muscle: Add clean makefile, generate plist, clean up

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: muscle: Add clean makefile, generate plist, clean up
From: Jason Bacon <bacon%NetBSD.org@localhost>
Date: Sat, 27 Oct 2018 15:07:41 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sat Oct 27 10:07:41 2018 -0500
Changeset:	367ff93f11fd974c2ffd3d0cb35dad98c8e36741

Modified Files:
	muscle/Makefile
	muscle/PLIST
	muscle/distinfo
	muscle/patches/patch-globalslinux.cpp
Added Files:
	muscle/files/Makefile
Removed Files:
	muscle/patches/patch-mk

Log Message:
muscle: Add clean makefile, generate plist, clean up

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=367ff93f11fd974c2ffd3d0cb35dad98c8e36741

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 muscle/Makefile                       |   9 +-
 muscle/PLIST                          |   1 +
 muscle/distinfo                       |   3 +-
 muscle/files/Makefile                 | 619 ++++++++++++++++++++++++++++++++++
 muscle/patches/patch-globalslinux.cpp |   2 +
 muscle/patches/patch-mk               |  29 --
 6 files changed, 627 insertions(+), 36 deletions(-)

diffs:
diff --git a/muscle/Makefile b/muscle/Makefile
index 5f7d39b7d1..1293d15b86 100644
--- a/muscle/Makefile
+++ b/muscle/Makefile
@@ -19,16 +19,17 @@ MAINTAINER=	bacon%NetBSD.org@localhost
 HOMEPAGE=	http://www.drive5.com/muscle/
 COMMENT=	MUltiple Sequence Comparison by Log-Expectation
 
-DEPENDS+=	dos2unix:../../converters/dos2unix
+DEPENDS+=	dos2unix>0:../../converters/dos2unix
 
-# LICENSE=	
+LICENSE=	public-domain
 
 ONLY_FOR_PLATFORM=	 *-*-x86_64 *-*-i386
 
 USE_LANGUAGES=	c c++
 
 WRKSRC=		${WRKDIR}/muscle${PV}/src
-BUILD_TARGET=	 muscle
+MAKE_FILE=	${FILESDIR}/Makefile
+CXXFLAGS+=	-std=c++11
 
 PV=		3.8.31
 
@@ -40,6 +41,4 @@ pre-patch:
 do-install:
 	${INSTALL_PROGRAM} ${WRKSRC}/muscle ${DESTDIR}${PREFIX}/bin
 
-# CentOS doesn't have zlib in the base, so uncomment if needed.
-# .include "../../devel/zlib/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/muscle/PLIST b/muscle/PLIST
index 48d96a5493..699551c6a8 100644
--- a/muscle/PLIST
+++ b/muscle/PLIST
@@ -1 +1,2 @@
 @comment $NetBSD$
+bin/muscle
diff --git a/muscle/distinfo b/muscle/distinfo
index 13accfe49a..387dc15381 100644
--- a/muscle/distinfo
+++ b/muscle/distinfo
@@ -4,5 +4,4 @@ SHA1 (muscle3.8.31_src.tar.gz) = 2fe55db73ff4e7ac6d4ca692f8f213d1c5071dac
 RMD160 (muscle3.8.31_src.tar.gz) = 18c9cf465f330a77d6a06ff9323c311a6f6be662
 SHA512 (muscle3.8.31_src.tar.gz) = 2baf2aae354ae1e3f529e627be2ace86e89dd15567e1f642a625b63f08ebe3d4bd7315080c7d786d95e3eda8703545ec74af9fe83ad1523d55d00137fb7274ce
 Size (muscle3.8.31_src.tar.gz) = 515267 bytes
-SHA1 (patch-globalslinux.cpp) = 6d6d531400ce120603e9759d571396869b864a9c
-SHA1 (patch-mk) = 1f257ec0272ed1b8630c1506180b357c702226cc
+SHA1 (patch-globalslinux.cpp) = f8579d7538eb8b4283be7109964f25406dd812f5
diff --git a/muscle/files/Makefile b/muscle/files/Makefile
new file mode 100644
index 0000000000..16f2e5c86e
--- /dev/null
+++ b/muscle/files/Makefile
@@ -0,0 +1,619 @@
+
+BIN     = muscle
+
+# Keep this in sync with src/mk
+OBJS=   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 ob
jscore2.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
+
+CC      ?= cc
+CXX     ?= c++
+LD      ?= c++
+
+.PHONY: all
+
+all: ${BIN}
+
+${BIN}: ${OBJS}
+	${CXX} -o ${BIN} ${OBJS}
+
+aligngivenpath.o: aligngivenpath.cpp muscle.h types.h enums.h intmath.h \
+ alpha.h params.h msa.h pwpath.h profile.h
+	${CXX} -c ${CXXFLAGS} aligngivenpath.cpp
+
+aligngivenpathsw.o: aligngivenpathsw.cpp muscle.h types.h enums.h \
+ intmath.h alpha.h params.h msa.h pwpath.h profile.h
+	${CXX} -c ${CXXFLAGS} aligngivenpathsw.cpp
+
+aligntwomsas.o: aligntwomsas.cpp muscle.h types.h enums.h intmath.h \
+ alpha.h params.h msa.h profile.h pwpath.h textfile.h timing.h
+	${CXX} -c ${CXXFLAGS} aligntwomsas.cpp
+
+aligntwoprofs.o: aligntwoprofs.cpp muscle.h types.h enums.h intmath.h \
+ alpha.h params.h msa.h profile.h pwpath.h
+	${CXX} -c ${CXXFLAGS} aligntwoprofs.cpp
+
+aln.o: aln.cpp muscle.h types.h enums.h intmath.h alpha.h params.h msa.h \
+ textfile.h
+	${CXX} -c ${CXXFLAGS} aln.cpp
+
+alpha.o: alpha.cpp muscle.h types.h enums.h intmath.h alpha.h params.h
+	${CXX} -c ${CXXFLAGS} alpha.cpp
+
+anchors.o: anchors.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h msa.h objscore.h
+	${CXX} -c ${CXXFLAGS} anchors.cpp
+
+bittraceback.o: bittraceback.cpp muscle.h types.h enums.h intmath.h \
+ alpha.h params.h pwpath.h
+	${CXX} -c ${CXXFLAGS} bittraceback.cpp
+
+blosum62.o: blosum62.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h
+	${CXX} -c ${CXXFLAGS} blosum62.cpp
+
+blosumla.o: blosumla.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h
+	${CXX} -c ${CXXFLAGS} blosumla.cpp
+
+clust.o: clust.cpp muscle.h types.h enums.h intmath.h alpha.h params.h \
+ clust.h clustset.h
+	${CXX} -c ${CXXFLAGS} clust.cpp
+
+cluster.o: cluster.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h cluster.h distfunc.h
+	${CXX} -c ${CXXFLAGS} cluster.cpp
+
+clwwt.o: clwwt.cpp muscle.h types.h enums.h intmath.h alpha.h params.h \
+ tree.h msa.h
+	${CXX} -c ${CXXFLAGS} clwwt.cpp
+
+color.o: color.cpp muscle.h types.h enums.h intmath.h alpha.h params.h \
+ msa.h
+	${CXX} -c ${CXXFLAGS} color.cpp
+
+cons.o: cons.cpp muscle.h types.h enums.h intmath.h alpha.h params.h \
+ msa.h
+	${CXX} -c ${CXXFLAGS} cons.cpp
+
+diaglist.o: diaglist.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h diaglist.h pwpath.h
+	${CXX} -c ${CXXFLAGS} diaglist.cpp
+
+diffobjscore.o: diffobjscore.cpp muscle.h types.h enums.h intmath.h \
+ alpha.h params.h msa.h objscore.h profile.h pwpath.h
+	${CXX} -c ${CXXFLAGS} diffobjscore.cpp
+
+diffpaths.o: diffpaths.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h pwpath.h
+	${CXX} -c ${CXXFLAGS} diffpaths.cpp
+
+difftrees.o: difftrees.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h tree.h
+	${CXX} -c ${CXXFLAGS} difftrees.cpp
+
+difftreese.o: difftreese.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h tree.h
+	${CXX} -c ${CXXFLAGS} difftreese.cpp
+
+distcalc.o: distcalc.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h distfunc.h distcalc.h msa.h
+	${CXX} -c ${CXXFLAGS} distcalc.cpp
+
+distfunc.o: distfunc.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h distfunc.h
+	${CXX} -c ${CXXFLAGS} distfunc.cpp
+
+distpwkimura.o: distpwkimura.cpp muscle.h types.h enums.h intmath.h \
+ alpha.h params.h distfunc.h msa.h seqvect.h seq.h pwpath.h
+	${CXX} -c ${CXXFLAGS} distpwkimura.cpp
+
+domuscle.o: domuscle.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h textfile.h seqvect.h seq.h distfunc.h msa.h tree.h profile.h \
+ pwpath.h timing.h
+	${CXX} -c ${CXXFLAGS} domuscle.cpp
+
+dosp.o: dosp.cpp muscle.h types.h enums.h intmath.h alpha.h params.h \
+ textfile.h msa.h objscore.h tree.h profile.h pwpath.h
+	${CXX} -c ${CXXFLAGS} dosp.cpp
+
+dpreglist.o: dpreglist.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h dpreglist.h diaglist.h
+	${CXX} -c ${CXXFLAGS} dpreglist.cpp
+
+drawtree.o: drawtree.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h tree.h
+	${CXX} -c ${CXXFLAGS} drawtree.cpp
+
+edgelist.o: edgelist.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h edgelist.h
+	${CXX} -c ${CXXFLAGS} edgelist.cpp
+
+enumopts.o: enumopts.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h enumopts.h
+	${CXX} -c ${CXXFLAGS} enumopts.cpp
+
+enumtostr.o: enumtostr.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h
+	${CXX} -c ${CXXFLAGS} enumtostr.cpp
+
+estring.o: estring.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h pwpath.h estring.h seq.h msa.h
+	${CXX} -c ${CXXFLAGS} estring.cpp
+
+fasta2.o: fasta2.cpp muscle.h types.h enums.h intmath.h alpha.h params.h
+	${CXX} -c ${CXXFLAGS} fasta2.cpp
+
+fasta.o: fasta.cpp muscle.h types.h enums.h intmath.h alpha.h params.h \
+ msa.h textfile.h
+	${CXX} -c ${CXXFLAGS} fasta.cpp
+
+fastclust.o: fastclust.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h seqvect.h seq.h distfunc.h clust.h clustsetdf.h clustset.h \
+ msa.h tree.h distcalc.h
+	${CXX} -c ${CXXFLAGS} fastclust.cpp
+
+fastdist.o: fastdist.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h distfunc.h seqvect.h seq.h
+	${CXX} -c ${CXXFLAGS} fastdist.cpp
+
+fastdistjones.o: fastdistjones.cpp muscle.h types.h enums.h intmath.h \
+ alpha.h params.h distfunc.h seqvect.h seq.h
+	${CXX} -c ${CXXFLAGS} fastdistjones.cpp
+
+fastdistkbit.o: fastdistkbit.cpp muscle.h types.h enums.h intmath.h \
+ alpha.h params.h distfunc.h seqvect.h seq.h
+	${CXX} -c ${CXXFLAGS} fastdistkbit.cpp
+
+fastdistkmer.o: fastdistkmer.cpp muscle.h types.h enums.h intmath.h \
+ alpha.h params.h msa.h seqvect.h seq.h distfunc.h
+	${CXX} -c ${CXXFLAGS} fastdistkmer.cpp
+
+fastdistmafft.o: fastdistmafft.cpp muscle.h types.h enums.h intmath.h \
+ alpha.h params.h distfunc.h seqvect.h seq.h
+	${CXX} -c ${CXXFLAGS} fastdistmafft.cpp
+
+fastdistnuc.o: fastdistnuc.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h distfunc.h seqvect.h seq.h
+	${CXX} -c ${CXXFLAGS} fastdistnuc.cpp
+
+fastscorepath2.o: fastscorepath2.cpp muscle.h types.h enums.h intmath.h \
+ alpha.h params.h profile.h msa.h pwpath.h
+	${CXX} -c ${CXXFLAGS} fastscorepath2.cpp
+
+finddiags.o: finddiags.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h profile.h msa.h pwpath.h diaglist.h
+	${CXX} -c ${CXXFLAGS} finddiags.cpp
+
+finddiagsn.o: finddiagsn.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h profile.h msa.h pwpath.h diaglist.h
+	${CXX} -c ${CXXFLAGS} finddiagsn.cpp
+
+glbalign352.o: glbalign352.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h pwpath.h timing.h textfile.h msa.h profile.h
+	${CXX} -c ${CXXFLAGS} glbalign352.cpp
+
+glbalign.o: glbalign.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h pwpath.h timing.h textfile.h msa.h profile.h
+	${CXX} -c ${CXXFLAGS} glbalign.cpp
+
+glbaligndiag.o: glbaligndiag.cpp muscle.h types.h enums.h intmath.h \
+ alpha.h params.h dpreglist.h diaglist.h pwpath.h profile.h msa.h \
+ timing.h
+	${CXX} -c ${CXXFLAGS} glbaligndiag.cpp
+
+glbalignla.o: glbalignla.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h profile.h msa.h pwpath.h
+	${CXX} -c ${CXXFLAGS} glbalignla.cpp
+
+glbalignle.o: glbalignle.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h profile.h msa.h pwpath.h
+	${CXX} -c ${CXXFLAGS} glbalignle.cpp
+
+glbalignns.o: glbalignns.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h profile.h msa.h pwpath.h
+	${CXX} -c ${CXXFLAGS} glbalignns.cpp
+
+glbalignsimple.o: glbalignsimple.cpp muscle.h types.h enums.h intmath.h \
+ alpha.h params.h pwpath.h profile.h msa.h
+	${CXX} -c ${CXXFLAGS} glbalignsimple.cpp
+
+glbalignsp.o: glbalignsp.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h profile.h msa.h pwpath.h
+	${CXX} -c ${CXXFLAGS} glbalignsp.cpp
+
+glbalignspn.o: glbalignspn.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h profile.h msa.h pwpath.h
+	${CXX} -c ${CXXFLAGS} glbalignspn.cpp
+
+glbalignss.o: glbalignss.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h profile.h msa.h pwpath.h seq.h
+	${CXX} -c ${CXXFLAGS} glbalignss.cpp
+
+glbalndimer.o: glbalndimer.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h pwpath.h profile.h msa.h gapscoredimer.h
+	${CXX} -c ${CXXFLAGS} glbalndimer.cpp
+
+globals.o: globals.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h
+	${CXX} -c ${CXXFLAGS} globals.cpp
+
+globalslinux.o: globalslinux.cpp muscle.h types.h enums.h intmath.h \
+ alpha.h params.h
+	${CXX} -c ${CXXFLAGS} globalslinux.cpp
+
+globalsosx.o: globalsosx.cpp
+	${CXX} -c ${CXXFLAGS} globalsosx.cpp
+
+globalsother.o: globalsother.cpp muscle.h types.h enums.h intmath.h \
+ alpha.h params.h
+	${CXX} -c ${CXXFLAGS} globalsother.cpp
+
+globalswin32.o: globalswin32.cpp muscle.h types.h enums.h intmath.h \
+ alpha.h params.h
+	${CXX} -c ${CXXFLAGS} globalswin32.cpp
+
+gonnet.o: gonnet.cpp muscle.h types.h enums.h intmath.h alpha.h params.h \
+ gonnet.h
+	${CXX} -c ${CXXFLAGS} gonnet.cpp
+
+gotowt.o: gotowt.cpp
+	${CXX} -c ${CXXFLAGS} gotowt.cpp
+
+henikoffweight.o: henikoffweight.cpp muscle.h types.h enums.h intmath.h \
+ alpha.h params.h msa.h
+	${CXX} -c ${CXXFLAGS} henikoffweight.cpp
+
+henikoffweightpb.o: henikoffweightpb.cpp muscle.h types.h enums.h \
+ intmath.h alpha.h params.h msa.h
+	${CXX} -c ${CXXFLAGS} henikoffweightpb.cpp
+
+html.o: html.cpp muscle.h types.h enums.h intmath.h alpha.h params.h \
+ msa.h textfile.h
+	${CXX} -c ${CXXFLAGS} html.cpp
+
+hydro.o: hydro.cpp muscle.h types.h enums.h intmath.h alpha.h params.h \
+ profile.h msa.h pwpath.h
+	${CXX} -c ${CXXFLAGS} hydro.cpp
+
+intmath.o: intmath.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h
+	${CXX} -c ${CXXFLAGS} intmath.cpp
+
+local.o: local.cpp muscle.h types.h enums.h intmath.h alpha.h params.h \
+ textfile.h msa.h profile.h pwpath.h tree.h
+	${CXX} -c ${CXXFLAGS} local.cpp
+
+main.o: main.cpp muscle.h types.h enums.h intmath.h alpha.h params.h \
+ svnversion.h
+	${CXX} -c ${CXXFLAGS} main.cpp
+
+makerootmsab.o: makerootmsab.cpp muscle.h types.h enums.h intmath.h \
+ alpha.h params.h tree.h profile.h msa.h pwpath.h seqvect.h seq.h
+	${CXX} -c ${CXXFLAGS} makerootmsab.cpp
+
+makerootmsa.o: makerootmsa.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h tree.h seqvect.h seq.h profile.h msa.h pwpath.h estring.h
+	${CXX} -c ${CXXFLAGS} makerootmsa.cpp
+
+maketree.o: maketree.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h msa.h textfile.h tree.h
+	${CXX} -c ${CXXFLAGS} maketree.cpp
+
+mhack.o: mhack.cpp muscle.h types.h enums.h intmath.h alpha.h params.h \
+ seqvect.h seq.h msa.h
+	${CXX} -c ${CXXFLAGS} mhack.cpp
+
+mpam200.o: mpam200.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h
+	${CXX} -c ${CXXFLAGS} mpam200.cpp
+
+msa2.o: msa2.cpp muscle.h types.h enums.h intmath.h alpha.h params.h \
+ msa.h seqvect.h seq.h profile.h pwpath.h tree.h
+	${CXX} -c ${CXXFLAGS} msa2.cpp
+
+msa.o: msa.cpp muscle.h types.h enums.h intmath.h alpha.h params.h msa.h \
+ textfile.h seq.h
+	${CXX} -c ${CXXFLAGS} msa.cpp
+
+msadistkimura.o: msadistkimura.cpp muscle.h types.h enums.h intmath.h \
+ alpha.h params.h msa.h
+	${CXX} -c ${CXXFLAGS} msadistkimura.cpp
+
+msf.o: msf.cpp muscle.h types.h enums.h intmath.h alpha.h params.h msa.h \
+ textfile.h
+	${CXX} -c ${CXXFLAGS} msf.cpp
+
+muscle.o: muscle.cpp muscle.h types.h enums.h intmath.h alpha.h params.h \
+ msa.h seqvect.h seq.h tree.h profile.h pwpath.h
+	${CXX} -c ${CXXFLAGS} muscle.cpp
+
+muscleout.o: muscleout.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h msa.h textfile.h
+	${CXX} -c ${CXXFLAGS} muscleout.cpp
+
+nucmx.o: nucmx.cpp muscle.h types.h enums.h intmath.h alpha.h params.h
+	${CXX} -c ${CXXFLAGS} nucmx.cpp
+
+nwdasimple2.o: nwdasimple2.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h pwpath.h profile.h msa.h
+	${CXX} -c ${CXXFLAGS} nwdasimple2.cpp
+
+nwdasimple.o: nwdasimple.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h pwpath.h profile.h msa.h
+	${CXX} -c ${CXXFLAGS} nwdasimple.cpp
+
+nwdasmall.o: nwdasmall.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h pwpath.h profile.h msa.h
+	${CXX} -c ${CXXFLAGS} nwdasmall.cpp
+
+nwrec.o: nwrec.cpp
+	${CXX} -c ${CXXFLAGS} nwrec.cpp
+
+nwsmall.o: nwsmall.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h pwpath.h profile.h msa.h
+	${CXX} -c ${CXXFLAGS} nwsmall.cpp
+
+objscore2.o: objscore2.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h msa.h profile.h pwpath.h objscore.h
+	${CXX} -c ${CXXFLAGS} objscore2.cpp
+
+objscore.o: objscore.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h msa.h objscore.h profile.h pwpath.h timing.h
+	${CXX} -c ${CXXFLAGS} objscore.cpp
+
+objscoreda.o: objscoreda.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h msa.h profile.h pwpath.h objscore.h
+	${CXX} -c ${CXXFLAGS} objscoreda.cpp
+
+onexception.o: onexception.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h
+	${CXX} -c ${CXXFLAGS} onexception.cpp
+
+options.o: options.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h
+	${CXX} -c ${CXXFLAGS} options.cpp
+
+outweights.o: outweights.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h msa.h
+	${CXX} -c ${CXXFLAGS} outweights.cpp
+
+pam200mafft.o: pam200mafft.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h
+	${CXX} -c ${CXXFLAGS} pam200mafft.cpp
+
+params.o: params.cpp muscle.h types.h enums.h intmath.h alpha.h params.h \
+ objscore.h profile.h msa.h pwpath.h enumopts.h
+	${CXX} -c ${CXXFLAGS} params.cpp
+
+phy2.o: phy2.cpp muscle.h types.h enums.h intmath.h alpha.h params.h \
+ tree.h
+	${CXX} -c ${CXXFLAGS} phy2.cpp
+
+phy3.o: phy3.cpp muscle.h types.h enums.h intmath.h alpha.h params.h \
+ tree.h edgelist.h
+	${CXX} -c ${CXXFLAGS} phy3.cpp
+
+phy4.o: phy4.cpp muscle.h types.h enums.h intmath.h alpha.h params.h \
+ tree.h
+	${CXX} -c ${CXXFLAGS} phy4.cpp
+
+phy.o: phy.cpp muscle.h types.h enums.h intmath.h alpha.h params.h tree.h
+	${CXX} -c ${CXXFLAGS} phy.cpp
+
+phyfromclust.o: phyfromclust.cpp muscle.h types.h enums.h intmath.h \
+ alpha.h params.h tree.h clust.h
+	${CXX} -c ${CXXFLAGS} phyfromclust.cpp
+
+phyfromfile.o: phyfromfile.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h tree.h textfile.h
+	${CXX} -c ${CXXFLAGS} phyfromfile.cpp
+
+physeq.o: physeq.cpp muscle.h types.h enums.h intmath.h alpha.h params.h \
+ msa.h textfile.h
+	${CXX} -c ${CXXFLAGS} physeq.cpp
+
+phytofile.o: phytofile.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h tree.h textfile.h
+	${CXX} -c ${CXXFLAGS} phytofile.cpp
+
+posgap.o: posgap.cpp muscle.h types.h enums.h intmath.h alpha.h params.h
+	${CXX} -c ${CXXFLAGS} posgap.cpp
+
+ppscore.o: ppscore.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h textfile.h msa.h tree.h profile.h pwpath.h objscore.h
+	${CXX} -c ${CXXFLAGS} ppscore.cpp
+
+profdb.o: profdb.cpp muscle.h types.h enums.h intmath.h alpha.h params.h \
+ textfile.h seqvect.h seq.h distfunc.h msa.h tree.h clust.h profile.h \
+ pwpath.h clustsetmsa.h clustset.h msadist.h
+	${CXX} -c ${CXXFLAGS} profdb.cpp
+
+profile.o: profile.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h textfile.h msa.h tree.h profile.h pwpath.h objscore.h
+	${CXX} -c ${CXXFLAGS} profile.cpp
+
+profilefrommsa.o: profilefrommsa.cpp muscle.h types.h enums.h intmath.h \
+ alpha.h params.h msa.h profile.h pwpath.h
+	${CXX} -c ${CXXFLAGS} profilefrommsa.cpp
+
+progalign.o: progalign.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h tree.h seqvect.h seq.h profile.h msa.h pwpath.h distfunc.h \
+ textfile.h estring.h
+	${CXX} -c ${CXXFLAGS} progalign.cpp
+
+progress.o: progress.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h
+	${CXX} -c ${CXXFLAGS} progress.cpp
+
+progressivealign.o: progressivealign.cpp muscle.h types.h enums.h \
+ intmath.h alpha.h params.h tree.h seqvect.h seq.h profile.h msa.h \
+ pwpath.h distfunc.h
+	${CXX} -c ${CXXFLAGS} progressivealign.cpp
+
+pwpath.o: pwpath.cpp muscle.h types.h enums.h intmath.h alpha.h params.h \
+ pwpath.h seq.h textfile.h msa.h
+	${CXX} -c ${CXXFLAGS} pwpath.cpp
+
+readmx.o: readmx.cpp muscle.h types.h enums.h intmath.h alpha.h params.h \
+ textfile.h
+	${CXX} -c ${CXXFLAGS} readmx.cpp
+
+realigndiffs.o: realigndiffs.cpp muscle.h types.h enums.h intmath.h \
+ alpha.h params.h msa.h tree.h profile.h pwpath.h
+	${CXX} -c ${CXXFLAGS} realigndiffs.cpp
+
+realigndiffse.o: realigndiffse.cpp muscle.h types.h enums.h intmath.h \
+ alpha.h params.h msa.h tree.h profile.h pwpath.h seqvect.h seq.h \
+ estring.h
+	${CXX} -c ${CXXFLAGS} realigndiffse.cpp
+
+refine.o: refine.cpp muscle.h types.h enums.h intmath.h alpha.h params.h \
+ textfile.h seqvect.h seq.h distfunc.h msa.h tree.h clust.h profile.h \
+ pwpath.h clustsetmsa.h clustset.h msadist.h
+	${CXX} -c ${CXXFLAGS} refine.cpp
+
+refinehoriz.o: refinehoriz.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h tree.h msa.h pwpath.h profile.h scorehistory.h objscore.h
+	${CXX} -c ${CXXFLAGS} refinehoriz.cpp
+
+refinesubfams.o: refinesubfams.cpp muscle.h types.h enums.h intmath.h \
+ alpha.h params.h msa.h tree.h clust.h profile.h pwpath.h
+	${CXX} -c ${CXXFLAGS} refinesubfams.cpp
+
+refinetree.o: refinetree.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h msa.h tree.h profile.h pwpath.h
+	${CXX} -c ${CXXFLAGS} refinetree.cpp
+
+refinetreee.o: refinetreee.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h msa.h tree.h profile.h pwpath.h
+	${CXX} -c ${CXXFLAGS} refinetreee.cpp
+
+refinevert.o: refinevert.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h profile.h msa.h pwpath.h seqvect.h seq.h clust.h tree.h
+	${CXX} -c ${CXXFLAGS} refinevert.cpp
+
+refinew.o: refinew.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h msa.h seqvect.h seq.h textfile.h
+	${CXX} -c ${CXXFLAGS} refinew.cpp
+
+savebest.o: savebest.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h msa.h textfile.h
+	${CXX} -c ${CXXFLAGS} savebest.cpp
+
+scoredist.o: scoredist.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h msa.h distfunc.h seqvect.h seq.h pwpath.h
+	${CXX} -c ${CXXFLAGS} scoredist.cpp
+
+scoregaps.o: scoregaps.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h msa.h objscore.h
+	${CXX} -c ${CXXFLAGS} scoregaps.cpp
+
+scorehistory.o: scorehistory.cpp muscle.h types.h enums.h intmath.h \
+ alpha.h params.h scorehistory.h
+	${CXX} -c ${CXXFLAGS} scorehistory.cpp
+
+scoremx.o: scoremx.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h profile.h msa.h pwpath.h
+	${CXX} -c ${CXXFLAGS} scoremx.cpp
+
+scorepp.o: scorepp.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h profile.h msa.h pwpath.h
+	${CXX} -c ${CXXFLAGS} scorepp.cpp
+
+seq.o: seq.cpp muscle.h types.h enums.h intmath.h alpha.h params.h seq.h \
+ textfile.h msa.h
+	${CXX} -c ${CXXFLAGS} seq.cpp
+
+seqvect.o: seqvect.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h seqvect.h seq.h textfile.h msa.h
+	${CXX} -c ${CXXFLAGS} seqvect.cpp
+
+setblosumweights.o: setblosumweights.cpp muscle.h types.h enums.h \
+ intmath.h alpha.h params.h msa.h cluster.h distfunc.h
+	${CXX} -c ${CXXFLAGS} setblosumweights.cpp
+
+setgscweights.o: setgscweights.cpp muscle.h types.h enums.h intmath.h \
+ alpha.h params.h msa.h cluster.h distfunc.h
+	${CXX} -c ${CXXFLAGS} setgscweights.cpp
+
+setnewhandler.o: setnewhandler.cpp muscle.h types.h enums.h intmath.h \
+ alpha.h params.h
+	${CXX} -c ${CXXFLAGS} setnewhandler.cpp
+
+spfast.o: spfast.cpp muscle.h types.h enums.h intmath.h alpha.h params.h \
+ profile.h msa.h pwpath.h
+	${CXX} -c ${CXXFLAGS} spfast.cpp
+
+sptest.o: sptest.cpp muscle.h types.h enums.h intmath.h alpha.h params.h \
+ objscore.h msa.h textfile.h pwpath.h
+	${CXX} -c ${CXXFLAGS} sptest.cpp
+
+stabilize.o: stabilize.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h msa.h
+	${CXX} -c ${CXXFLAGS} stabilize.cpp
+
+subfam.o: subfam.cpp muscle.h types.h enums.h intmath.h alpha.h params.h \
+ tree.h textfile.h msa.h seqvect.h seq.h profile.h pwpath.h
+	${CXX} -c ${CXXFLAGS} subfam.cpp
+
+subfams.o: subfams.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h distfunc.h
+	${CXX} -c ${CXXFLAGS} subfams.cpp
+
+sw.o: sw.cpp muscle.h types.h enums.h intmath.h alpha.h params.h pwpath.h \
+ profile.h msa.h
+	${CXX} -c ${CXXFLAGS} sw.cpp
+
+termgaps.o: termgaps.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h profile.h msa.h pwpath.h
+	${CXX} -c ${CXXFLAGS} termgaps.cpp
+
+textfile.o: textfile.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h textfile.h
+	${CXX} -c ${CXXFLAGS} textfile.cpp
+
+threewaywt.o: threewaywt.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h tree.h
+	${CXX} -c ${CXXFLAGS} threewaywt.cpp
+
+tomhydro.o: tomhydro.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h profile.h msa.h pwpath.h
+	${CXX} -c ${CXXFLAGS} tomhydro.cpp
+
+traceback.o: traceback.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h profile.h msa.h pwpath.h
+	${CXX} -c ${CXXFLAGS} traceback.cpp
+
+tracebackopt.o: tracebackopt.cpp muscle.h types.h enums.h intmath.h \
+ alpha.h params.h pwpath.h
+	${CXX} -c ${CXXFLAGS} tracebackopt.cpp
+
+tracebacksw.o: tracebacksw.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h profile.h msa.h pwpath.h
+	${CXX} -c ${CXXFLAGS} tracebacksw.cpp
+
+treefrommsa.o: treefrommsa.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h msa.h tree.h clust.h clustsetmsa.h clustset.h msadist.h \
+ distcalc.h
+	${CXX} -c ${CXXFLAGS} treefrommsa.cpp
+
+typetostr.o: typetostr.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h
+	${CXX} -c ${CXXFLAGS} typetostr.cpp
+
+upgma2.o: upgma2.cpp muscle.h types.h enums.h intmath.h alpha.h params.h \
+ tree.h distcalc.h
+	${CXX} -c ${CXXFLAGS} upgma2.cpp
+
+usage.o: usage.cpp muscle.h types.h enums.h intmath.h alpha.h params.h
+	${CXX} -c ${CXXFLAGS} usage.cpp
+
+validateids.o: validateids.cpp muscle.h types.h enums.h intmath.h alpha.h \
+ params.h msa.h tree.h seqvect.h seq.h
+	${CXX} -c ${CXXFLAGS} validateids.cpp
+
+vtml2.o: vtml2.cpp muscle.h types.h enums.h intmath.h alpha.h params.h
+	${CXX} -c ${CXXFLAGS} vtml2.cpp
+
+writescorefile.o: writescorefile.cpp muscle.h types.h enums.h intmath.h \
+ alpha.h params.h msa.h
+	${CXX} -c ${CXXFLAGS} writescorefile.cpp
diff --git a/muscle/patches/patch-globalslinux.cpp b/muscle/patches/patch-globalslinux.cpp
index 13e0efc6aa..eaa05107dd 100644
--- a/muscle/patches/patch-globalslinux.cpp
+++ b/muscle/patches/patch-globalslinux.cpp
@@ -1,5 +1,7 @@
 $NetBSD$
 
+# Portability
+
 --- globalslinux.cpp.orig	Tue Nov 30 05:09:50 2004
 +++ globalslinux.cpp	Mon Jul  4 11:13:18 2005
 @@ -7,6 +7,12 @@
diff --git a/muscle/patches/patch-mk b/muscle/patches/patch-mk
deleted file mode 100644
index 95fac23f20..0000000000
--- a/muscle/patches/patch-mk
+++ /dev/null
@@ -1,29 +0,0 @@
-$NetBSD$
-
---- 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 pro
filefrommsa 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
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