Attachment 143873 Details for Bug 191130 – svn diff

[patch] svn diff

muscle.diff (text/plain), 8.13 KB, created by Motomichi Matsuzaki on 2014-06-17 15:01:16 UTC

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Creator: Motomichi Matsuzaki

Created: 2014-06-17 15:01:16 UTC

Size: 8.13 KB

patch

obsolete

>Index: Makefile
>===================================================================
>--- Makefile	(revision 358125)
>+++ Makefile	(working copy)
>@@ -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>
>Index: distinfo
>===================================================================
>--- distinfo	(revision 358125)
>+++ distinfo	(working copy)
>@@ -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
>Index: files/patch-Makefile
>===================================================================
>--- files/patch-Makefile	(revision 358125)
>+++ files/patch-Makefile	(working copy)
>@@ -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)
>Index: files/patch-intmath.cpp
>===================================================================
>--- files/patch-intmath.cpp	(revision 358125)
>+++ files/patch-intmath.cpp	(working copy)
>@@ -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)
>Index: files/patch-mk
>===================================================================
>--- files/patch-mk	(revision 0)
>+++ files/patch-mk	(working copy)
>@@ -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
>
>Property changes on: files/patch-mk
>___________________________________________________________________
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>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

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Attachments on bug 191130: 143873