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Mon, 13 Jan 2020 17:42:23 +0000 (UTC) (envelope-from fernape@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id 00DHgN1e085324; Mon, 13 Jan 2020 17:42:23 GMT (envelope-from fernape@FreeBSD.org) Received: (from fernape@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id 00DHgMR8085225; Mon, 13 Jan 2020 17:42:22 GMT (envelope-from fernape@FreeBSD.org) Message-Id: <202001131742.00DHgMR8085225@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: fernape set sender to fernape@FreeBSD.org using -f From: =?UTF-8?Q?Fernando_Apestegu=c3=ada?= Date: Mon, 13 Jan 2020 17:42:22 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r522911 - in head/biology/muscle: . files X-SVN-Group: ports-head X-SVN-Commit-Author: fernape X-SVN-Commit-Paths: in head/biology/muscle: . files X-SVN-Commit-Revision: 522911 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 13 Jan 2020 17:42:23 -0000 Author: fernape Date: Mon Jan 13 17:42:22 2020 New Revision: 522911 URL: https://svnweb.freebsd.org/changeset/ports/522911 Log: biology/muscle: update to 3.8.1551 * Bug fix for long sequences. * Unbreak '/dev/tty' problem during a build * Update maintainer's mail address PR: 243206 Submitted by: mzaki@e-mail.ne.jp (maintainer) Added: head/biology/muscle/files/patch-Makefile (contents, props changed) Deleted: head/biology/muscle/files/patch-mk Modified: head/biology/muscle/Makefile head/biology/muscle/distinfo head/biology/muscle/files/patch-globalslinux.cpp Modified: head/biology/muscle/Makefile ============================================================================== --- head/biology/muscle/Makefile Mon Jan 13 17:42:18 2020 (r522910) +++ head/biology/muscle/Makefile Mon Jan 13 17:42:22 2020 (r522911) @@ -2,27 +2,21 @@ # $FreeBSD$ PORTNAME= muscle -PORTVERSION= 3.8.31 +PORTVERSION= 3.8.1551 CATEGORIES= biology -MASTER_SITES= http://www.drive5.com/muscle/downloads${PORTVERSION}/ -DISTNAME= ${PORTNAME}${PORTVERSION}_src +MASTER_SITES= http://www.drive5.com/muscle/ +DISTNAME= ${PORTNAME}_src_${PORTVERSION} -MAINTAINER= mzaki@m.u-tokyo.ac.jp +MAINTAINER= mzaki@e-mail.ne.jp COMMENT= MUltiple Sequence Comparison by Log-Expectation -FETCH_ARGS= -A +LICENSE= PD -WRKSRC= ${WRKDIR}/${PORTNAME}${PORTVERSION}/src - -USES= dos2unix +USES= dos2unix gmake +NO_WRKSUBDIR= yes DOS2UNIX_GLOB= *.cpp -ALL_TARGET= muscle - PLIST_FILES= bin/muscle - -ONLY_FOR_ARCHS= amd64 i386 -ONLY_FOR_ARCHS_REASON= Fails to install: tries to modify /dev/tty do-install: ${INSTALL_PROGRAM} ${WRKSRC}/muscle ${STAGEDIR}${PREFIX}/bin Modified: head/biology/muscle/distinfo ============================================================================== --- head/biology/muscle/distinfo Mon Jan 13 17:42:18 2020 (r522910) +++ head/biology/muscle/distinfo Mon Jan 13 17:42:22 2020 (r522911) @@ -1,2 +1,3 @@ -SHA256 (muscle3.8.31_src.tar.gz) = 43c5966a82133bd7da5921e8142f2f592c2b5f53d802f0527a2801783af809ad -SIZE (muscle3.8.31_src.tar.gz) = 515267 +TIMESTAMP = 1578543217 +SHA256 (muscle_src_3.8.1551.tar.gz) = c70c552231cd3289f1bad51c9bd174804c18bb3adcf47f501afec7a68f9c482e +SIZE (muscle_src_3.8.1551.tar.gz) = 190019 Added: head/biology/muscle/files/patch-Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/muscle/files/patch-Makefile Mon Jan 13 17:42:22 2020 (r522911) @@ -0,0 +1,28 @@ +--- Makefile.orig 2014-07-12 16:42:52 UTC ++++ Makefile +@@ -10,8 +10,8 @@ + # this is fixed by deleting "-static" from the LDLIBS line. + + CFLAGS = -O3 -funroll-loops -Winline -DNDEBUG=1 +-LDLIBS = -lm -static +-# LDLIBS = -lm ++#LDLIBS = -lm -static ++LDLIBS = -lm + + OBJ = .o + EXE = +@@ -19,7 +19,7 @@ EXE = + RM = rm -f + CP = cp + +-GPP = g++ ++GPP = $(CXX) + LD = $(GPP) $(CFLAGS) + CPP = $(GPP) -c $(CFLAGS) + +@@ -33,4 +33,4 @@ $(CPPOBJ): %.o: %.cpp + + muscle: $(CPPOBJ) + $(LD) -o muscle $(CPPOBJ) $(LDLIBS) +- strip muscle ++# strip muscle Modified: head/biology/muscle/files/patch-globalslinux.cpp ============================================================================== --- head/biology/muscle/files/patch-globalslinux.cpp Mon Jan 13 17:42:18 2020 (r522910) +++ head/biology/muscle/files/patch-globalslinux.cpp Mon Jan 13 17:42:22 2020 (r522911) @@ -1,5 +1,5 @@ ---- globalslinux.cpp.orig Tue Nov 30 05:09:50 2004 -+++ globalslinux.cpp Mon Jul 4 11:13:18 2005 +--- globalslinux.cpp.orig 2020-01-09 04:20:25 UTC ++++ globalslinux.cpp @@ -7,6 +7,12 @@ #include #include @@ -13,7 +13,7 @@ const int ONE_MB = 1000000; const int MEM_WARNING_THRESHOLD = 20*ONE_MB; -@@ -39,6 +45,34 @@ +@@ -39,6 +45,34 @@ const char *GetCmdLine() return szCmdLine; } @@ -48,7 +48,7 @@ double GetMemUseMB() { static char statm[64]; -@@ -83,6 +117,7 @@ +@@ -74,6 +108,7 @@ double GetMemUseMB() return ((double) Pages * (double) PageSize)/1e6; } @@ -56,7 +56,7 @@ void SaveCmdLine(int argc, char *argv[]) { -@@ -118,6 +153,28 @@ +@@ -109,6 +144,28 @@ void CheckMemUse() dPeakMemUseMB = dMB; } @@ -85,7 +85,7 @@ double GetRAMSizeMB() { const double DEFAULT_RAM = 500; -@@ -168,5 +225,6 @@ +@@ -159,5 +216,6 @@ double GetRAMSizeMB() int Bytes = atoi(pMem+9)*1000; return ((double) Bytes)/1e6; }