svn commit: r358182 - in head/biology/muscle: . files
Raphael Kubo da Costa
rakuco at FreeBSD.org
Tue Jun 17 21:36:07 UTC 2014
Author: rakuco
Date: Tue Jun 17 21:36:06 2014
New Revision: 358182
URL: http://svnweb.freebsd.org/changeset/ports/358182
QAT: https://qat.redports.org/buildarchive/r358182/
Log:
Update to 3.8.31.
PR: 191130
Submitted by: mzaki at m.u-tokyo.ac.jp (maintainer)
Added:
head/biology/muscle/files/patch-mk (contents, props changed)
Deleted:
head/biology/muscle/files/patch-Makefile
head/biology/muscle/files/patch-intmath.cpp
Modified:
head/biology/muscle/Makefile
head/biology/muscle/distinfo
Modified: head/biology/muscle/Makefile
==============================================================================
--- head/biology/muscle/Makefile Tue Jun 17 20:52:50 2014 (r358181)
+++ head/biology/muscle/Makefile Tue Jun 17 21:36:06 2014 (r358182)
@@ -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 at 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>
Modified: head/biology/muscle/distinfo
==============================================================================
--- head/biology/muscle/distinfo Tue Jun 17 20:52:50 2014 (r358181)
+++ head/biology/muscle/distinfo Tue Jun 17 21:36:06 2014 (r358182)
@@ -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
Added: head/biology/muscle/files/patch-mk
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/muscle/files/patch-mk Tue Jun 17 21:36:06 2014 (r358182)
@@ -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 profilefrom
msa 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 objscor
e2.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
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