Attachment 210555 Details for Bug 243206 – svn diff for biology/muscle to 3.8.1551

[patch] svn diff for biology/muscle to 3.8.1551

muscle-3.8.1551.diff (text/plain), 8.20 KB, created by Motomichi Matsuzaki on 2020-01-09 05:16:30 UTC

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Creator: Motomichi Matsuzaki

Created: 2020-01-09 05:16:30 UTC

Size: 8.20 KB

patch

obsolete

>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

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Attachments on bug 243206: 210555 | 210754