From nobody Mon Dec 6 01:03:03 2021 X-Original-To: dev-commits-ports-all@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id DCACD18C8956; Mon, 6 Dec 2021 01:03:03 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4J6lXl4NGGz4hs3; Mon, 6 Dec 2021 01:03:03 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 760E62217B; Mon, 6 Dec 2021 01:03:03 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 1B6133xj038662; Mon, 6 Dec 2021 01:03:03 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 1B6133s5038661; Mon, 6 Dec 2021 01:03:03 GMT (envelope-from git) Date: Mon, 6 Dec 2021 01:03:03 GMT Message-Id: <202112060103.1B6133s5038661@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Muhammad Moinur Rahman Subject: git: 908f72ff107d - main - biology/seaview: Update version 5.0.4=>5.0.5 List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-all@freebsd.org X-BeenThere: dev-commits-ports-all@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: bofh X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 908f72ff107dea687ffd3bee46bb00028f34cdac Auto-Submitted: auto-generated ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1638752583; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=AtVJtMbRogdFpJyfsLrHsISUzkowgN81lpK8DHGepO0=; b=OjuoxzLt1vyNd8U2kM0FCTNz9ShH09sXVxuq+lsH/CZvFEZDLPTAmkdo037a+/emgslPYP LwfBH2MGPZXm+cvq6xXJMe69H1tJ0+WJ+l87a6Di8KMNIy1PlQp0Y9Qkf/3e+G5PztIXAF 0a9wp/U9B63o6tbqSzoYVZ7lE9fwpucbfpuCGL0WffzpdlH0EgRYneE3Q9FbJ0t3YLPpn7 7id15okzTmxuPHX7TvhowAE+88y2ge0wFe0uMv5KuRHLME7O1MbVpPu2K3SnOSjVyJTCpY dXP4oM3m6ObfxcikRRb9OJU6fL/dZcHwjOYDVriCL+1d3TRtvbwS32ed5BdDrw== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1638752583; a=rsa-sha256; cv=none; b=Wb3HGboV5SI4iN3B57baEIrMHKTdEyi3e35SafzzhPjrudhpS/x3mJg4GUjFJcOb7uO8vb knmbT60T1rVZKvpQ8qBn95v1dNyhDCD5AW4oGmXqs+e+MU9z79KRGBjQzgCaTJHLDV07o5 eHzC7xDoIcEuHKkizZGW9BltFs8eIjw4YVjm+6Mw9H9Cr1Ue3u6oBUhN1h+hY/eyqGKdo8 +GaGNgbH6eiAE5nErDeW3QuDNvl+68D4g1Eq4TpWqBHcJcjB2IUYyPB4plXxP+oOObQm2r S8diEjfI6qjIUGCuwlnQo0/qv3vF6cbB5aXkuIYn37n1xpszGKTVhs5B0vDuGQ== ARC-Authentication-Results: i=1; mx1.freebsd.org; none X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by bofh: URL: https://cgit.FreeBSD.org/ports/commit/?id=908f72ff107dea687ffd3bee46bb00028f34cdac commit 908f72ff107dea687ffd3bee46bb00028f34cdac Author: Muhammad Moinur Rahman AuthorDate: 2021-12-05 22:44:15 +0000 Commit: Muhammad Moinur Rahman 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)