Index: Makefile
===================================================================
--- Makefile	(revision 522467)
+++ Makefile	(working copy)
@@ -2,28 +2,22 @@
 # $FreeBSD$
 
 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
 
Index: distinfo
===================================================================
--- distinfo	(revision 522467)
+++ distinfo	(working copy)
@@ -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
Index: files/patch-Makefile
===================================================================
--- files/patch-Makefile	(nonexistent)
+++ files/patch-Makefile	(working copy)
@@ -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

Property changes on: files/patch-Makefile
___________________________________________________________________
Added: fbsd:nokeywords
## -0,0 +1 ##
+yes
\ No newline at end of property
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Index: files/patch-globalslinux.cpp
===================================================================
--- files/patch-globalslinux.cpp	(revision 522467)
+++ files/patch-globalslinux.cpp	(working copy)
@@ -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 <errno.h>
  #include <stdio.h>
@@ -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;
  	}
Index: files/patch-mk
===================================================================
--- files/patch-mk	(revision 522467)
+++ files/patch-mk	(nonexistent)
@@ -1,27 +0,0 @@
---- 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

Property changes on: files/patch-mk
___________________________________________________________________
Deleted: fbsd:nokeywords
## -1 +0,0 ##
-yes
\ No newline at end of property
Deleted: svn:eol-style
## -1 +0,0 ##
-native
\ No newline at end of property
Deleted: svn:mime-type
## -1 +0,0 ##
-text/plain
\ No newline at end of property