csrc_dnapars.c deleted file mode 100644 index ecf81d66f4ae..000000000000 --- a/biology/seaview/files/patch-csrc_dnapars.c +++ /dev/null @@ -1,70 +0,0 @@ ---- csrc/dnapars.c.orig 2019-11-29 14:00:33 UTC -+++ csrc/dnapars.c -@@ -77,41 +77,44 @@ void load_tree(long treei); - /* function prototypes */ - - --Char infilename[FNMLNGTH], outfilename[FNMLNGTH], intreename[FNMLNGTH], *outtreename, -+extern Char infilename[FNMLNGTH], outfilename[FNMLNGTH], intreename[FNMLNGTH], *outtreename, - weightfilename[FNMLNGTH]; - char basechar[32]="ACMGRSVTWYHKDBNO???????????????"; --node *root; --long chars, col, msets, ith, njumble, jumb, maxtrees; -+extern node *root; -+extern long chars, col, msets, ith, njumble, jumb; -+long maxtrees; - /* chars = number of sites in actual sequences */ --long inseed, inseed0; --double threshold; --boolean jumble, usertree, thresh, weights, thorough, rearrfirst, -- trout, progress, stepbox, ancseq, mulsets, justwts, firstset, mulf, -- multf; -+extern long inseed, inseed0; -+extern double threshold; -+extern boolean jumble, usertree, thresh, weights, -+ trout, progress, stepbox, ancseq, mulsets, justwts, firstset; -+boolean thorough, rearrfirst, mulf, multf; - steptr oldweight; --longer seed; --pointarray treenode; /* pointers to all nodes in tree */ --long *enterorder; -+extern longer seed; -+extern pointarray treenode; /* pointers to all nodes in tree */ -+extern long *enterorder; - long *zeros; - - /* local variables for Pascal maketree, propagated globally for C version: */ - --long minwhich; -+extern 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; -+extern boolean lastrearr, recompute; -+extern double nsteps[maxuser]; -+extern long **fsteps; -+extern node *there; -+node *oldnufork; -+extern long *place; -+extern bestelm *bestrees; -+extern long *threshwt; - baseptr nothing; --gbases *garbage; --node *temp, *temp1, *temp2, *tempsum, *temprm, *tempadd, *tempf, *tmp, *tmp1, -+extern gbases *garbage; -+extern node *temp, *temp1; -+node *temp2, *tempsum, *temprm, *tempadd, *tempf, *tmp, *tmp1, - *tmp2, *tmp3, *tmprm, *tmpadd; --boolean *names; -+extern boolean *names; - node *grbg; --char *progname; -+extern char *progname; - - - static void getoptions(int arg_maxtrees, dnapars_S_option s_option)
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