From owner-dev-commits-ports-main@freebsd.org Sat Aug 14 08:58:47 2021 Return-Path: Delivered-To: dev-commits-ports-main@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id 8F380668B4B; Sat, 14 Aug 2021 08:58:47 +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 4GmvVH3Y4yz3FyT; Sat, 14 Aug 2021 08:58:47 +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 5F9451F3A9; Sat, 14 Aug 2021 08:58:47 +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 17E8wlSx010368; Sat, 14 Aug 2021 08:58:47 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 17E8wldB010367; Sat, 14 Aug 2021 08:58:47 GMT (envelope-from git) Date: Sat, 14 Aug 2021 08:58:47 GMT Message-Id: <202108140858.17E8wldB010367@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Alexey Dokuchaev Subject: git: 0ee21a35d161 - main - biology/seaview: in preparation to FLTK update, unbreak the port MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: danfe X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 0ee21a35d161900f6f0333200c5139bece030139 Auto-Submitted: auto-generated X-BeenThere: dev-commits-ports-main@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: Commits to the main branch of the FreeBSD ports repository List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 14 Aug 2021 08:58:47 -0000 The branch main has been updated by danfe: URL: https://cgit.FreeBSD.org/ports/commit/?id=0ee21a35d161900f6f0333200c5139bece030139 commit 0ee21a35d161900f6f0333200c5139bece030139 Author: Alexey Dokuchaev AuthorDate: 2021-08-14 08:56:18 +0000 Commit: Alexey Dokuchaev CommitDate: 2021-08-14 08:58:03 +0000 biology/seaview: in preparation to FLTK update, unbreak the port Ensure there is only one variable definition per each object, as the C (and C++) standards mandated for years and is now enforced by modern toolchains. --- biology/seaview/Makefile | 7 +-- biology/seaview/files/patch-csrc_dnapars.c | 70 ++++++++++++++++++++++++++++++ 2 files changed, 74 insertions(+), 3 deletions(-) diff --git a/biology/seaview/Makefile b/biology/seaview/Makefile index 922134459401..3508d87dfddc 100644 --- a/biology/seaview/Makefile +++ b/biology/seaview/Makefile @@ -12,9 +12,6 @@ COMMENT= Multiple DNA/protein sequence alignment editor LICENSE= GPLv3 -BROKEN_FreeBSD_13= ld: error: duplicate symbol: progname -BROKEN_FreeBSD_14= ld: error: duplicate symbol: progname - LIB_DEPENDS= libfltk.so:x11-toolkits/fltk \ libfontconfig.so:x11-fonts/fontconfig \ libpng.so:graphics/png @@ -40,6 +37,10 @@ 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: (cd ${WRKSRC} && ${INSTALL_PROGRAM} seaview \ diff --git a/biology/seaview/files/patch-csrc_dnapars.c b/biology/seaview/files/patch-csrc_dnapars.c new file mode 100644 index 000000000000..ecf81d66f4ae --- /dev/null +++ b/biology/seaview/files/patch-csrc_dnapars.c @@ -0,0 +1,70 @@ +--- 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)