Update to 3.8.31.

PR:		191130
Submitted by:	mzaki@m.u-tokyo.ac.jp (maintainer)

5 files changed, 37 insertions, 89 deletions

diff --git a/biology/muscle/Makefile b/biology/muscle/Makefile
index 91f9a6eb20a4..83033be028a7 100644
--- a/biology/muscle/Makefile
+++ b/biology/muscle/Makefile
@@ -2,36 +2,26 @@
 # $FreeBSD$
 
 PORTNAME=	muscle
-PORTVERSION=	3.6
+PORTVERSION=	3.8.31
 CATEGORIES=	biology
 MASTER_SITES=	http://www.drive5.com/muscle/downloads${PORTVERSION}/
 DISTNAME=	${PORTNAME}${PORTVERSION}_src
 
-.if !defined(NOPORTDOCS)
-EXTRACT_ONLY=	${DISTNAME}${EXTRACT_SUFX}
-DISTFILES=	${EXTRACT_ONLY}
-PORTDOCS=	${PORTNAME}.pdf ${PORTNAME}.html
-MASTER_SITES+=	http://www.drive5.com/muscle/:docs
-.for file in ${PORTDOCS}
-DISTFILES+=	${file}:docs
-.endfor
-.endif
-
 MAINTAINER=	mzaki@m.u-tokyo.ac.jp
-COMMENT=	Multiple Sequence Comparison by Log-Expectation
+COMMENT=	MUltiple Sequence Comparison by Log-Expectation
 
 FETCH_ARGS=	-A
 
-USES=		dos2unix gmake
-DOS2UNIX_FILES=	*.cpp
+WRKSRC=		${WRKDIR}/${PORTNAME}${PORTVERSION}/src
+
+USES=		dos2unix
+DOS2UNIX_GLOB=	*.cpp
+
+ALL_TARGET=	muscle
 
 PLIST_FILES=	bin/muscle
 
 do-install:
 	${INSTALL_PROGRAM} ${WRKSRC}/muscle ${STAGEDIR}${PREFIX}/bin
-.if !defined(NOPORTDOCS)
-	@${MKDIR} ${STAGEDIR}${DOCSDIR}
-	${INSTALL_DATA} ${PORTDOCS:S|^|${DISTDIR}/|} ${STAGEDIR}${DOCSDIR}
-.endif
 
 .include <bsd.port.mk>
diff --git a/biology/muscle/distinfo b/biology/muscle/distinfo
index 42dd8c5ca7c9..12b54cc9e1ad 100644
--- a/biology/muscle/distinfo
+++ b/biology/muscle/distinfo
@@ -1,6 +1,2 @@
-SHA256 (muscle3.6_src.tar.gz) = 32b818a51f421e1d687f513dc31374a330470950151a5e7df961e64781699431
-SIZE (muscle3.6_src.tar.gz) = 185267
-SHA256 (muscle.pdf) = a28fd0afc0919c176a9a1cedb3b46cadb24a53c575089305cc4b2967ec4a5fc9
-SIZE (muscle.pdf) = 239031
-SHA256 (muscle.html) = 4df43445f08d99e18da71a06438cc8fc3ba42b6709e19c8cfea0c31788dc17b6
-SIZE (muscle.html) = 94645
+SHA256 (muscle3.8.31_src.tar.gz) = 43c5966a82133bd7da5921e8142f2f592c2b5f53d802f0527a2801783af809ad
+SIZE (muscle3.8.31_src.tar.gz) = 515267
diff --git a/biology/muscle/files/patch-Makefile b/biology/muscle/files/patch-Makefile
deleted file mode 100644
index b53296b7fe4a..000000000000
--- a/biology/muscle/files/patch-Makefile
+++ /dev/null
@@ -1,35 +0,0 @@
---- Makefile.orig	Fri Sep  9 07:26:04 2005
-+++ Makefile	Tue Dec 20 18:50:33 2005
-@@ -9,28 +9,14 @@
- # On OSX, using -static gives the error "ld: can't locate file for: -lcrt0.o",
- # this is fixed by deleting "-static" from the LDLIBS line.
- 
--CFLAGS = -O3 -funroll-loops -Winline -DNDEBUG=1
--LDLIBS = -lm -static
--# LDLIBS = -lm
--
--OBJ = .o
--EXE =
--
--RM = rm -f
--CP = cp
--
--GPP = g++
--LD = $(GPP) $(CFLAGS)
--CPP = $(GPP) -c $(CFLAGS) 
-+CC = g++
-+CXXFLAGS += -O3 -funroll-loops -Winline -DNDEBUG=1
-+LDLIBS = -lm -lkvm
- 
- all: muscle
- 
- CPPSRC = $(sort $(wildcard *.cpp))
- CPPOBJ	= $(subst .cpp,.o,$(CPPSRC))
- 
--$(CPPOBJ): %.o: %.cpp
--	$(CPP) $< -o $@
--
- muscle: $(CPPOBJ)
--	$(LD) -o muscle $(CPPOBJ) $(LDLIBS)
--	strip muscle
-+	$(LINK.o) -o $@ $^ $(LDLIBS)
diff --git a/biology/muscle/files/patch-intmath.cpp b/biology/muscle/files/patch-intmath.cpp
deleted file mode 100644
index 0ad4ca73e2e3..000000000000
--- a/biology/muscle/files/patch-intmath.cpp
+++ /dev/null
@@ -1,30 +0,0 @@
---- intmath.cpp.orig	Tue Nov 30 05:09:50 2004
-+++ intmath.cpp	Mon Jul  4 07:49:45 2005
-@@ -8,13 +8,6 @@
- 	return (PROB) pow(2.0, (double) Score/INTSCALE);
- 	}
- 
--static const double log2e = log2(exp(1.0));
--
--double lnTolog2(double ln)
--	{
--	return ln*log2e;
--	}
--
- double log2(double x)
- 	{
- 	if (0 == x)
-@@ -24,6 +17,13 @@
- // Multiply by inverse of log(2) just in case multiplication
- // is faster than division.
- 	return log(x)*dInvLn2;
-+	}
-+
-+static const double log2e = log2(exp(1.0));
-+
-+double lnTolog2(double ln)
-+	{
-+	return ln*log2e;
- 	}
- 
- SCORE ProbToScore(PROB Prob)
diff --git a/biology/muscle/files/patch-mk b/biology/muscle/files/patch-mk
new file mode 100644
index 000000000000..79f0707ad8b6
--- /dev/null
+++ b/biology/muscle/files/patch-mk
@@ -0,0 +1,27 @@
+--- mk.orig	2010-05-02 08:15:42.000000000 +0900
++++ mk	2014-06-17 23:45:55.000000000 +0900
+@@ -1,4 +1,4 @@
+-#!/bin/bash
++#!/bin/sh
+ CPPNames='aligngivenpath aligngivenpathsw aligntwomsas aligntwoprofs aln alpha anchors bittraceback blosum62 blosumla clust cluster clwwt color cons diaglist diffobjscore diffpaths difftrees difftreese distcalc distfunc distpwkimura domuscle dosp dpreglist drawtree edgelist enumopts enumtostr estring fasta fasta2 fastclust fastdist fastdistjones fastdistkbit fastdistkmer fastdistmafft fastdistnuc fastscorepath2 finddiags finddiagsn glbalign glbalign352 glbaligndiag glbalignle glbalignsimple glbalignsp glbalignspn glbalignss glbalndimer globals globalslinux globalsosx globalsother globalswin32 gonnet henikoffweight henikoffweightpb html hydro intmath local main makerootmsa makerootmsab maketree mhack mpam200 msa msa2 msadistkimura msf muscle muscleout nucmx nwdasimple nwdasimple2 nwdasmall nwrec nwsmall objscore objscore2 objscoreda onexception options outweights pam200mafft params phy phy2 phy3 phy4 phyfromclust phyfromfile physeq phytofile posgap ppscore profdb profile profilefrommsa progalign progress progressivealign pwpath readmx realigndiffs realigndiffse refine refinehoriz refinesubfams refinetree refinetreee refinevert refinew savebest scoredist scoregaps scorehistory scorepp seq seqvect setblosumweights setgscweights setnewhandler spfast sptest stabilize subfam subfams sw termgaps textfile threewaywt tomhydro traceback tracebackopt tracebacksw treefrommsa typetostr upgma2 usage validateids vtml2 writescorefile'
+ ObjNames='aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.o alpha.o anchors.o bittraceback.o blosum62.o blosumla.o clust.o cluster.o clwwt.o color.o cons.o diaglist.o diffobjscore.o diffpaths.o difftrees.o difftreese.o distcalc.o distfunc.o distpwkimura.o domuscle.o dosp.o dpreglist.o drawtree.o edgelist.o enumopts.o enumtostr.o estring.o fasta.o fasta2.o fastclust.o fastdist.o fastdistjones.o fastdistkbit.o fastdistkmer.o fastdistmafft.o fastdistnuc.o fastscorepath2.o finddiags.o finddiagsn.o glbalign.o glbalign352.o glbaligndiag.o glbalignle.o glbalignsimple.o glbalignsp.o glbalignspn.o glbalignss.o glbalndimer.o globals.o globalslinux.o globalsosx.o globalsother.o globalswin32.o gonnet.o henikoffweight.o henikoffweightpb.o html.o hydro.o intmath.o local.o main.o makerootmsa.o makerootmsab.o maketree.o mhack.o mpam200.o msa.o msa2.o msadistkimura.o msf.o muscle.o muscleout.o nucmx.o nwdasimple.o nwdasimple2.o nwdasmall.o nwrec.o nwsmall.o objscore.o objscore2.o objscoreda.o onexception.o options.o outweights.o pam200mafft.o params.o phy.o phy2.o phy3.o phy4.o phyfromclust.o phyfromfile.o physeq.o phytofile.o posgap.o ppscore.o profdb.o profile.o profilefrommsa.o progalign.o progress.o progressivealign.o pwpath.o readmx.o realigndiffs.o realigndiffse.o refine.o refinehoriz.o refinesubfams.o refinetree.o refinetreee.o refinevert.o refinew.o savebest.o scoredist.o scoregaps.o scorehistory.o scorepp.o seq.o seqvect.o setblosumweights.o setgscweights.o setnewhandler.o spfast.o sptest.o stabilize.o subfam.o subfams.o sw.o termgaps.o textfile.o threewaywt.o tomhydro.o traceback.o tracebackopt.o tracebacksw.o treefrommsa.o typetostr.o upgma2.o usage.o validateids.o vtml2.o writescorefile.o'
+ 
+@@ -6,16 +6,15 @@
+ for CPPName in $CPPNames
+ do
+   echo $CPPName >> /dev/tty
+-  g++ $ENV_GCC_OPTS -c -O3 -msse2 -mfpmath=sse -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 $CPPName.cpp -o $CPPName.o  >> muscle.make.stdout.txt 2>> muscle.make.stderr.txt
++  ${CXX} $ENV_GCC_OPTS -c -O3 -msse2 -mfpmath=sse -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 $CPPName.cpp -o $CPPName.o  >> muscle.make.stdout.txt 2>> muscle.make.stderr.txt
+ done
+ 
+ LINK_OPTS=
+ if [ `uname -s` == Linux ] ; then
+     LINK_OPTS=-static
+ fi
+-g++ $LINK_OPTS $ENV_LINK_OPTS -g -o muscle $ObjNames  >> muscle.make.stdout.txt 2>> muscle.make.stderr.txt
++${CXX} $LINK_OPTS $ENV_LINK_OPTS -g -o muscle $ObjNames  >> muscle.make.stdout.txt 2>> muscle.make.stderr.txt
+ tail muscle.make.stderr.txt
+ 
+-strip muscle
+ ls -lh muscle
+ sum muscle