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Message-Id: <20130907025041.96465d47c8df0c050b7e1a2d@yahoo.com>
Date: Sat, 7 Sep 2013 02:50:41 +0900
From: KATO Tsuguru <tkato432@yahoo.com>
To: FreeBSD-gnats-submit@FreeBSD.org
Subject: biology/fasta3: Update to version 36.3.6c

>Number:         181883
>Category:       ports
>Synopsis:       biology/fasta3: Update to version 36.3.6c
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    pawel
>State:          closed
>Quarter:        
>Keywords:       
>Date-Required:  
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Fri Sep 06 18:10:03 UTC 2013
>Closed-Date:    Tue Oct 29 19:32:34 UTC 2013
>Last-Modified:  Tue Oct 29 19:40:00 UTC 2013
>Originator:     KATO Tsuguru
>Release:        FreeBSD 8.4-RELEASE-p3 i386
>Organization:
>Environment:
>Description:
- Update to version 36.3.6c

>How-To-Repeat:
>Fix:

diff -urN /usr/ports/biology/fasta3/Makefile biology/fasta3/Makefile
--- /usr/ports/biology/fasta3/Makefile	2013-09-05 01:47:14.000000000 +0900
+++ biology/fasta3/Makefile	2013-09-07 00:00:00.000000000 +0900
@@ -2,7 +2,7 @@
 # $FreeBSD: head/biology/fasta3/Makefile 323293 2013-07-19 14:08:02Z wen $
 
 PORTNAME=	fasta3
-PORTVERSION=	36.3.6
+PORTVERSION=	36.3.6c
 CATEGORIES=	biology
 MASTER_SITES=	http://faculty.virginia.edu/wrpearson/fasta/fasta36/
 DISTNAME=	fasta-${PORTVERSION}
@@ -10,18 +10,31 @@
 MAINTAINER=	ports@FreeBSD.org
 COMMENT=	Collection of programs for searching DNA and protein databases
 
+OPTIONS_DEFINE=	DOCS EXAMPLES
+
 NO_CDROM=	May not be sold or incorporated into a commercial product
+
 WRKSRC=		${WRKDIR}/${DISTNAME}
 BUILD_WRKSRC=	${WRKSRC}/src
 INSTALL_WRKSRC=	${BUILD_WRKSRC}
-SUB_FILES=	pkg-message
+
 MAKEFILE=	Makefile.freebsd
+MAKE_ENV=	THR_LIBS="-pthread" XDIR="${PREFIX}/bin" \
+		FASTA_HOST="$$(${UNAME} -n)"
 
-XDIR=		${PREFIX}/bin
-FASTA_HOST!=	/usr/bin/uname -n
+SUB_FILES=	pkg-message
+
+PLIST_SUB=	VER="${PORTVERSION:R:R}"
 
-MAKE_ENV+=	THR_LIBS=${PTHREAD_LIBS} XDIR=${XDIR} \
-		FASTA_HOST='"${FASTA_HOST}"'
+MLINKS=		fasta36.1 tfasta35.1 fasta36.1 fastx35.1 \
+		fasta36.1 tfastx35.1 fasta36.1 fasty35.1 \
+		fasta36.1 tfasty35.1 fasta36.1 ssearch35.1 \
+		fasta36.1 fastf35.1 fasta36.1 fasts35.1 \
+		fasta36.1 tfasts35.1 fasta36.1 fastm35.1 \
+		fasta36.1 tfastf35.1 fasta36.1 ggsearch35.1 \
+		fasta36.1 lalign35.1 fasta36.1 prss35.1 \
+		fasta36.1 prfx35.1
+MAN1=		fasta36.1 fastf3.1 fasts3.1 prss3.1 map_db.1 ps_lav.1
 
 FASTA3_DOCS=	README.versions \
 		fasta_func.doc readme.* fasta.defaults \
@@ -29,39 +42,36 @@
 DATA=		data/*.mat
 EXAMPLES=	seq/*.aa seq/*.lc seq/*.seq seq/*.lib
 
-MAN1=		fasta36.1 fastf3.1 fasts3.1 prss3.1 map_db.1 ps_lav.1
-MLINKS=		fasta36.1 tfasta35.1 fasta36.1 fastx35.1 fasta36.1 tfastx35.1 \
-		fasta36.1 fasty35.1 fasta36.1 tfasty35.1 fasta36.1 ssearch35.1 \
-		fasta36.1 fastf35.1 fasta36.1 fasts35.1 fasta36.1 tfasts35.1 \
-		fasta36.1 fastm35.1 fasta36.1 tfastf35.1 fasta36.1 ggsearch35.1 \
-		fasta36.1 lalign35.1 fasta36.1 prss35.1 fasta36.1 prfx35.1
-PLIST_SUB=	VER=${PORTVERSION:R:R}
+.include <bsd.port.options.mk>
 
 post-patch:
-	@ ${CP} ${WRKSRC}/make/${MAKEFILE} ${BUILD_WRKSRC}/
+	@${CP} ${WRKSRC}/make/${MAKEFILE} ${BUILD_WRKSRC}
+
 post-install:
-	${INSTALL_PROGRAM} ${WRKSRC}/bin/* ${PREFIX}/bin/
-	${INSTALL_DATA} ${WRKSRC}/conf/fastlibs ${PREFIX}/etc/fastlibs.sample
-	@ ${MKDIR} ${DATADIR}
+	(cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} * ${PREFIX}/bin)
+	(cd ${WRKSRC}/conf && ${INSTALL_DATA} fastlibs ${PREFIX}/etc/fastlibs.sample)
+	@${MKDIR} ${DATADIR}
 .for data in ${DATA}
-	${INSTALL_DATA} ${WRKSRC}/${data} ${DATADIR}
-.endfor
-	@ ${MKDIR} ${EXAMPLESDIR}
-.for ex in ${EXAMPLES}
-	${INSTALL_DATA} ${WRKSRC}/${ex} ${EXAMPLESDIR}
+	(cd ${WRKSRC} && ${INSTALL_DATA} ${data} ${DATADIR})
 .endfor
 .for manpage in ${MAN1}
-	${INSTALL_MAN} ${WRKSRC}/doc/${manpage} ${MAN1PREFIX}/man/man1/
+	(cd ${WRKSRC}/doc && ${INSTALL_MAN} ${manpage} ${MAN1PREFIX}/man/man1)
+.endfor
+.if ${PORT_OPTIONS:MDOCS}
+	@${MKDIR} ${DOCSDIR}
+.for i in COPYRIGHT FASTA_LIST README
+	(cd ${WRKSRC} && ${INSTALL_DATA} ${i} ${DOCSDIR})
 .endfor
-.if !defined(NOPORTDOCS)
-	@ ${MKDIR} ${DOCSDIR}
-	${INSTALL_DATA} ${WRKSRC}/README ${DOCSDIR}
-	${INSTALL_DATA} ${WRKSRC}/COPYRIGHT ${DOCSDIR}
-	${INSTALL_DATA} ${WRKSRC}/FASTA_LIST ${DOCSDIR}
 .for docfile in ${FASTA3_DOCS}
-	@ ${INSTALL_DATA} ${WRKSRC}/doc/${docfile} ${DOCSDIR}
+	(cd ${WRKSRC}/doc && ${INSTALL_DATA} ${docfile} ${DOCSDIR})
+.endfor
+.endif
+.if ${PORT_OPTIONS:MEXAMPLES}
+	@${MKDIR} ${EXAMPLESDIR}
+.for ex in ${EXAMPLES}
+	(cd ${WRKSRC} && ${INSTALL_DATA} ${ex} ${EXAMPLESDIR})
 .endfor
 .endif
-	@ ${CAT} ${PKGMESSAGE}
+	@${CAT} ${PKGMESSAGE}
 
 .include <bsd.port.mk>
diff -urN /usr/ports/biology/fasta3/distinfo biology/fasta3/distinfo
--- /usr/ports/biology/fasta3/distinfo	2013-09-05 01:47:14.000000000 +0900
+++ biology/fasta3/distinfo	2013-09-07 00:00:00.000000000 +0900
@@ -1,2 +1,2 @@
-SHA256 (fasta-36.3.6.tar.gz) = d6c526c307941fe8c98a16406cb01df6bb5712d3c2b7f4a90e126ceba682db6f
-SIZE (fasta-36.3.6.tar.gz) = 995298
+SHA256 (fasta-36.3.6c.tar.gz) = a6abe630a061ddf9d52064aedf5466896b410fccf7adc8802bce8363e7c9e8dd
+SIZE (fasta-36.3.6c.tar.gz) = 996137
diff -urN /usr/ports/biology/fasta3/pkg-plist biology/fasta3/pkg-plist
--- /usr/ports/biology/fasta3/pkg-plist	2013-09-05 01:47:14.000000000 +0900
+++ biology/fasta3/pkg-plist	2013-09-07 00:00:00.000000000 +0900
@@ -17,11 +17,17 @@
 bin/tfastx%%VER%%
 bin/tfasty%%VER%%
 etc/fastlibs.sample
-%%PORTDOCS%%%%DOCSDIR%%/README
 %%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT
 %%PORTDOCS%%%%DOCSDIR%%/FASTA_LIST
+%%PORTDOCS%%%%DOCSDIR%%/README
 %%PORTDOCS%%%%DOCSDIR%%/README.versions
+%%PORTDOCS%%%%DOCSDIR%%/changes_v34.html
+%%PORTDOCS%%%%DOCSDIR%%/changes_v35.html
+%%PORTDOCS%%%%DOCSDIR%%/changes_v36.html
+%%PORTDOCS%%%%DOCSDIR%%/fasta.defaults
+%%PORTDOCS%%%%DOCSDIR%%/fasta.options
 %%PORTDOCS%%%%DOCSDIR%%/fasta_func.doc
+%%PORTDOCS%%%%DOCSDIR%%/fasta_versions.html
 %%PORTDOCS%%%%DOCSDIR%%/readme.v30
 %%PORTDOCS%%%%DOCSDIR%%/readme.v30t6
 %%PORTDOCS%%%%DOCSDIR%%/readme.v30t7
@@ -33,57 +39,51 @@
 %%PORTDOCS%%%%DOCSDIR%%/readme.v35
 %%PORTDOCS%%%%DOCSDIR%%/readme.v36
 %%PORTDOCS%%%%DOCSDIR%%/readme.w32
-%%PORTDOCS%%%%DOCSDIR%%/fasta.defaults
-%%PORTDOCS%%%%DOCSDIR%%/fasta.options
-%%PORTDOCS%%%%DOCSDIR%%/fasta_versions.html
-%%PORTDOCS%%%%DOCSDIR%%/changes_v34.html
-%%PORTDOCS%%%%DOCSDIR%%/changes_v35.html
-%%PORTDOCS%%%%DOCSDIR%%/changes_v36.html
-%%EXAMPLESDIR%%/dyr_human.aa
-%%EXAMPLESDIR%%/egmsmg.aa
-%%EXAMPLESDIR%%/gstt1_drome.aa
-%%EXAMPLESDIR%%/gtm1_human.aa
-%%EXAMPLESDIR%%/gtt1_drome.aa
-%%EXAMPLESDIR%%/h10_human.aa
-%%EXAMPLESDIR%%/hahu.aa
-%%EXAMPLESDIR%%/lcbo.aa
-%%EXAMPLESDIR%%/m1r.aa
-%%EXAMPLESDIR%%/m2.aa
-%%EXAMPLESDIR%%/mchu.aa
-%%EXAMPLESDIR%%/mgstm1.aa
-%%EXAMPLESDIR%%/ms1.aa
-%%EXAMPLESDIR%%/musplfm.aa
-%%EXAMPLESDIR%%/mwkw.aa
-%%EXAMPLESDIR%%/mwrtc1.aa
-%%EXAMPLESDIR%%/myosin_bp.aa
-%%EXAMPLESDIR%%/n0.aa
-%%EXAMPLESDIR%%/n1.aa
-%%EXAMPLESDIR%%/n2.aa
-%%EXAMPLESDIR%%/n2s.aa
-%%EXAMPLESDIR%%/n2t.aa
-%%EXAMPLESDIR%%/ngt.aa
-%%EXAMPLESDIR%%/ngts.aa
-%%EXAMPLESDIR%%/oohu.aa
-%%EXAMPLESDIR%%/prio_atepa.aa
-%%EXAMPLESDIR%%/qrhuld.aa
-%%EXAMPLESDIR%%/titin_hum.aa
-%%EXAMPLESDIR%%/xurt8c.aa
-%%EXAMPLESDIR%%/xurtg.aa
-%%EXAMPLESDIR%%/mgstm1.lc
-%%EXAMPLESDIR%%/xurt8c.lc
-%%EXAMPLESDIR%%/bovgh.seq
-%%EXAMPLESDIR%%/bovprl.seq
-%%EXAMPLESDIR%%/gst.seq
-%%EXAMPLESDIR%%/hsgstm1b.seq
-%%EXAMPLESDIR%%/humgstd.seq
-%%EXAMPLESDIR%%/mgstm1.seq
-%%EXAMPLESDIR%%/mgstm1_genclone.seq
-%%EXAMPLESDIR%%/mgtt2_x.seq
-%%EXAMPLESDIR%%/titin_hum.seq
-%%EXAMPLESDIR%%/mu.lib
-%%EXAMPLESDIR%%/n2_fs.lib
-%%EXAMPLESDIR%%/n_fs.lib
-%%EXAMPLESDIR%%/prot_test.lib
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bovgh.seq
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bovprl.seq
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dyr_human.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/egmsmg.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/gst.seq
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/gstt1_drome.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/gtm1_human.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/gtt1_drome.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/h10_human.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hahu.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hsgstm1b.seq
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/humgstd.seq
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lcbo.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/m1r.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/m2.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mchu.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgstm1.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgstm1.lc
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgstm1.seq
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgstm1_genclone.seq
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgtt2_x.seq
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ms1.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mu.lib
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/musplfm.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mwkw.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mwrtc1.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/myosin_bp.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n0.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n1.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n2.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n2_fs.lib
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n2s.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n2t.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n_fs.lib
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ngt.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ngts.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/oohu.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prio_atepa.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prot_test.lib
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/qrhuld.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/titin_hum.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/titin_hum.seq
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/xurt8c.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/xurt8c.lc
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/xurtg.aa
 %%DATADIR%%/blosum45.mat
 %%DATADIR%%/blosum50.mat
 %%DATADIR%%/blosum62.mat
@@ -97,6 +97,6 @@
 %%DATADIR%%/pam250.mat
 %%DATADIR%%/rna.mat
 %%DATADIR%%/vtml160.mat
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
-@dirrm %%EXAMPLESDIR%%
 @dirrm %%DATADIR%%
+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%
+%%PORTDOCS%%@dirrm %%DOCSDIR%%
>Release-Note:
>Audit-Trail:
Responsible-Changed-From-To: freebsd-ports-bugs->miwi 
Responsible-Changed-By: edwin 
Responsible-Changed-When: Fri Sep 6 18:12:52 UTC 2013 
Responsible-Changed-Why:  
miwi@ wants this submitter's PRs (via the GNATS Auto Assign Tool) 

http://www.freebsd.org/cgi/query-pr.cgi?pr=181883 
Responsible-Changed-From-To: miwi->freebsd-ports-bugs 
Responsible-Changed-By: bdrewery 
Responsible-Changed-When: Sun Sep 22 09:11:52 CDT 2013 
Responsible-Changed-Why:  
Back to the heap due to timeout 

http://www.freebsd.org/cgi/query-pr.cgi?pr=181883 

From: KATO Tsuguru <tkato432@yahoo.com>
To: bug-followup@FreeBSD.org
Cc:  
Subject: Re: ports/181883: biology/fasta3: Update to version 36.3.6c
Date: Wed, 30 Oct 2013 02:50:31 +0900

 This is a multi-part message in MIME format.
 
 --Multipart=_Wed__30_Oct_2013_02_50_31_+0900_Dt.rccrvI5XLIxQ7
 Content-Type: text/plain; charset=US-ASCII
 Content-Transfer-Encoding: 7bit
 
 Version 36.3.6d has been released.
 
 --Multipart=_Wed__30_Oct_2013_02_50_31_+0900_Dt.rccrvI5XLIxQ7
 Content-Type: text/x-diff;
  name="biology_fasta3.diff"
 Content-Disposition: attachment;
  filename="biology_fasta3.diff"
 Content-Transfer-Encoding: 7bit
 
 diff -urN /usr/ports/biology/fasta3/Makefile biology/fasta3/Makefile
 --- /usr/ports/biology/fasta3/Makefile	2013-09-22 01:13:54.000000000 +0900
 +++ biology/fasta3/Makefile	2013-10-30 00:00:00.000000000 +0900
 @@ -2,7 +2,7 @@
  # $FreeBSD: head/biology/fasta3/Makefile 327709 2013-09-20 15:55:44Z bapt $
  
  PORTNAME=	fasta3
 -PORTVERSION=	36.3.6
 +PORTVERSION=	36.3.6d
  CATEGORIES=	biology
  MASTER_SITES=	http://faculty.virginia.edu/wrpearson/fasta/fasta36/
  DISTNAME=	fasta-${PORTVERSION}
 @@ -10,59 +10,62 @@
  MAINTAINER=	ports@FreeBSD.org
  COMMENT=	Collection of programs for searching DNA and protein databases
  
 +OPTIONS_DEFINE=	DOCS EXAMPLES
 +
  NO_CDROM=	May not be sold or incorporated into a commercial product
 +
  WRKSRC=		${WRKDIR}/${DISTNAME}
  BUILD_WRKSRC=	${WRKSRC}/src
  INSTALL_WRKSRC=	${BUILD_WRKSRC}
 -SUB_FILES=	pkg-message
 +
  MAKEFILE=	Makefile.freebsd
 +MAKE_ENV=	THR_LIBS="-pthread" XDIR="${STAGEDIR}${PREFIX}/bin" \
 +		FASTA_HOST="$$(${UNAME} -n)"
  
 -XDIR=		${PREFIX}/bin
 -FASTA_HOST!=	/usr/bin/uname -n
 +SUB_FILES=	pkg-message
  
 -MAKE_ENV+=	THR_LIBS=${PTHREAD_LIBS} XDIR=${XDIR} \
 -		FASTA_HOST='"${FASTA_HOST}"'
 +PLIST_SUB=	VER="${PORTVERSION:R:R}"
  
 -FASTA3_DOCS=	README.versions \
 +MAN1_LINKS=	fastf35.1 fasts35.1 fastm35.1 fastx35.1 fasty35.1 \
 +		ggsearch35.1 lalign35.1 ssearch35.1 tfasta35.1 tfastf35.1 \
 +		tfasts35.1 tfastx35.1 tfasty35.1 prfx35.1 prss35.1
 +MAN1_FILES=	fasta36.1 fastf3.1 fasts3.1 prss3.1 map_db.1 ps_lav.1
 +DOC_FILES=	README.versions \
  		fasta_func.doc readme.* fasta.defaults \
  		fasta.options fasta_versions.html changes*.html
  DATA=		data/*.mat
  EXAMPLES=	seq/*.aa seq/*.lc seq/*.seq seq/*.lib
  
 -MAN1=		fasta36.1 fastf3.1 fasts3.1 prss3.1 map_db.1 ps_lav.1
 -MLINKS=		fasta36.1 tfasta35.1 fasta36.1 fastx35.1 fasta36.1 tfastx35.1 \
 -		fasta36.1 fasty35.1 fasta36.1 tfasty35.1 fasta36.1 ssearch35.1 \
 -		fasta36.1 fastf35.1 fasta36.1 fasts35.1 fasta36.1 tfasts35.1 \
 -		fasta36.1 fastm35.1 fasta36.1 tfastf35.1 fasta36.1 ggsearch35.1 \
 -		fasta36.1 lalign35.1 fasta36.1 prss35.1 fasta36.1 prfx35.1
 -PLIST_SUB=	VER=${PORTVERSION:R:R}
 +.include <bsd.port.options.mk>
  
 -NO_STAGE=	yes
  post-patch:
 -	@ ${CP} ${WRKSRC}/make/${MAKEFILE} ${BUILD_WRKSRC}/
 +	@${CP} ${WRKSRC}/make/${MAKEFILE} ${BUILD_WRKSRC}
 +
  post-install:
 -	${INSTALL_PROGRAM} ${WRKSRC}/bin/* ${PREFIX}/bin/
 -	${INSTALL_DATA} ${WRKSRC}/conf/fastlibs ${PREFIX}/etc/fastlibs.sample
 -	@ ${MKDIR} ${DATADIR}
 +	(cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} * ${STAGEDIR}${PREFIX}/bin)
 +	(cd ${WRKSRC}/conf && ${INSTALL_DATA} fastlibs \
 +		${STAGEDIR}${PREFIX}/etc/fastlibs.sample)
 +	@${MKDIR} ${STAGEDIR}${DATADIR}
  .for data in ${DATA}
 -	${INSTALL_DATA} ${WRKSRC}/${data} ${DATADIR}
 +	(cd ${WRKSRC} && ${INSTALL_DATA} ${data} ${STAGEDIR}${DATADIR})
  .endfor
 -	@ ${MKDIR} ${EXAMPLESDIR}
 -.for ex in ${EXAMPLES}
 -	${INSTALL_DATA} ${WRKSRC}/${ex} ${EXAMPLESDIR}
 +.for manpage in ${MAN1_FILES}
 +	(cd ${WRKSRC}/doc && ${INSTALL_MAN} ${manpage} \
 +		${STAGEDIR}${MAN1PREFIX}/man/man1)
 +.endfor
 +.for links in ${MAN1_LINKS}
 +	(${LN} -sf fasta36.1 ${STAGEDIR}${MAN1PREFIX}/man/man1/${links})
  .endfor
 -.for manpage in ${MAN1}
 -	${INSTALL_MAN} ${WRKSRC}/doc/${manpage} ${MAN1PREFIX}/man/man1/
 +	@${MKDIR} ${STAGEDIR}${DOCSDIR}
 +.for i in COPYRIGHT FASTA_LIST README
 +	(cd ${WRKSRC} && ${INSTALL_DATA} ${i} ${STAGEDIR}${DOCSDIR})
  .endfor
 -.if !defined(NOPORTDOCS)
 -	@ ${MKDIR} ${DOCSDIR}
 -	${INSTALL_DATA} ${WRKSRC}/README ${DOCSDIR}
 -	${INSTALL_DATA} ${WRKSRC}/COPYRIGHT ${DOCSDIR}
 -	${INSTALL_DATA} ${WRKSRC}/FASTA_LIST ${DOCSDIR}
 -.for docfile in ${FASTA3_DOCS}
 -	@ ${INSTALL_DATA} ${WRKSRC}/doc/${docfile} ${DOCSDIR}
 +.for docfile in ${DOC_FILES}
 +	(cd ${WRKSRC}/doc && ${INSTALL_DATA} ${docfile} ${STAGEDIR}${DOCSDIR})
 +.endfor
 +	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
 +.for ex in ${EXAMPLES}
 +	(cd ${WRKSRC} && ${INSTALL_DATA} ${ex} ${STAGEDIR}${EXAMPLESDIR})
  .endfor
 -.endif
 -	@ ${CAT} ${PKGMESSAGE}
  
  .include <bsd.port.mk>
 diff -urN /usr/ports/biology/fasta3/distinfo biology/fasta3/distinfo
 --- /usr/ports/biology/fasta3/distinfo	2013-09-05 01:47:14.000000000 +0900
 +++ biology/fasta3/distinfo	2013-10-30 00:00:00.000000000 +0900
 @@ -1,2 +1,2 @@
 -SHA256 (fasta-36.3.6.tar.gz) = d6c526c307941fe8c98a16406cb01df6bb5712d3c2b7f4a90e126ceba682db6f
 -SIZE (fasta-36.3.6.tar.gz) = 995298
 +SHA256 (fasta-36.3.6d.tar.gz) = 6392741abecc8b25daeee53389584f48cee8a8ea7340c7f8cc97e149720a5730
 +SIZE (fasta-36.3.6d.tar.gz) = 997714
 diff -urN /usr/ports/biology/fasta3/files/patch-Makefile.freebsd biology/fasta3/files/patch-Makefile.freebsd
 --- /usr/ports/biology/fasta3/files/patch-Makefile.freebsd	2013-09-05 01:47:14.000000000 +0900
 +++ biology/fasta3/files/patch-Makefile.freebsd	2013-10-30 00:00:00.000000000 +0900
 @@ -13,7 +13,7 @@
   
   BIN = ../bin
  -XDIR =		/usr/local/bin
 -+XDIR =		${LOCALBASE}/bin
 ++XDIR?=		${LOCALBASE}/bin
   
   LIB_M+=		-lm
   
 diff -urN /usr/ports/biology/fasta3/pkg-plist biology/fasta3/pkg-plist
 --- /usr/ports/biology/fasta3/pkg-plist	2013-09-05 01:47:14.000000000 +0900
 +++ biology/fasta3/pkg-plist	2013-10-30 00:00:00.000000000 +0900
 @@ -17,11 +17,38 @@
  bin/tfastx%%VER%%
  bin/tfasty%%VER%%
  etc/fastlibs.sample
 -%%PORTDOCS%%%%DOCSDIR%%/README
 +man/man1/fasta36.1.gz
 +man/man1/fastf3.1.gz
 +man/man1/fastf35.1.gz
 +man/man1/fastm35.1.gz
 +man/man1/fasts3.1.gz
 +man/man1/fasts35.1.gz
 +man/man1/fastx35.1.gz
 +man/man1/fasty35.1.gz
 +man/man1/ggsearch35.1.gz
 +man/man1/lalign35.1.gz
 +man/man1/map_db.1.gz
 +man/man1/prfx35.1.gz
 +man/man1/prss3.1.gz
 +man/man1/prss35.1.gz
 +man/man1/ps_lav.1.gz
 +man/man1/ssearch35.1.gz
 +man/man1/tfasta35.1.gz
 +man/man1/tfastf35.1.gz
 +man/man1/tfasts35.1.gz
 +man/man1/tfastx35.1.gz
 +man/man1/tfasty35.1.gz
  %%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT
  %%PORTDOCS%%%%DOCSDIR%%/FASTA_LIST
 +%%PORTDOCS%%%%DOCSDIR%%/README
  %%PORTDOCS%%%%DOCSDIR%%/README.versions
 +%%PORTDOCS%%%%DOCSDIR%%/changes_v34.html
 +%%PORTDOCS%%%%DOCSDIR%%/changes_v35.html
 +%%PORTDOCS%%%%DOCSDIR%%/changes_v36.html
 +%%PORTDOCS%%%%DOCSDIR%%/fasta.defaults
 +%%PORTDOCS%%%%DOCSDIR%%/fasta.options
  %%PORTDOCS%%%%DOCSDIR%%/fasta_func.doc
 +%%PORTDOCS%%%%DOCSDIR%%/fasta_versions.html
  %%PORTDOCS%%%%DOCSDIR%%/readme.v30
  %%PORTDOCS%%%%DOCSDIR%%/readme.v30t6
  %%PORTDOCS%%%%DOCSDIR%%/readme.v30t7
 @@ -33,57 +60,51 @@
  %%PORTDOCS%%%%DOCSDIR%%/readme.v35
  %%PORTDOCS%%%%DOCSDIR%%/readme.v36
  %%PORTDOCS%%%%DOCSDIR%%/readme.w32
 -%%PORTDOCS%%%%DOCSDIR%%/fasta.defaults
 -%%PORTDOCS%%%%DOCSDIR%%/fasta.options
 -%%PORTDOCS%%%%DOCSDIR%%/fasta_versions.html
 -%%PORTDOCS%%%%DOCSDIR%%/changes_v34.html
 -%%PORTDOCS%%%%DOCSDIR%%/changes_v35.html
 -%%PORTDOCS%%%%DOCSDIR%%/changes_v36.html
 -%%EXAMPLESDIR%%/dyr_human.aa
 -%%EXAMPLESDIR%%/egmsmg.aa
 -%%EXAMPLESDIR%%/gstt1_drome.aa
 -%%EXAMPLESDIR%%/gtm1_human.aa
 -%%EXAMPLESDIR%%/gtt1_drome.aa
 -%%EXAMPLESDIR%%/h10_human.aa
 -%%EXAMPLESDIR%%/hahu.aa
 -%%EXAMPLESDIR%%/lcbo.aa
 -%%EXAMPLESDIR%%/m1r.aa
 -%%EXAMPLESDIR%%/m2.aa
 -%%EXAMPLESDIR%%/mchu.aa
 -%%EXAMPLESDIR%%/mgstm1.aa
 -%%EXAMPLESDIR%%/ms1.aa
 -%%EXAMPLESDIR%%/musplfm.aa
 -%%EXAMPLESDIR%%/mwkw.aa
 -%%EXAMPLESDIR%%/mwrtc1.aa
 -%%EXAMPLESDIR%%/myosin_bp.aa
 -%%EXAMPLESDIR%%/n0.aa
 -%%EXAMPLESDIR%%/n1.aa
 -%%EXAMPLESDIR%%/n2.aa
 -%%EXAMPLESDIR%%/n2s.aa
 -%%EXAMPLESDIR%%/n2t.aa
 -%%EXAMPLESDIR%%/ngt.aa
 -%%EXAMPLESDIR%%/ngts.aa
 -%%EXAMPLESDIR%%/oohu.aa
 -%%EXAMPLESDIR%%/prio_atepa.aa
 -%%EXAMPLESDIR%%/qrhuld.aa
 -%%EXAMPLESDIR%%/titin_hum.aa
 -%%EXAMPLESDIR%%/xurt8c.aa
 -%%EXAMPLESDIR%%/xurtg.aa
 -%%EXAMPLESDIR%%/mgstm1.lc
 -%%EXAMPLESDIR%%/xurt8c.lc
 -%%EXAMPLESDIR%%/bovgh.seq
 -%%EXAMPLESDIR%%/bovprl.seq
 -%%EXAMPLESDIR%%/gst.seq
 -%%EXAMPLESDIR%%/hsgstm1b.seq
 -%%EXAMPLESDIR%%/humgstd.seq
 -%%EXAMPLESDIR%%/mgstm1.seq
 -%%EXAMPLESDIR%%/mgstm1_genclone.seq
 -%%EXAMPLESDIR%%/mgtt2_x.seq
 -%%EXAMPLESDIR%%/titin_hum.seq
 -%%EXAMPLESDIR%%/mu.lib
 -%%EXAMPLESDIR%%/n2_fs.lib
 -%%EXAMPLESDIR%%/n_fs.lib
 -%%EXAMPLESDIR%%/prot_test.lib
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bovgh.seq
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bovprl.seq
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dyr_human.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/egmsmg.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/gst.seq
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/gstt1_drome.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/gtm1_human.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/gtt1_drome.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/h10_human.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hahu.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hsgstm1b.seq
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/humgstd.seq
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lcbo.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/m1r.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/m2.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mchu.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgstm1.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgstm1.lc
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgstm1.seq
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgstm1_genclone.seq
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgtt2_x.seq
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ms1.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mu.lib
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/musplfm.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mwkw.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mwrtc1.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/myosin_bp.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n0.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n1.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n2.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n2_fs.lib
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n2s.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n2t.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n_fs.lib
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ngt.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ngts.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/oohu.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prio_atepa.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prot_test.lib
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/qrhuld.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/titin_hum.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/titin_hum.seq
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/xurt8c.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/xurt8c.lc
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/xurtg.aa
  %%DATADIR%%/blosum45.mat
  %%DATADIR%%/blosum50.mat
  %%DATADIR%%/blosum62.mat
 @@ -97,6 +118,6 @@
  %%DATADIR%%/pam250.mat
  %%DATADIR%%/rna.mat
  %%DATADIR%%/vtml160.mat
 -%%PORTDOCS%%@dirrm %%DOCSDIR%%
 -@dirrm %%EXAMPLESDIR%%
  @dirrm %%DATADIR%%
 +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%
 +%%PORTDOCS%%@dirrm %%DOCSDIR%%
 
 --Multipart=_Wed__30_Oct_2013_02_50_31_+0900_Dt.rccrvI5XLIxQ7--
Responsible-Changed-From-To: freebsd-ports-bugs->pawel 
Responsible-Changed-By: pawel 
Responsible-Changed-When: Tue Oct 29 18:44:28 UTC 2013 
Responsible-Changed-Why:  
I'll take it. 

http://www.freebsd.org/cgi/query-pr.cgi?pr=181883 
State-Changed-From-To: open->closed 
State-Changed-By: pawel 
State-Changed-When: Tue Oct 29 19:32:33 UTC 2013 
State-Changed-Why:  
Committed. Thanks! 

http://www.freebsd.org/cgi/query-pr.cgi?pr=181883 

From: dfilter@FreeBSD.ORG (dfilter service)
To: bug-followup@FreeBSD.org
Cc:  
Subject: Re: ports/181883: commit references a PR
Date: Tue, 29 Oct 2013 19:32:30 +0000 (UTC)

 Author: pawel
 Date: Tue Oct 29 19:32:15 2013
 New Revision: 331982
 URL: http://svnweb.freebsd.org/changeset/ports/331982
 
 Log:
   Update to version 36.3.6d
   
   PR:		ports/181883
   Submitted by:	KATO Tsuguru <tkato432@yahoo.com>
 
 Modified:
   head/biology/fasta3/Makefile
   head/biology/fasta3/distinfo   (contents, props changed)
   head/biology/fasta3/files/patch-Makefile.freebsd   (contents, props changed)
   head/biology/fasta3/pkg-descr
   head/biology/fasta3/pkg-plist   (contents, props changed)
 
 Modified: head/biology/fasta3/Makefile
 ==============================================================================
 --- head/biology/fasta3/Makefile	Tue Oct 29 19:11:18 2013	(r331981)
 +++ head/biology/fasta3/Makefile	Tue Oct 29 19:32:15 2013	(r331982)
 @@ -2,7 +2,7 @@
  # $FreeBSD$
  
  PORTNAME=	fasta3
 -PORTVERSION=	36.3.6
 +PORTVERSION=	36.3.6d
  CATEGORIES=	biology
  MASTER_SITES=	http://faculty.virginia.edu/wrpearson/fasta/fasta36/
  DISTNAME=	fasta-${PORTVERSION}
 @@ -10,59 +10,60 @@ DISTNAME=	fasta-${PORTVERSION}
  MAINTAINER=	ports@FreeBSD.org
  COMMENT=	Collection of programs for searching DNA and protein databases
  
 +OPTIONS_DEFINE=	DOCS EXAMPLES
 +
  NO_CDROM=	May not be sold or incorporated into a commercial product
 +
  WRKSRC=		${WRKDIR}/${DISTNAME}
  BUILD_WRKSRC=	${WRKSRC}/src
  INSTALL_WRKSRC=	${BUILD_WRKSRC}
 -SUB_FILES=	pkg-message
 +
  MAKEFILE=	Makefile.freebsd
 +MAKE_ENV=	THR_LIBS="-pthread" XDIR="${STAGEDIR}${PREFIX}/bin" \
 +		FASTA_HOST="$$(${UNAME} -n)"
  
 -XDIR=		${PREFIX}/bin
 -FASTA_HOST!=	/usr/bin/uname -n
 +SUB_FILES=	pkg-message
  
 -MAKE_ENV+=	THR_LIBS=${PTHREAD_LIBS} XDIR=${XDIR} \
 -		FASTA_HOST='"${FASTA_HOST}"'
 +PLIST_SUB=	VER="${PORTVERSION:R:R}"
  
 -FASTA3_DOCS=	README.versions \
 +MAN1_LINKS=	fastf35.1 fasts35.1 fastm35.1 fastx35.1 fasty35.1 \
 +		ggsearch35.1 lalign35.1 ssearch35.1 tfasta35.1 tfastf35.1 \
 +		tfasts35.1 tfastx35.1 tfasty35.1 prfx35.1 prss35.1
 +MAN1_FILES=	fasta36.1 fastf3.1 fasts3.1 prss3.1 map_db.1 ps_lav.1
 +DOC_FILES=	README.versions \
  		fasta_func.doc readme.* fasta.defaults \
  		fasta.options fasta_versions.html changes*.html
  DATA=		data/*.mat
  EXAMPLES=	seq/*.aa seq/*.lc seq/*.seq seq/*.lib
  
 -MAN1=		fasta36.1 fastf3.1 fasts3.1 prss3.1 map_db.1 ps_lav.1
 -MLINKS=		fasta36.1 tfasta35.1 fasta36.1 fastx35.1 fasta36.1 tfastx35.1 \
 -		fasta36.1 fasty35.1 fasta36.1 tfasty35.1 fasta36.1 ssearch35.1 \
 -		fasta36.1 fastf35.1 fasta36.1 fasts35.1 fasta36.1 tfasts35.1 \
 -		fasta36.1 fastm35.1 fasta36.1 tfastf35.1 fasta36.1 ggsearch35.1 \
 -		fasta36.1 lalign35.1 fasta36.1 prss35.1 fasta36.1 prfx35.1
 -PLIST_SUB=	VER=${PORTVERSION:R:R}
 -
 -NO_STAGE=	yes
  post-patch:
 -	@ ${CP} ${WRKSRC}/make/${MAKEFILE} ${BUILD_WRKSRC}/
 +	@${CP} ${WRKSRC}/make/${MAKEFILE} ${BUILD_WRKSRC}
 +
  post-install:
 -	${INSTALL_PROGRAM} ${WRKSRC}/bin/* ${PREFIX}/bin/
 -	${INSTALL_DATA} ${WRKSRC}/conf/fastlibs ${PREFIX}/etc/fastlibs.sample
 -	@ ${MKDIR} ${DATADIR}
 +	(cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} * ${STAGEDIR}${PREFIX}/bin)
 +	(cd ${WRKSRC}/conf && ${INSTALL_DATA} fastlibs \
 +		${STAGEDIR}${PREFIX}/etc/fastlibs.sample)
 +	@${MKDIR} ${STAGEDIR}${DATADIR}
  .for data in ${DATA}
 -	${INSTALL_DATA} ${WRKSRC}/${data} ${DATADIR}
 +	(cd ${WRKSRC} && ${INSTALL_DATA} ${data} ${STAGEDIR}${DATADIR})
  .endfor
 -	@ ${MKDIR} ${EXAMPLESDIR}
 -.for ex in ${EXAMPLES}
 -	${INSTALL_DATA} ${WRKSRC}/${ex} ${EXAMPLESDIR}
 +.for manpage in ${MAN1_FILES}
 +	(cd ${WRKSRC}/doc && ${INSTALL_MAN} ${manpage} \
 +		${STAGEDIR}${MAN1PREFIX}/man/man1)
 +.endfor
 +.for links in ${MAN1_LINKS}
 +	(${LN} -sf fasta36.1 ${STAGEDIR}${MAN1PREFIX}/man/man1/${links})
  .endfor
 -.for manpage in ${MAN1}
 -	${INSTALL_MAN} ${WRKSRC}/doc/${manpage} ${MAN1PREFIX}/man/man1/
 +	@${MKDIR} ${STAGEDIR}${DOCSDIR}
 +.for i in COPYRIGHT FASTA_LIST README
 +	(cd ${WRKSRC} && ${INSTALL_DATA} ${i} ${STAGEDIR}${DOCSDIR})
  .endfor
 -.if !defined(NOPORTDOCS)
 -	@ ${MKDIR} ${DOCSDIR}
 -	${INSTALL_DATA} ${WRKSRC}/README ${DOCSDIR}
 -	${INSTALL_DATA} ${WRKSRC}/COPYRIGHT ${DOCSDIR}
 -	${INSTALL_DATA} ${WRKSRC}/FASTA_LIST ${DOCSDIR}
 -.for docfile in ${FASTA3_DOCS}
 -	@ ${INSTALL_DATA} ${WRKSRC}/doc/${docfile} ${DOCSDIR}
 +.for docfile in ${DOC_FILES}
 +	(cd ${WRKSRC}/doc && ${INSTALL_DATA} ${docfile} ${STAGEDIR}${DOCSDIR})
 +.endfor
 +	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
 +.for ex in ${EXAMPLES}
 +	(cd ${WRKSRC} && ${INSTALL_DATA} ${ex} ${STAGEDIR}${EXAMPLESDIR})
  .endfor
 -.endif
 -	@ ${CAT} ${PKGMESSAGE}
  
  .include <bsd.port.mk>
 
 Modified: head/biology/fasta3/distinfo
 ==============================================================================
 --- head/biology/fasta3/distinfo	Tue Oct 29 19:11:18 2013	(r331981)
 +++ head/biology/fasta3/distinfo	Tue Oct 29 19:32:15 2013	(r331982)
 @@ -1,2 +1,2 @@
 -SHA256 (fasta-36.3.6.tar.gz) = d6c526c307941fe8c98a16406cb01df6bb5712d3c2b7f4a90e126ceba682db6f
 -SIZE (fasta-36.3.6.tar.gz) = 995298
 +SHA256 (fasta-36.3.6d.tar.gz) = 6392741abecc8b25daeee53389584f48cee8a8ea7340c7f8cc97e149720a5730
 +SIZE (fasta-36.3.6d.tar.gz) = 997714
 
 Modified: head/biology/fasta3/files/patch-Makefile.freebsd
 ==============================================================================
 --- head/biology/fasta3/files/patch-Makefile.freebsd	Tue Oct 29 19:11:18 2013	(r331981)
 +++ head/biology/fasta3/files/patch-Makefile.freebsd	Tue Oct 29 19:32:15 2013	(r331982)
 @@ -13,7 +13,7 @@
   
   BIN = ../bin
  -XDIR =		/usr/local/bin
 -+XDIR =		${LOCALBASE}/bin
 ++XDIR?=		${LOCALBASE}/bin
   
   LIB_M+=		-lm
   
 
 Modified: head/biology/fasta3/pkg-descr
 ==============================================================================
 --- head/biology/fasta3/pkg-descr	Tue Oct 29 19:11:18 2013	(r331981)
 +++ head/biology/fasta3/pkg-descr	Tue Oct 29 19:32:15 2013	(r331982)
 @@ -14,5 +14,4 @@ Molecular Biology 132:185-219.
  The FASTA3 suite is distributed freely subject to the condition that it may
  not be sold or incorporated into a commercial product.
  
 -Author: William R Pearson <wrp@virginia.edu>
  WWW: http://fasta.bioch.virginia.edu/
 
 Modified: head/biology/fasta3/pkg-plist
 ==============================================================================
 --- head/biology/fasta3/pkg-plist	Tue Oct 29 19:11:18 2013	(r331981)
 +++ head/biology/fasta3/pkg-plist	Tue Oct 29 19:32:15 2013	(r331982)
 @@ -17,11 +17,38 @@ bin/tfasts%%VER%%
  bin/tfastx%%VER%%
  bin/tfasty%%VER%%
  etc/fastlibs.sample
 -%%PORTDOCS%%%%DOCSDIR%%/README
 +man/man1/fasta36.1.gz
 +man/man1/fastf3.1.gz
 +man/man1/fastf35.1.gz
 +man/man1/fastm35.1.gz
 +man/man1/fasts3.1.gz
 +man/man1/fasts35.1.gz
 +man/man1/fastx35.1.gz
 +man/man1/fasty35.1.gz
 +man/man1/ggsearch35.1.gz
 +man/man1/lalign35.1.gz
 +man/man1/map_db.1.gz
 +man/man1/prfx35.1.gz
 +man/man1/prss3.1.gz
 +man/man1/prss35.1.gz
 +man/man1/ps_lav.1.gz
 +man/man1/ssearch35.1.gz
 +man/man1/tfasta35.1.gz
 +man/man1/tfastf35.1.gz
 +man/man1/tfasts35.1.gz
 +man/man1/tfastx35.1.gz
 +man/man1/tfasty35.1.gz
  %%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT
  %%PORTDOCS%%%%DOCSDIR%%/FASTA_LIST
 +%%PORTDOCS%%%%DOCSDIR%%/README
  %%PORTDOCS%%%%DOCSDIR%%/README.versions
 +%%PORTDOCS%%%%DOCSDIR%%/changes_v34.html
 +%%PORTDOCS%%%%DOCSDIR%%/changes_v35.html
 +%%PORTDOCS%%%%DOCSDIR%%/changes_v36.html
 +%%PORTDOCS%%%%DOCSDIR%%/fasta.defaults
 +%%PORTDOCS%%%%DOCSDIR%%/fasta.options
  %%PORTDOCS%%%%DOCSDIR%%/fasta_func.doc
 +%%PORTDOCS%%%%DOCSDIR%%/fasta_versions.html
  %%PORTDOCS%%%%DOCSDIR%%/readme.v30
  %%PORTDOCS%%%%DOCSDIR%%/readme.v30t6
  %%PORTDOCS%%%%DOCSDIR%%/readme.v30t7
 @@ -33,57 +60,51 @@ etc/fastlibs.sample
  %%PORTDOCS%%%%DOCSDIR%%/readme.v35
  %%PORTDOCS%%%%DOCSDIR%%/readme.v36
  %%PORTDOCS%%%%DOCSDIR%%/readme.w32
 -%%PORTDOCS%%%%DOCSDIR%%/fasta.defaults
 -%%PORTDOCS%%%%DOCSDIR%%/fasta.options
 -%%PORTDOCS%%%%DOCSDIR%%/fasta_versions.html
 -%%PORTDOCS%%%%DOCSDIR%%/changes_v34.html
 -%%PORTDOCS%%%%DOCSDIR%%/changes_v35.html
 -%%PORTDOCS%%%%DOCSDIR%%/changes_v36.html
 -%%EXAMPLESDIR%%/dyr_human.aa
 -%%EXAMPLESDIR%%/egmsmg.aa
 -%%EXAMPLESDIR%%/gstt1_drome.aa
 -%%EXAMPLESDIR%%/gtm1_human.aa
 -%%EXAMPLESDIR%%/gtt1_drome.aa
 -%%EXAMPLESDIR%%/h10_human.aa
 -%%EXAMPLESDIR%%/hahu.aa
 -%%EXAMPLESDIR%%/lcbo.aa
 -%%EXAMPLESDIR%%/m1r.aa
 -%%EXAMPLESDIR%%/m2.aa
 -%%EXAMPLESDIR%%/mchu.aa
 -%%EXAMPLESDIR%%/mgstm1.aa
 -%%EXAMPLESDIR%%/ms1.aa
 -%%EXAMPLESDIR%%/musplfm.aa
 -%%EXAMPLESDIR%%/mwkw.aa
 -%%EXAMPLESDIR%%/mwrtc1.aa
 -%%EXAMPLESDIR%%/myosin_bp.aa
 -%%EXAMPLESDIR%%/n0.aa
 -%%EXAMPLESDIR%%/n1.aa
 -%%EXAMPLESDIR%%/n2.aa
 -%%EXAMPLESDIR%%/n2s.aa
 -%%EXAMPLESDIR%%/n2t.aa
 -%%EXAMPLESDIR%%/ngt.aa
 -%%EXAMPLESDIR%%/ngts.aa
 -%%EXAMPLESDIR%%/oohu.aa
 -%%EXAMPLESDIR%%/prio_atepa.aa
 -%%EXAMPLESDIR%%/qrhuld.aa
 -%%EXAMPLESDIR%%/titin_hum.aa
 -%%EXAMPLESDIR%%/xurt8c.aa
 -%%EXAMPLESDIR%%/xurtg.aa
 -%%EXAMPLESDIR%%/mgstm1.lc
 -%%EXAMPLESDIR%%/xurt8c.lc
 -%%EXAMPLESDIR%%/bovgh.seq
 -%%EXAMPLESDIR%%/bovprl.seq
 -%%EXAMPLESDIR%%/gst.seq
 -%%EXAMPLESDIR%%/hsgstm1b.seq
 -%%EXAMPLESDIR%%/humgstd.seq
 -%%EXAMPLESDIR%%/mgstm1.seq
 -%%EXAMPLESDIR%%/mgstm1_genclone.seq
 -%%EXAMPLESDIR%%/mgtt2_x.seq
 -%%EXAMPLESDIR%%/titin_hum.seq
 -%%EXAMPLESDIR%%/mu.lib
 -%%EXAMPLESDIR%%/n2_fs.lib
 -%%EXAMPLESDIR%%/n_fs.lib
 -%%EXAMPLESDIR%%/prot_test.lib
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bovgh.seq
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bovprl.seq
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dyr_human.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/egmsmg.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/gst.seq
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/gstt1_drome.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/gtm1_human.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/gtt1_drome.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/h10_human.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hahu.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hsgstm1b.seq
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/humgstd.seq
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lcbo.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/m1r.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/m2.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mchu.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgstm1.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgstm1.lc
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgstm1.seq
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgstm1_genclone.seq
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgtt2_x.seq
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ms1.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mu.lib
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/musplfm.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mwkw.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mwrtc1.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/myosin_bp.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n0.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n1.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n2.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n2_fs.lib
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n2s.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n2t.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/n_fs.lib
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ngt.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ngts.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/oohu.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prio_atepa.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prot_test.lib
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/qrhuld.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/titin_hum.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/titin_hum.seq
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/xurt8c.aa
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/xurt8c.lc
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/xurtg.aa
  %%DATADIR%%/blosum45.mat
  %%DATADIR%%/blosum50.mat
  %%DATADIR%%/blosum62.mat
 @@ -97,6 +118,6 @@ etc/fastlibs.sample
  %%DATADIR%%/pam250.mat
  %%DATADIR%%/rna.mat
  %%DATADIR%%/vtml160.mat
 -%%PORTDOCS%%@dirrm %%DOCSDIR%%
 -@dirrm %%EXAMPLESDIR%%
  @dirrm %%DATADIR%%
 +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%
 +%%PORTDOCS%%@dirrm %%DOCSDIR%%
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>Unformatted:
