Attachment 164571 Details for Bug 205558 – Patch to upgrade biology/mafft to 7.266

Patch to upgrade biology/mafft to 7.266

mafft-7.266.diff (text/plain), 9.54 KB, created by cartwright on 2015-12-23 23:47:53 UTC

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Creator: cartwright

Created: 2015-12-23 23:47:53 UTC

Size: 9.54 KB

patch

obsolete

>Index: Makefile
>===================================================================
>--- Makefile	(revision 403942)
>+++ Makefile	(working copy)
>@@ -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 @@
> 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}
>+	@${MKDIR} ${STAGEDIR}${DOCSDIR}
> 	${INSTALL_DATA} ${WRKSRC}/test/* ${STAGEDIR}${EXAMPLESDIR}
>-	@${MKDIR} ${STAGEDIR}${DOCSDIR}
> 	${INSTALL_DATA} ${WRKSRC}/readme ${STAGEDIR}${DOCSDIR}
>-	${INSTALL_DATA} ${WRKSRC}/license ${STAGEDIR}${DOCSDIR}
> 
> .include <bsd.port.mk>
>Index: distinfo
>===================================================================
>--- distinfo	(revision 403942)
>+++ distinfo	(working copy)
>@@ -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
>Index: files/patch-core_Makefile
>===================================================================
>--- files/patch-core_Makefile	(revision 0)
>+++ files/patch-core_Makefile	(working copy)
>@@ -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
>
>Property changes on: files/patch-core_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-core_mltaln.h
>===================================================================
>--- files/patch-core_mltaln.h	(revision 0)
>+++ files/patch-core_mltaln.h	(working copy)
>@@ -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;
>
>Property changes on: files/patch-core_mltaln.h
>___________________________________________________________________
>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: pkg-plist
>===================================================================
>--- pkg-plist	(revision 403942)
>+++ pkg-plist	(working copy)
>@@ -51,7 +51,6 @@
> 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 @@
> %%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

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cartwright: maintainer-approval+

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Attachments on bug 205558: 164571 | 164572 | 164573