biology/muscle: update to 3.8.1551
* Bug fix for long sequences. * Unbreak '/dev/tty' problem during a build * Update maintainer's mail address PR: 243206 Submitted by: mzaki@e-mail.ne.jp (maintainer)
This commit is contained in:
Fernando Apesteguía
parent
e2e20b9e8e
commit
5fd9586f06
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=522911
@ -2,28 +2,22 @@
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# $FreeBSD$
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PORTNAME= muscle
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PORTVERSION= 3.8.31
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PORTVERSION= 3.8.1551
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CATEGORIES= biology
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MASTER_SITES= http://www.drive5.com/muscle/downloads${PORTVERSION}/
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DISTNAME= ${PORTNAME}${PORTVERSION}_src
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MASTER_SITES= http://www.drive5.com/muscle/
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DISTNAME= ${PORTNAME}_src_${PORTVERSION}
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MAINTAINER= mzaki@m.u-tokyo.ac.jp
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MAINTAINER= mzaki@e-mail.ne.jp
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COMMENT= MUltiple Sequence Comparison by Log-Expectation
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FETCH_ARGS= -A
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LICENSE= PD
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WRKSRC= ${WRKDIR}/${PORTNAME}${PORTVERSION}/src
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USES= dos2unix
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USES= dos2unix gmake
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NO_WRKSUBDIR= yes
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DOS2UNIX_GLOB= *.cpp
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ALL_TARGET= muscle
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PLIST_FILES= bin/muscle
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ONLY_FOR_ARCHS= amd64 i386
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ONLY_FOR_ARCHS_REASON= Fails to install: tries to modify /dev/tty
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do-install:
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${INSTALL_PROGRAM} ${WRKSRC}/muscle ${STAGEDIR}${PREFIX}/bin
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@ -1,2 +1,3 @@
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SHA256 (muscle3.8.31_src.tar.gz) = 43c5966a82133bd7da5921e8142f2f592c2b5f53d802f0527a2801783af809ad
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SIZE (muscle3.8.31_src.tar.gz) = 515267
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TIMESTAMP = 1578543217
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SHA256 (muscle_src_3.8.1551.tar.gz) = c70c552231cd3289f1bad51c9bd174804c18bb3adcf47f501afec7a68f9c482e
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SIZE (muscle_src_3.8.1551.tar.gz) = 190019
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28
biology/muscle/files/patch-Makefile
Normal file
28
biology/muscle/files/patch-Makefile
Normal file
@ -0,0 +1,28 @@
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--- Makefile.orig 2014-07-12 16:42:52 UTC
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+++ Makefile
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@@ -10,8 +10,8 @@
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# this is fixed by deleting "-static" from the LDLIBS line.
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CFLAGS = -O3 -funroll-loops -Winline -DNDEBUG=1
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-LDLIBS = -lm -static
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-# LDLIBS = -lm
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+#LDLIBS = -lm -static
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+LDLIBS = -lm
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OBJ = .o
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EXE =
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@@ -19,7 +19,7 @@ EXE =
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RM = rm -f
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CP = cp
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-GPP = g++
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+GPP = $(CXX)
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LD = $(GPP) $(CFLAGS)
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CPP = $(GPP) -c $(CFLAGS)
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@@ -33,4 +33,4 @@ $(CPPOBJ): %.o: %.cpp
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muscle: $(CPPOBJ)
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$(LD) -o muscle $(CPPOBJ) $(LDLIBS)
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- strip muscle
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+# strip muscle
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@ -1,5 +1,5 @@
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--- globalslinux.cpp.orig Tue Nov 30 05:09:50 2004
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+++ globalslinux.cpp Mon Jul 4 11:13:18 2005
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--- globalslinux.cpp.orig 2020-01-09 04:20:25 UTC
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+++ globalslinux.cpp
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@@ -7,6 +7,12 @@
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#include <errno.h>
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#include <stdio.h>
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@ -13,7 +13,7 @@
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const int ONE_MB = 1000000;
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const int MEM_WARNING_THRESHOLD = 20*ONE_MB;
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@@ -39,6 +45,34 @@
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@@ -39,6 +45,34 @@ const char *GetCmdLine()
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return szCmdLine;
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}
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@ -48,7 +48,7 @@
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double GetMemUseMB()
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{
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static char statm[64];
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@@ -83,6 +117,7 @@
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@@ -74,6 +108,7 @@ double GetMemUseMB()
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return ((double) Pages * (double) PageSize)/1e6;
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}
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@ -56,7 +56,7 @@
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void SaveCmdLine(int argc, char *argv[])
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{
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@@ -118,6 +153,28 @@
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@@ -109,6 +144,28 @@ void CheckMemUse()
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dPeakMemUseMB = dMB;
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}
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@ -85,7 +85,7 @@
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double GetRAMSizeMB()
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{
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const double DEFAULT_RAM = 500;
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@@ -168,5 +225,6 @@
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@@ -159,5 +216,6 @@ double GetRAMSizeMB()
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int Bytes = atoi(pMem+9)*1000;
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return ((double) Bytes)/1e6;
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}
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@ -1,27 +0,0 @@
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--- mk.orig 2010-05-02 08:15:42.000000000 +0900
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+++ mk 2014-06-17 23:45:55.000000000 +0900
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@@ -1,4 +1,4 @@
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-#!/bin/bash
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+#!/bin/sh
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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'
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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'
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@@ -6,16 +6,15 @@
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for CPPName in $CPPNames
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do
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echo $CPPName >> /dev/tty
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- 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
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+ ${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
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done
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LINK_OPTS=
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if [ `uname -s` == Linux ] ; then
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LINK_OPTS=-static
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fi
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-g++ $LINK_OPTS $ENV_LINK_OPTS -g -o muscle $ObjNames >> muscle.make.stdout.txt 2>> muscle.make.stderr.txt
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+${CXX} $LINK_OPTS $ENV_LINK_OPTS -g -o muscle $ObjNames >> muscle.make.stdout.txt 2>> muscle.make.stderr.txt
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tail muscle.make.stderr.txt
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-strip muscle
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ls -lh muscle
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sum muscle
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