- Update to 7.266

PR:		205558
Submitted by:	cartwright@asu.edu(maintainer)

5 files changed, 133 insertions, 42 deletions

diff --git a/biology/mafft/Makefile b/biology/mafft/Makefile
index 3663a0d374fc..da1188d8f524 100644
--- a/biology/mafft/Makefile
+++ b/biology/mafft/Makefile
@@ -2,7 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	mafft
-PORTVERSION=	7.221
+PORTVERSION=	7.266
 CATEGORIES=	biology
 MASTER_SITES=	http://mafft.cbrc.jp/alignment/software/
 DISTNAME=	${PORTNAME}-${PORTVERSION}-without-extensions-src
@@ -11,60 +11,37 @@ MAINTAINER=	cartwright@asu.edu
 COMMENT=	Multiple alignment program for amino acid or nucleotide sequences
 
 LICENSE=	BSD2CLAUSE
+LICENSE_FILE=	${WRKSRC}/license
 
 OPTIONS_DEFINE=	DOCS EXAMPLES
 
 WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}-without-extensions
 BUILD_WRKSRC=	${WRKSRC}/core
+INSTALL_WRKSRC=	${WRKSRC}/core
 
 USES=		gmake shebangfix tar:tgz
 
-SHEBANG_FILES=	core/mafftash_premafft.tmpl core/seekquencer_premafft.tmpl
+SHEBANG_FILES=	core/*.tmpl
 
-LIBEXEC_FILES=	dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign \
-		pair2hat3s multi2hat3s pairash addsingle splittbfast \
-		disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap \
-		countlen seq2regtable regtable2seq score getlag dndpre \
-		setcore replaceu restoreu setdirection makedirectionlist version
-PERL_LIBEXEC_FILES=	mafftash_premafft.pl seekquencer_premafft.pl
-SCRIPT_FILES=	mafft mafft-homologs.rb
-LN_FILES=	einsi fftns fftnsi ginsi linsi mafft-einsi mafft-fftns \
-		mafft-fftnsi mafft-ginsi mafft-linsi mafft-nwns mafft-nwnsi \
-		mafft-qinsi mafft-xinsi nwns nwnsi
-MAN1_FILES=	mafft.1 mafft-homologs.1
+MAKE_ENV=	INSTALL_LIB="${INSTALL_LIB}" \
+		INSTALL_DATA="${INSTALL_DATA}" \
+		INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
+		INSTALL_SCRIPT="${INSTALL_SCRIPT}" \
+		MKDIR="${MKDIR}" \
+		LN="${LN}"
 
-BROKEN_sparc64=		Does not install on sparc64: depends on thread-local storage
+.include <bsd.port.options.mk>
 
 post-patch:
-	@${REINPLACE_CMD} -e 's|^PREFIX = .*$$||' \
-		-e 's|^MANDIR = .*$$|MANDIR = $$(MANPREFIX)/man/man1|' \
-		-e 's|^CC = .*$$||' \
-		-e 's|^CFLAGS = .*$$||' \
+.if ${ARCH} == sparc64
+	@${REINPLACE_CMD} -e 's|ENABLE_MULTITHREAD = -Denablemultithread||' \
 		${BUILD_WRKSRC}/Makefile
+.endif
 
-do-install:
-	@${MKDIR} ${STAGEDIR}${PREFIX}/libexec/${PORTNAME}
-.for exec in ${LIBEXEC_FILES}
-	${INSTALL_PROGRAM} ${WRKSRC}/binaries/${exec} ${STAGEDIR}${PREFIX}/libexec/${PORTNAME}
-.endfor
-.for exec in ${PERL_LIBEXEC_FILES}
-	${INSTALL_SCRIPT} ${WRKSRC}/binaries/${exec} ${STAGEDIR}${PREFIX}/libexec/${PORTNAME}
-.endfor
-.for exec in ${SCRIPT_FILES}
-	${INSTALL_SCRIPT} ${WRKSRC}/scripts/${exec} ${STAGEDIR}${PREFIX}/bin
-.endfor
-.for exec in ${LN_FILES}
-	${LN} -sf mafft ${STAGEDIR}${PREFIX}/bin/${exec}
-.endfor
-	${LN} -sf ../libexec/${PORTNAME}/mafft-distance ${STAGEDIR}${PREFIX}/bin/mafft-distance
-	${LN} -sf ../libexec/${PORTNAME}/mafft-profile ${STAGEDIR}${PREFIX}/bin/mafft-profile
-.for man in ${MAN1_FILES}
-	${INSTALL_MAN} ${WRKSRC}/binaries/${man} ${STAGEDIR}${MAN1PREFIX}/man/man1
-.endfor
+post-install:
 	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
-	${INSTALL_DATA} ${WRKSRC}/test/* ${STAGEDIR}${EXAMPLESDIR}
 	@${MKDIR} ${STAGEDIR}${DOCSDIR}
+	${INSTALL_DATA} ${WRKSRC}/test/* ${STAGEDIR}${EXAMPLESDIR}
 	${INSTALL_DATA} ${WRKSRC}/readme ${STAGEDIR}${DOCSDIR}
-	${INSTALL_DATA} ${WRKSRC}/license ${STAGEDIR}${DOCSDIR}
 
 .include <bsd.port.mk>
diff --git a/biology/mafft/distinfo b/biology/mafft/distinfo
index 199a7bc6e942..82b25f1f2b56 100644
--- a/biology/mafft/distinfo
+++ b/biology/mafft/distinfo
@@ -1,2 +1,2 @@
-SHA256 (mafft-7.221-without-extensions-src.tgz) = 6d9cdcc04684c8c8ff61888dffc0396b48c713e4519a99f54e04c4a7179d2776
-SIZE (mafft-7.221-without-extensions-src.tgz) = 376075
+SHA256 (mafft-7.266-without-extensions-src.tgz) = 59d4921e13377bb2c8e1f0a007e94b3e698e2c546ce8facc9daa530bc673e707
+SIZE (mafft-7.266-without-extensions-src.tgz) = 440576
diff --git a/biology/mafft/files/patch-core_Makefile b/biology/mafft/files/patch-core_Makefile
new file mode 100644
index 000000000000..24857082308f
--- /dev/null
+++ b/biology/mafft/files/patch-core_Makefile
@@ -0,0 +1,103 @@
+--- core/Makefile.orig	2015-11-26 01:42:39 UTC
++++ core/Makefile
+@@ -1,8 +1,7 @@
+-PREFIX = /usr/local
+-LIBDIR = $(PREFIX)/libexec/mafft
+-BINDIR = $(PREFIX)/bin
+-MANDIR = $(PREFIX)/share/man/man1
+-DESTDIR = 
++prefix = ${STAGEDIR}${PREFIX}
++LIBDIR = $(prefix)/libexec/mafft
++BINDIR = $(prefix)/bin
++MANDIR = $(prefix)/man/man1
+ 
+ #MNO_CYGWIN = -mno-cygwin
+ 
+@@ -10,29 +9,17 @@ ENABLE_MULTITHREAD = -Denablemultithread
+ # Comment out the above line if your compiler 
+ # does not support TLS (thread-local strage).
+ 
+-CC = gcc
+-CFLAGS = -O3
+-#CFLAGS = -O3 -fPIC
+-# add -fPIC when building .so files
+-
+-#CC = icc
+-#CFLAGS = -fast
+-# if you have icc, use this.
+-
+-#CFLAGS =  -O0  -fPIC -pedantic -Wall -std=c99 -g -pg -DMALLOC_CHECK_=3
+-#CFLAGS =  -O0  -fPIC -pedantic -Wall -std=c99 -g -pg -DMALLOC_CHECK_=3  -fprofile-arcs -ftest-coverage 
+-#CFLAGS =  -O0  -fPIC -pedantic -Wall -std=c99 -g -DMALLOC_CHECK_=3 # for shark, valgrind
+-
+-
+-MYCFLAGS = $(MNO_CYGWIN) $(ENABLE_MULTITHREAD) $(CFLAGS)
++MYCFLAGS = $(ENABLE_MULTITHREAD) $(CFLAGS)
+ 
+ ifdef ENABLE_MULTITHREAD
+-LIBS = -lm  -lpthread
++LIBS = -lm  -pthread
+ else
+ LIBS = -lm
+ endif
+ 
+-INSTALL = install
++LNFILES = linsi ginsi fftns fftnsi nwns nwnsi einsi \
++	mafft-linsi mafft-ginsi mafft-fftns mafft-fftnsi mafft-nwns \
++	mafft-nwnsi mafft-einsi mafft-xinsi mafft-qinsi
+ 
+ PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign \
+ 		pair2hat3s multi2hat3s pairash addsingle \
+@@ -131,12 +118,6 @@ MANPAGES = mafft.1 mafft-homologs.1
+ 
+ 
+ all : $(PERLPROGS) $(PROGS) $(SCRIPTS)
+-	cp $(SCRIPTS) ../scripts
+-	chmod 755 ../scripts/*
+-	cp $(PERLPROGS) $(PROGS) ../binaries
+-	chmod 755 ../binaries/*
+-	cp $(MANPAGES) ../binaries
+-	@echo done.
+ 
+ sos : $(SOS)
+ dylibs : $(DYLIBS)
+@@ -524,31 +505,13 @@ clean :
+ #	rm -f ../binaries/* ../scripts/*
+ 
+ install : all
+-	mkdir -p $(DESTDIR)$(LIBDIR)
+-	chmod 755 $(DESTDIR)$(LIBDIR)
+-	mkdir -p $(DESTDIR)$(BINDIR)
+-	chmod 755 $(DESTDIR)$(BINDIR)
+-	chmod 755 $(SCRIPTS)
+-	$(INSTALL) $(SCRIPTS)  $(DESTDIR)$(BINDIR)
+-	chmod 755 $(PROGS) ||:     # in MinGW, it's ok if this fails
+-	$(INSTALL) -s $(PROGS) $(DESTDIR)$(LIBDIR)
+-	$(INSTALL) $(PERLPROGS) $(DESTDIR)$(LIBDIR)
+-	$(INSTALL) -m 644 $(MANPAGES) $(DESTDIR)$(LIBDIR)
++	$(MKDIR) $(DESTDIR)$(LIBDIR) $(DESTDIR)$(BINDIR) $(DESTDIR)$(MANDIR)
++	$(INSTALL_SCRIPT) $(SCRIPTS)  $(DESTDIR)$(BINDIR)
++	$(INSTALL_PROGRAM) $(PROGS) $(DESTDIR)$(LIBDIR)
++	$(INSTALL_SCRIPT) $(PERLPROGS) $(DESTDIR)$(LIBDIR)
++	$(INSTALL_DATA) $(MANPAGES) $(DESTDIR)$(MANDIR)
+ 
+-	( cd $(DESTDIR)$(BINDIR); \
+-rm -f linsi ginsi einsi fftns fftnsi nwns nwnsi xinsi qinsi; \
+-rm -f mafft-linsi mafft-ginsi mafft-einsi mafft-fftns mafft-fftnsi mafft-nwns mafft-nwnsi mafft-xinsi mafft-qinsi mafft-randomcore.rb ; \
+-ln -s mafft linsi; ln -s mafft ginsi; ln -s mafft fftns; \
+-ln -s mafft fftnsi; ln -s mafft nwns; ln -s mafft nwnsi; \
+-ln -s mafft einsi; \
+-ln -s mafft mafft-linsi; ln -s mafft mafft-ginsi; ln -s mafft mafft-fftns; \
+-ln -s mafft mafft-fftnsi; ln -s mafft mafft-nwns; ln -s mafft mafft-nwnsi; \
+-ln -s mafft mafft-einsi; ln -s mafft mafft-xinsi; ln -s mafft mafft-qinsi;\
+-rm -f mafft-profile mafft-profile.exe; ln -s $(LIBDIR)/mafft-profile .; \
+-rm -f mafft-distance mafft-distance.exe; ln -s $(LIBDIR)/mafft-distance . )
++	$(foreach f,$(LNFILES),$(LN) -s mafft $(DESTDIR)$(BINDIR)/$(f);)
+ 
+-	mkdir -p $(DESTDIR)$(MANDIR)
+-	chmod 755 $(DESTDIR)$(MANDIR)
+-	$(INSTALL) -m 644 $(MANPAGES) $(DESTDIR)$(MANDIR)
+-# remove incorrectly installed manpages by previous versions
+-#	rm -f /usr/local/man/man1/mafft.1 /usr/local/man/man1/mafft-homologs.1 
++	$(LN) -s ../libexec/mafft/mafft-profile $(DESTDIR)$(BINDIR)/mafft-profile
++	$(LN) -s ../libexec/mafft/mafft-distance $(DESTDIR)$(BINDIR)/mafft-distance
diff --git a/biology/mafft/files/patch-core_mltaln.h b/biology/mafft/files/patch-core_mltaln.h
new file mode 100644
index 000000000000..afb91b0f3355
--- /dev/null
+++ b/biology/mafft/files/patch-core_mltaln.h
@@ -0,0 +1,11 @@
+--- core/mltaln.h.orig	2015-11-26 01:42:39 UTC
++++ core/mltaln.h
+@@ -182,6 +182,8 @@ extern int conjuctionfortbfast();
+ extern int fastconjuction();
+ extern char seqcheck( char ** );
+ 
++extern int deletenewinsertions_whole_eq( int on, int an, char **oseq, char **aseq, int **deletelist );
++
+ typedef struct _LocalHom
+ {
+ 	int nokori;
diff --git a/biology/mafft/pkg-plist b/biology/mafft/pkg-plist
index bc0982b4d887..37594a5eaf41 100644
--- a/biology/mafft/pkg-plist
+++ b/biology/mafft/pkg-plist
@@ -51,7 +51,6 @@ libexec/mafft/tbfast
 libexec/mafft/version
 man/man1/mafft-homologs.1.gz
 man/man1/mafft.1.gz
-%%PORTDOCS%%%%DOCSDIR%%/license
 %%PORTDOCS%%%%DOCSDIR%%/readme
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.dpparttree
@@ -59,6 +58,7 @@ man/man1/mafft.1.gz
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.fftnsi
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.gins1
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.ginsi
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.ginsi.allowshift
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.lins1
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.linsi
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.parttree