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Message-Id: <20121009025549.29ff8f044ce7b1a0f6910dd6@yahoo.com>
Date: Tue, 9 Oct 2012 02:55:49 +0900
From: KATO Tsuguru <tkato432@yahoo.com>
To: FreeBSD-gnats-submit@FreeBSD.org
Subject: biology/blat: Update to version 35

>Number:         172496
>Category:       ports
>Synopsis:       biology/blat: Update to version 35
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          closed
>Quarter:        
>Keywords:       
>Date-Required:  
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Mon Oct 08 18:00:27 UTC 2012
>Closed-Date:    Wed Nov 20 15:34:14 UTC 2013
>Last-Modified:  Wed Nov 20 15:34:14 UTC 2013
>Originator:     KATO Tsuguru
>Release:        FreeBSD 7.4-RELEASE-p10 i386
>Organization:
>Environment:
>Description:
- Update to version 35

New file:
files/patch-makefile

Remove file:
pkg-plist

>How-To-Repeat:
>Fix:

diff -urN /usr/ports/biology/blat/Makefile biology/blat/Makefile
--- /usr/ports/biology/blat/Makefile	2012-10-01 23:45:16.000000000 +0900
+++ biology/blat/Makefile	2012-10-03 06:08:01.000000000 +0900
@@ -2,44 +2,65 @@
 # $FreeBSD: ports/biology/blat/Makefile,v 1.8 2012/10/01 14:45:16 tabthorpe Exp $
 
 PORTNAME=	blat
-PORTVERSION=	34
+PORTVERSION=	35
 CATEGORIES=	biology
-MASTER_SITES=	http://www.soe.ucsc.edu/~kent/src/
+MASTER_SITES=	http://hgwdev.cse.ucsc.edu/~kent/src/
 DISTNAME=	${PORTNAME}Src${PORTVERSION}
 
 MAINTAINER=	ports@FreeBSD.org
 COMMENT=	A fast tool for local sequence similarity searches
 
+LIB_DEPENDS=	png15:${PORTSDIR}/graphics/png
+
+OPTIONS_DEFINE=	DOCS
+
+WRKSRC=		${WRKDIR}/${PORTNAME}Src
+
 USE_ZIP=	yes
+USE_OPENSSL=	yes
 USE_GMAKE=	yes
 MAKEFILE=	makefile
-WRKSRC=		${WRKDIR}/${PORTNAME}Src
-MAKE_ENV+=	HOME="${WRKSRC}/${BINDIR}" MACHTYPE="${ARCH}"
+MAKE_ENV=	MACHTYPE="${ARCH}" SSLDIR="${OPENSSLBASE}/include/openssl" \
+		PNGLIB="${LDFLAGS}" PNGINCL="${CPPFLAGS}" \
+		HOME="${WRKSRC}/${BINDIR}" STRIP="${TRUE}"
+MAKE_JOBS_SAFE=yes
+
+CPPFLAGS+=	$$(libpng-config --I_opts)
+LDFLAGS+=	$$(libpng-config --ldflags)
 
 SUB_FILES=	pkg-message
 
+PORTDOCS=	README
+PLIST_FILES=	${EXECUTABLES:S,^,bin/,} \
+		lib/blat/webBlat/webBlat \
+		lib/blat/webBlat/install.txt
+PLIST_DIRS=	lib/blat/webBlat \
+		lib/blat
+
 EXECUTABLES=	blat faToNib faToTwoBit gfClient gfServer nibFrag \
 		pslPretty pslReps pslSort twoBitInfo twoBitToFa
 
+.include <bsd.port.options.mk>
+
 post-patch:
 	@${MKDIR} ${WRKSRC}/bin/${ARCH}
 	@${MKDIR} ${WRKSRC}/lib/${ARCH}
-	@${REINPLACE_CMD} -E 's,^(CC|CFLAGS)=,\1 ?=,g;s,-Werror,,g' \
-		${WRKSRC}/inc/common.mk
+	@${REINPLACE_CMD} -e \
+		's|^CC=|CC?=| ; \
+		 s|COPT=.*|COPT=|' ${WRKSRC}/inc/common.mk
 
 do-install:
 .for exe in ${EXECUTABLES}
-	${INSTALL_PROGRAM} ${WRKSRC}/bin/${ARCH}/${exe} ${PREFIX}/bin
+	(cd ${WRKSRC}/bin/${ARCH} && ${INSTALL_PROGRAM} ${exe} ${PREFIX}/bin)
 .endfor
-	${MKDIR} ${DATADIR}/webBlat
-	${INSTALL_PROGRAM} ${WRKSRC}/webBlat/webBlat ${DATADIR}/webBlat
-	${INSTALL_DATA} ${WRKSRC}/webBlat/install.txt ${DATADIR}/webBlat
-.if !defined(NOPORTDOCS)
-	${MKDIR} ${DOCSDIR}
-	${INSTALL_DATA} ${WRKSRC}/README ${DOCSDIR}
+	@${MKDIR} ${PREFIX}/lib/blat/webBlat
+	(cd ${WRKSRC}/webBlat \
+		&& ${INSTALL_PROGRAM} webBlat ${PREFIX}/lib/blat/webBlat \
+		&& ${INSTALL_DATA} install.txt ${PREFIX}/lib/blat/webBlat)
+.if ${PORT_OPTIONS:MDOCS}
+	@${MKDIR} ${DOCSDIR}
+	(cd ${WRKSRC} && ${INSTALL_DATA} README ${DOCSDIR})
 .endif
-
-post-install:
 	@${CAT} ${PKGMESSAGE}
 
 .include <bsd.port.mk>
diff -urN /usr/ports/biology/blat/distinfo biology/blat/distinfo
--- /usr/ports/biology/blat/distinfo	2011-03-19 21:29:29.000000000 +0900
+++ biology/blat/distinfo	2012-10-03 04:51:43.000000000 +0900
@@ -1,2 +1,2 @@
-SHA256 (blatSrc34.zip) = b764828fdf8ef4c9994ae4b6148340a776493475edb573b6adf63ae7ca9b2629
-SIZE (blatSrc34.zip) = 2142975
+SHA256 (blatSrc35.zip) = 2fb53c9489f9bd95f4119a526e6911f107a759eeb228ccc53b3bebb3aa6e50ab
+SIZE (blatSrc35.zip) = 1887567
diff -urN /usr/ports/biology/blat/files/patch-makefile biology/blat/files/patch-makefile
--- /usr/ports/biology/blat/files/patch-makefile	1970-01-01 09:00:00.000000000 +0900
+++ biology/blat/files/patch-makefile	2012-10-03 05:45:18.000000000 +0900
@@ -0,0 +1,36 @@
+--- makefile.orig	2012-08-14 09:15:05.000000000 +0900
++++ makefile	2012-10-03 05:40:34.000000000 +0900
+@@ -1,18 +1,19 @@
+ all:
+-	cd lib && ${MAKE}
+-	cd jkOwnLib && ${MAKE}
+-	cd blat && $(MAKE)
+-	cd gfClient && $(MAKE)
+-	cd gfServer && $(MAKE)
+-	cd hg/pslPretty && $(MAKE)
+-	cd hg/pslReps && $(MAKE)
+-	cd hg/pslSort && $(MAKE)
+-	cd utils/nibFrag && $(MAKE)
+-	cd utils/faToNib && $(MAKE)
+-	cd utils/faToTwoBit && $(MAKE)
+-	cd utils/twoBitToFa && $(MAKE)
+-	cd utils/twoBitInfo && $(MAKE)
+-	cd webBlat && $(MAKE)
++		
++	$(MAKE) -C lib
++	$(MAKE) -C jkOwnLib
++	$(MAKE) -C blat
++	$(MAKE) -C gfClient
++	$(MAKE) -C gfServer
++	$(MAKE) -C hg/pslPretty
++	$(MAKE) -C hg/pslReps
++	$(MAKE) -C hg/pslSort
++	$(MAKE) -C utils/nibFrag
++	$(MAKE) -C utils/faToNib
++	$(MAKE) -C utils/faToTwoBit
++	$(MAKE) -C utils/twoBitToFa
++	$(MAKE) -C utils/twoBitInfo
++	$(MAKE) -C webBlat
+ 
+ clean:
+ 	rm -f */*.o */*/*.o lib/*/*.a
diff -urN /usr/ports/biology/blat/files/pkg-message.in biology/blat/files/pkg-message.in
--- /usr/ports/biology/blat/files/pkg-message.in	2006-03-15 19:26:12.000000000 +0900
+++ biology/blat/files/pkg-message.in	2012-10-03 04:55:04.000000000 +0900
@@ -3,6 +3,6 @@
  A CGI script (webBlat) and instructions on how to set up a BLAT web server
  have been installed in 
  
- %%DATADIR%%
+ %%PREFIX%%/lib/blat
 
 ===============================================================================
diff -urN /usr/ports/biology/blat/pkg-descr biology/blat/pkg-descr
--- /usr/ports/biology/blat/pkg-descr	2006-03-15 19:26:11.000000000 +0900
+++ biology/blat/pkg-descr	2012-10-03 06:06:19.000000000 +0900
@@ -1,9 +1,9 @@
-BLAT is a bioinformatics software tool which performs rapid mRNA/DNA
-and cross-species protein alignments. BLAT is more accurate and 500
-times faster than popular existing tools for mRNA/DNA alignments and 50
-times faster for protein alignments at sensitivity settings typically
-used when comparing vertebrate sequences. (Source: Kent, W.J. 2002. BLAT
--- The BLAST-Like Alignment Tool. Genome Research 4: 656-664.
+BLAT is a bioinformatics software tool which performs rapid mRNA/DNA and
+cross-species protein alignments. BLAT is more accurate and 500 times
+faster than popular existing tools for mRNA/DNA alignments and 50 times
+faster for protein alignments at sensitivity settings typically used
+when comparing vertebrate sequences. (Source: Kent, W.J. 2002. BLAT --
+The BLAST-Like Alignment Tool. Genome Research 4: 656-664.
 http://dx.doi.org/10.1101/gr.229202)
 
 BLAT is not BLAST. DNA BLAT works by keeping an index of the entire
@@ -11,4 +11,4 @@
 bit less than a gigabyte of RAM, BLAT can deliver high performance on a
 reasonably priced Linux box.
 
-WWW: http://www.genomeblat.com
+WWW: http://users.soe.ucsc.edu/~kent/
diff -urN /usr/ports/biology/blat/pkg-plist biology/blat/pkg-plist
--- /usr/ports/biology/blat/pkg-plist	2006-03-15 19:26:11.000000000 +0900
+++ biology/blat/pkg-plist	1970-01-01 09:00:00.000000000 +0900
@@ -1,17 +0,0 @@
-bin/blat
-bin/faToNib
-bin/faToTwoBit
-bin/gfClient
-bin/gfServer
-bin/nibFrag
-bin/pslPretty
-bin/pslReps
-bin/pslSort
-bin/twoBitInfo
-bin/twoBitToFa
-%%PORTDOCS%%%%DOCSDIR%%/README
-%%DATADIR%%/webBlat/webBlat
-%%DATADIR%%/webBlat/install.txt
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
-@dirrm %%DATADIR%%/webBlat
-@dirrm %%DATADIR%%
>Release-Note:
>Audit-Trail:
Responsible-Changed-From-To: freebsd-ports-bugs->miwi 
Responsible-Changed-By: edwin 
Responsible-Changed-When: Mon Oct 8 18:00:48 UTC 2012 
Responsible-Changed-Why:  
miwi@ wants his PRs (via the GNATS Auto Assign Tool) 

http://www.freebsd.org/cgi/query-pr.cgi?pr=172496 
Responsible-Changed-From-To: miwi->freebsd-ports-bugs 
Responsible-Changed-By: bapt 
Responsible-Changed-When: Mon Oct 29 09:40:37 UTC 2012 
Responsible-Changed-Why:  
Reassign to the heap miwi being overloaded for now 

http://www.freebsd.org/cgi/query-pr.cgi?pr=172496 
Responsible-Changed-From-To: freebsd-ports-bugs->araujo 
Responsible-Changed-By: araujo 
Responsible-Changed-When: Tue Dec 11 13:02:13 UTC 2012 
Responsible-Changed-Why:  
I'll take it. 

http://www.freebsd.org/cgi/query-pr.cgi?pr=172496 
State-Changed-From-To: open->feedback 
State-Changed-By: araujo 
State-Changed-When: Fri Jan 18 06:30:07 UTC 2013 
State-Changed-Why:  
Does not build. Check at: 
http://people.freebsd.org/~araujo/port/blat-35.log 

http://www.freebsd.org/cgi/query-pr.cgi?pr=172496 

From: KATO Tsuguru <tkato432@yahoo.com>
To: bug-followup@FreeBSD.org
Cc:  
Subject: Re: ports/172496: biology/blat: Update to version 35
Date: Sat, 19 Jan 2013 02:55:44 +0900

 This is a multi-part message in MIME format.
 
 --Multipart=_Sat__19_Jan_2013_02_55_44_+0900_YH50h7eZEl7eiFYn
 Content-Type: text/plain; charset=US-ASCII
 Content-Transfer-Encoding: 7bit
 
 Here is the corrected patch.
 
 --Multipart=_Sat__19_Jan_2013_02_55_44_+0900_YH50h7eZEl7eiFYn
 Content-Type: text/x-diff;
  name="biology_blat.diff"
 Content-Disposition: attachment;
  filename="biology_blat.diff"
 Content-Transfer-Encoding: 7bit
 
 diff -urN /usr/ports/biology/blat/Makefile biology/blat/Makefile
 --- /usr/ports/biology/blat/Makefile	2012-11-08 06:54:28.000000000 +0900
 +++ biology/blat/Makefile	2013-01-18 21:10:13.000000000 +0900
 @@ -2,44 +2,69 @@
  # $FreeBSD: head/biology/blat/Makefile 305130 2012-10-01 14:45:16Z tabthorpe $
  
  PORTNAME=	blat
 -PORTVERSION=	34
 +PORTVERSION=	35
  CATEGORIES=	biology
 -MASTER_SITES=	http://www.soe.ucsc.edu/~kent/src/
 +MASTER_SITES=	http://hgwdev.cse.ucsc.edu/~kent/src/
  DISTNAME=	${PORTNAME}Src${PORTVERSION}
  
  MAINTAINER=	ports@FreeBSD.org
 -COMMENT=	A fast tool for local sequence similarity searches
 +COMMENT=	Fast tool for local sequence similarity searches
 +
 +LIB_DEPENDS=	png15:${PORTSDIR}/graphics/png
 +
 +OPTIONS_DEFINE=	DOCS
 +
 +WRKSRC=		${WRKDIR}/${PORTNAME}Src
  
  USE_ZIP=	yes
 +USE_OPENSSL=	yes
  USE_GMAKE=	yes
  MAKEFILE=	makefile
 -WRKSRC=		${WRKDIR}/${PORTNAME}Src
 -MAKE_ENV+=	HOME="${WRKSRC}/${BINDIR}" MACHTYPE="${ARCH}"
 +MAKE_ENV=	MACHTYPE="${ARCH}" SSLDIR="${OPENSSLBASE}/include/openssl" \
 +		PNGLIB="${LDFLAGS}" PNGINCL="${CPPFLAGS}" \
 +		HOME="${WRKSRC}/${BINDIR}" STRIP="${TRUE}"
 +MAKE_JOBS_SAFE=yes
 +
 +CPPFLAGS+=	$$(libpng-config --I_opts)
 +LDFLAGS+=	$$(libpng-config --ldflags)
  
  SUB_FILES=	pkg-message
  
 +PORTDOCS=	README
 +PLIST_FILES=	${EXECUTABLES:S,^,bin/,} \
 +		lib/blat/webBlat/webBlat \
 +		lib/blat/webBlat/install.txt
 +PLIST_DIRS=	lib/blat/webBlat \
 +		lib/blat
 +
  EXECUTABLES=	blat faToNib faToTwoBit gfClient gfServer nibFrag \
  		pslPretty pslReps pslSort twoBitInfo twoBitToFa
  
 +.include <bsd.port.options.mk>
 +
  post-patch:
  	@${MKDIR} ${WRKSRC}/bin/${ARCH}
  	@${MKDIR} ${WRKSRC}/lib/${ARCH}
 -	@${REINPLACE_CMD} -E 's,^(CC|CFLAGS)=,\1 ?=,g;s,-Werror,,g' \
 -		${WRKSRC}/inc/common.mk
 +	@${REINPLACE_CMD} -e \
 +		's|cd |$$(MAKE) -C | ; \
 +		 s| &&.*||' ${WRKSRC}/makefile
 +	@${REINPLACE_CMD} -e \
 +		's|^CC=|CC?=| ; \
 +		 s|COPT=.*|COPT=|' ${WRKSRC}/inc/common.mk
  
  do-install:
  .for exe in ${EXECUTABLES}
 -	${INSTALL_PROGRAM} ${WRKSRC}/bin/${ARCH}/${exe} ${PREFIX}/bin
 +	(cd ${WRKSRC}/bin/${ARCH} && ${INSTALL_PROGRAM} ${exe} ${PREFIX}/bin)
  .endfor
 -	${MKDIR} ${DATADIR}/webBlat
 -	${INSTALL_PROGRAM} ${WRKSRC}/webBlat/webBlat ${DATADIR}/webBlat
 -	${INSTALL_DATA} ${WRKSRC}/webBlat/install.txt ${DATADIR}/webBlat
 -.if !defined(NOPORTDOCS)
 -	${MKDIR} ${DOCSDIR}
 -	${INSTALL_DATA} ${WRKSRC}/README ${DOCSDIR}
 +	@${MKDIR} ${PREFIX}/lib/blat/webBlat
 +	(cd ${WRKSRC}/webBlat \
 +		&& ${INSTALL_PROGRAM} webBlat ${PREFIX}/lib/blat/webBlat)
 +	(cd ${WRKSRC}/webBlat \
 +		&& ${INSTALL_DATA} install.txt ${PREFIX}/lib/blat/webBlat)
 +.if ${PORT_OPTIONS:MDOCS}
 +	@${MKDIR} ${DOCSDIR}
 +	(cd ${WRKSRC} && ${INSTALL_DATA} README ${DOCSDIR})
  .endif
 -
 -post-install:
  	@${CAT} ${PKGMESSAGE}
  
  .include <bsd.port.mk>
 diff -urN /usr/ports/biology/blat/distinfo biology/blat/distinfo
 --- /usr/ports/biology/blat/distinfo	2012-11-08 06:54:28.000000000 +0900
 +++ biology/blat/distinfo	2012-10-03 04:51:43.000000000 +0900
 @@ -1,2 +1,2 @@
 -SHA256 (blatSrc34.zip) = b764828fdf8ef4c9994ae4b6148340a776493475edb573b6adf63ae7ca9b2629
 -SIZE (blatSrc34.zip) = 2142975
 +SHA256 (blatSrc35.zip) = 2fb53c9489f9bd95f4119a526e6911f107a759eeb228ccc53b3bebb3aa6e50ab
 +SIZE (blatSrc35.zip) = 1887567
 diff -urN /usr/ports/biology/blat/files/pkg-message.in biology/blat/files/pkg-message.in
 --- /usr/ports/biology/blat/files/pkg-message.in	2012-11-08 06:54:28.000000000 +0900
 +++ biology/blat/files/pkg-message.in	2012-10-03 04:55:04.000000000 +0900
 @@ -3,6 +3,6 @@
   A CGI script (webBlat) and instructions on how to set up a BLAT web server
   have been installed in 
   
 - %%DATADIR%%
 + %%PREFIX%%/lib/blat
  
  ===============================================================================
 diff -urN /usr/ports/biology/blat/pkg-descr biology/blat/pkg-descr
 --- /usr/ports/biology/blat/pkg-descr	2012-11-08 06:54:28.000000000 +0900
 +++ biology/blat/pkg-descr	2012-10-03 06:06:19.000000000 +0900
 @@ -1,9 +1,9 @@
 -BLAT is a bioinformatics software tool which performs rapid mRNA/DNA
 -and cross-species protein alignments. BLAT is more accurate and 500
 -times faster than popular existing tools for mRNA/DNA alignments and 50
 -times faster for protein alignments at sensitivity settings typically
 -used when comparing vertebrate sequences. (Source: Kent, W.J. 2002. BLAT
 --- The BLAST-Like Alignment Tool. Genome Research 4: 656-664.
 +BLAT is a bioinformatics software tool which performs rapid mRNA/DNA and
 +cross-species protein alignments. BLAT is more accurate and 500 times
 +faster than popular existing tools for mRNA/DNA alignments and 50 times
 +faster for protein alignments at sensitivity settings typically used
 +when comparing vertebrate sequences. (Source: Kent, W.J. 2002. BLAT --
 +The BLAST-Like Alignment Tool. Genome Research 4: 656-664.
  http://dx.doi.org/10.1101/gr.229202)
  
  BLAT is not BLAST. DNA BLAT works by keeping an index of the entire
 @@ -11,4 +11,4 @@
  bit less than a gigabyte of RAM, BLAT can deliver high performance on a
  reasonably priced Linux box.
  
 -WWW: http://www.genomeblat.com
 +WWW: http://users.soe.ucsc.edu/~kent/
 diff -urN /usr/ports/biology/blat/pkg-plist biology/blat/pkg-plist
 --- /usr/ports/biology/blat/pkg-plist	2012-11-08 06:54:28.000000000 +0900
 +++ biology/blat/pkg-plist	1970-01-01 09:00:00.000000000 +0900
 @@ -1,17 +0,0 @@
 -bin/blat
 -bin/faToNib
 -bin/faToTwoBit
 -bin/gfClient
 -bin/gfServer
 -bin/nibFrag
 -bin/pslPretty
 -bin/pslReps
 -bin/pslSort
 -bin/twoBitInfo
 -bin/twoBitToFa
 -%%PORTDOCS%%%%DOCSDIR%%/README
 -%%DATADIR%%/webBlat/webBlat
 -%%DATADIR%%/webBlat/install.txt
 -%%PORTDOCS%%@dirrm %%DOCSDIR%%
 -@dirrm %%DATADIR%%/webBlat
 -@dirrm %%DATADIR%%
 
 --Multipart=_Sat__19_Jan_2013_02_55_44_+0900_YH50h7eZEl7eiFYn--
State-Changed-From-To: feedback->open 
State-Changed-By: araujo 
State-Changed-When: Wed Feb 27 07:21:57 UTC 2013 
State-Changed-Why:  
Feedback received. 

http://www.freebsd.org/cgi/query-pr.cgi?pr=172496 
State-Changed-From-To: open->feedback 
State-Changed-By: araujo 
State-Changed-When: Fri May 24 09:12:22 UTC 2013 
State-Changed-Why:  
It does not build properly: 
https://redports.org/~araujo/20130524085341-38121-122263/blat-35.log 

http://www.freebsd.org/cgi/query-pr.cgi?pr=172496 

From: KATO Tsuguru <tkato432@yahoo.com>
To: bug-followup@FreeBSD.org
Cc:  
Subject: Re: ports/172496: biology/blat: Update to version 35
Date: Sat, 25 May 2013 03:30:01 +0900

 I've never seen such result on locally installed tinderbox-4.0.0.
 Parhups it would be caused by some specific problem with Redports.

From: KATO Tsuguru <tkato432@yahoo.com>
To: bug-followup@FreeBSD.org
Cc:  
Subject: Re: ports/172496: biology/blat: Update to version 35
Date: Fri, 21 Jun 2013 03:00:01 +0900

 This is a multi-part message in MIME format.
 
 --Multipart=_Fri__21_Jun_2013_03_00_01_+0900_eX6VNSh1+aUo=Z5P
 Content-Type: text/plain; charset=US-ASCII
 Content-Transfer-Encoding: 7bit
 
 Remake of the patch against current tree.
 
 --Multipart=_Fri__21_Jun_2013_03_00_01_+0900_eX6VNSh1+aUo=Z5P
 Content-Type: text/x-diff;
  name="biology_blat.diff"
 Content-Disposition: attachment;
  filename="biology_blat.diff"
 Content-Transfer-Encoding: 7bit
 
 diff -urN /usr/ports/biology/blat/Makefile biology/blat/Makefile
 --- /usr/ports/biology/blat/Makefile	2013-06-20 05:53:08.000000000 +0900
 +++ biology/blat/Makefile	2013-06-21 00:00:00.000000000 +0900
 @@ -2,54 +2,69 @@
  # $FreeBSD: head/biology/blat/Makefile 321304 2013-06-19 18:43:13Z bsam $
  
  PORTNAME=	blat
 -PORTVERSION=	34
 +PORTVERSION=	35
  CATEGORIES=	biology
 -MASTER_SITES=	http://www.soe.ucsc.edu/~kent/src/
 +MASTER_SITES=	http://hgwdev.cse.ucsc.edu/~kent/src/
  DISTNAME=	${PORTNAME}Src${PORTVERSION}
  
  MAINTAINER=	ports@FreeBSD.org
  COMMENT=	Fast tool for local sequence similarity searches
  
 +LIB_DEPENDS=	png15:${PORTSDIR}/graphics/png
 +
 +OPTIONS_DEFINE=	DOCS
 +
 +WRKSRC=		${WRKDIR}/${PORTNAME}Src
 +
  USE_ZIP=	yes
 +USE_OPENSSL=	yes
  USE_GMAKE=	yes
  MAKEFILE=	makefile
 -WRKSRC=		${WRKDIR}/${PORTNAME}Src
 -MAKE_ENV+=	HOME="${WRKSRC}/${BINDIR}" MACHTYPE="${ARCH}"
 +MAKE_ENV=	MACHTYPE="${ARCH}" SSLDIR="${OPENSSLBASE}/include/openssl" \
 +		PNGLIB="${LDFLAGS}" PNGINCL="${CPPFLAGS}" \
 +		HOME="${WRKSRC}/${BINDIR}" STRIP="${TRUE}"
 +MAKE_JOBS_SAFE=yes
 +
 +CPPFLAGS+=	$$(libpng-config --I_opts)
 +LDFLAGS+=	$$(libpng-config --ldflags)
  
  SUB_FILES=	pkg-message
  
 +PORTDOCS=	README
 +PLIST_FILES=	${EXECUTABLES:S,^,bin/,} \
 +		lib/blat/webBlat/webBlat \
 +		lib/blat/webBlat/install.txt
 +PLIST_DIRS=	lib/blat/webBlat \
 +		lib/blat
 +
  EXECUTABLES=	blat faToNib faToTwoBit gfClient gfServer nibFrag \
  		pslPretty pslReps pslSort twoBitInfo twoBitToFa
  
 -PLIST_FILES+=	${EXECUTABLES:S,^,bin/,}
 -PORTDOCS=	README
 -PORTDATA=	*
 -
 -OPTIONS_DEFINE=	DOCS
 +.include <bsd.port.options.mk>
  
  post-patch:
  	@${MKDIR} ${WRKSRC}/bin/${ARCH}
  	@${MKDIR} ${WRKSRC}/lib/${ARCH}
 -	@${REINPLACE_CMD} -E 's,^(CC|CFLAGS)=,\1 ?=,g;s,-Werror,,g' \
 -		${WRKSRC}/inc/common.mk
 -
 -.include <bsd.port.options.mk>
 +	@${REINPLACE_CMD} -e \
 +		's|cd |$$(MAKE) -C | ; \
 +		 s| &&.*||' ${WRKSRC}/makefile
 +	@${REINPLACE_CMD} -e \
 +		's|^CC=|CC?=| ; \
 +		 s|COPT=.*|COPT=|' ${WRKSRC}/inc/common.mk
  
  do-install:
  .for exe in ${EXECUTABLES}
 -	${INSTALL_PROGRAM} ${WRKSRC}/bin/${ARCH}/${exe} ${PREFIX}/bin
 +	(cd ${WRKSRC}/bin/${ARCH} && ${INSTALL_PROGRAM} ${exe} ${PREFIX}/bin)
  .endfor
 -	@${MKDIR} ${DATADIR}/webBlat
 -	${INSTALL_PROGRAM} ${WRKSRC}/webBlat/webBlat ${DATADIR}/webBlat
 -	${INSTALL_DATA} ${WRKSRC}/webBlat/install.txt ${DATADIR}/webBlat
 +	@${MKDIR} ${PREFIX}/lib/blat/webBlat
 +	(cd ${WRKSRC}/webBlat \
 +		&& ${INSTALL_PROGRAM} webBlat ${PREFIX}/lib/blat/webBlat)
 +	(cd ${WRKSRC}/webBlat \
 +		&& ${INSTALL_DATA} install.txt ${PREFIX}/lib/blat/webBlat)
  .if ${PORT_OPTIONS:MDOCS}
  	@${MKDIR} ${DOCSDIR}
 -	${INSTALL_DATA} ${WRKSRC}/README ${DOCSDIR}
 +	(cd ${WRKSRC} && ${INSTALL_DATA} README ${DOCSDIR})
  .endif
 -
 -post-install:
 -	@${ECHO_MSG}
  	@${CAT} ${PKGMESSAGE}
 -	@${ECHO_MSG}
  
  .include <bsd.port.mk>
 diff -urN /usr/ports/biology/blat/distinfo biology/blat/distinfo
 --- /usr/ports/biology/blat/distinfo	2012-11-08 06:54:28.000000000 +0900
 +++ biology/blat/distinfo	2013-06-21 00:00:00.000000000 +0900
 @@ -1,2 +1,2 @@
 -SHA256 (blatSrc34.zip) = b764828fdf8ef4c9994ae4b6148340a776493475edb573b6adf63ae7ca9b2629
 -SIZE (blatSrc34.zip) = 2142975
 +SHA256 (blatSrc35.zip) = 2fb53c9489f9bd95f4119a526e6911f107a759eeb228ccc53b3bebb3aa6e50ab
 +SIZE (blatSrc35.zip) = 1887567
 diff -urN /usr/ports/biology/blat/files/pkg-message.in biology/blat/files/pkg-message.in
 --- /usr/ports/biology/blat/files/pkg-message.in	2012-11-08 06:54:28.000000000 +0900
 +++ biology/blat/files/pkg-message.in	2013-06-21 00:00:00.000000000 +0900
 @@ -3,6 +3,6 @@
   A CGI script (webBlat) and instructions on how to set up a BLAT web server
   have been installed in 
   
 - %%DATADIR%%
 + %%PREFIX%%/lib/blat
  
  ===============================================================================
 diff -urN /usr/ports/biology/blat/pkg-descr biology/blat/pkg-descr
 --- /usr/ports/biology/blat/pkg-descr	2012-11-08 06:54:28.000000000 +0900
 +++ biology/blat/pkg-descr	2013-06-21 00:00:00.000000000 +0900
 @@ -1,9 +1,9 @@
 -BLAT is a bioinformatics software tool which performs rapid mRNA/DNA
 -and cross-species protein alignments. BLAT is more accurate and 500
 -times faster than popular existing tools for mRNA/DNA alignments and 50
 -times faster for protein alignments at sensitivity settings typically
 -used when comparing vertebrate sequences. (Source: Kent, W.J. 2002. BLAT
 --- The BLAST-Like Alignment Tool. Genome Research 4: 656-664.
 +BLAT is a bioinformatics software tool which performs rapid mRNA/DNA and
 +cross-species protein alignments. BLAT is more accurate and 500 times
 +faster than popular existing tools for mRNA/DNA alignments and 50 times
 +faster for protein alignments at sensitivity settings typically used
 +when comparing vertebrate sequences. (Source: Kent, W.J. 2002. BLAT --
 +The BLAST-Like Alignment Tool. Genome Research 4: 656-664.
  http://dx.doi.org/10.1101/gr.229202)
  
  BLAT is not BLAST. DNA BLAT works by keeping an index of the entire
 @@ -11,4 +11,4 @@
  bit less than a gigabyte of RAM, BLAT can deliver high performance on a
  reasonably priced Linux box.
  
 -WWW: http://www.genomeblat.com
 +WWW: http://users.soe.ucsc.edu/~kent/
 
 --Multipart=_Fri__21_Jun_2013_03_00_01_+0900_eX6VNSh1+aUo=Z5P--
State-Changed-From-To: feedback->open 
State-Changed-By: araujo 
State-Changed-When: Tue Jun 25 03:06:53 UTC 2013 
State-Changed-Why:  
- Still have the same issue to build.  - I have not time enought to take 
care of it anymore. 


Responsible-Changed-From-To: araujo->freebsd-ports-bugs 
Responsible-Changed-By: araujo 
Responsible-Changed-When: Tue Jun 25 03:06:53 UTC 2013 
Responsible-Changed-Why:  
- Still have the same issue to build. I have not time enought to take 
care of it anymore. 

http://www.freebsd.org/cgi/query-pr.cgi?pr=172496 

From: KATO Tsuguru <tkato432@yahoo.com>
To: bug-followup@FreeBSD.org
Cc:  
Subject: Re: ports/172496: biology/blat: Update to version 35
Date: Fri, 1 Nov 2013 04:25:33 +0900

 This is a multi-part message in MIME format.
 
 --Multipart=_Fri__1_Nov_2013_04_25_33_+0900_fsq_ImQqfDQNdKuY
 Content-Type: text/plain; charset=US-ASCII
 Content-Transfer-Encoding: 7bit
 
 Remake of the patch against current tree.
 
 --Multipart=_Fri__1_Nov_2013_04_25_33_+0900_fsq_ImQqfDQNdKuY
 Content-Type: text/x-diff;
  name="biology_blat.diff"
 Content-Disposition: attachment;
  filename="biology_blat.diff"
 Content-Transfer-Encoding: 7bit
 
 diff -urN /usr/ports/biology/blat/Makefile biology/blat/Makefile
 --- /usr/ports/biology/blat/Makefile	2013-09-22 01:13:54.000000000 +0900
 +++ biology/blat/Makefile	2013-11-01 00:00:00.000000000 +0900
 @@ -2,55 +2,68 @@
  # $FreeBSD: head/biology/blat/Makefile 327709 2013-09-20 15:55:44Z bapt $
  
  PORTNAME=	blat
 -PORTVERSION=	34
 +PORTVERSION=	35
  CATEGORIES=	biology
 -MASTER_SITES=	http://www.soe.ucsc.edu/~kent/src/
 +MASTER_SITES=	http://hgwdev.cse.ucsc.edu/~kent/src/
  DISTNAME=	${PORTNAME}Src${PORTVERSION}
  
  MAINTAINER=	ports@FreeBSD.org
  COMMENT=	Fast tool for local sequence similarity searches
  
 +LIB_DEPENDS=	libpng15.so:${PORTSDIR}/graphics/png
 +
 +OPTIONS_DEFINE=	DOCS
 +
 +WRKSRC=		${WRKDIR}/${PORTNAME}Src
 +
  USE_ZIP=	yes
 +USE_OPENSSL=	yes
  USE_GMAKE=	yes
  MAKEFILE=	makefile
 -WRKSRC=		${WRKDIR}/${PORTNAME}Src
 -MAKE_ENV+=	HOME="${WRKSRC}/${BINDIR}" MACHTYPE="${ARCH}"
 +MAKE_ENV=	MACHTYPE="${ARCH}" SSLDIR="${OPENSSLBASE}/include/openssl" \
 +		PNGLIB="${LDFLAGS}" PNGINCL="${CPPFLAGS}" \
 +		HOME="${WRKSRC}/${BINDIR}" STRIP="${TRUE}"
 +
 +CPPFLAGS+=	$$(libpng-config --I_opts)
 +LDFLAGS+=	$$(libpng-config --ldflags)
  
  SUB_FILES=	pkg-message
  
 +PORTDOCS=	README
 +PLIST_FILES=	${EXECUTABLES:S,^,bin/,} \
 +		lib/blat/webBlat/webBlat \
 +		lib/blat/webBlat/install.txt
 +PLIST_DIRS=	lib/blat/webBlat \
 +		lib/blat
 +
  EXECUTABLES=	blat faToNib faToTwoBit gfClient gfServer nibFrag \
  		pslPretty pslReps pslSort twoBitInfo twoBitToFa
  
 -PLIST_FILES+=	${EXECUTABLES:S,^,bin/,}
 -PORTDOCS=	README
 -PORTDATA=	*
 -
 -OPTIONS_DEFINE=	DOCS
 +.include <bsd.port.options.mk>
  
 -NO_STAGE=	yes
  post-patch:
  	@${MKDIR} ${WRKSRC}/bin/${ARCH}
  	@${MKDIR} ${WRKSRC}/lib/${ARCH}
 -	@${REINPLACE_CMD} -E 's,^(CC|CFLAGS)=,\1 ?=,g;s,-Werror,,g' \
 -		${WRKSRC}/inc/common.mk
 -
 -.include <bsd.port.options.mk>
 +	@${FIND} ${WRKSRC} -name "makefile" | ${XARGS} ${REINPLACE_CMD} -e \
 +		's|$${DESTDIR}||g'
 +	@${REINPLACE_CMD} -e \
 +		's|cd |$$(MAKE) -C | ; \
 +		 s| &&.*||' ${WRKSRC}/makefile
 +	@${REINPLACE_CMD} -e \
 +		's|^CC=|CC?=| ; \
 +		 s|COPT=.*|COPT=|' ${WRKSRC}/inc/common.mk
  
  do-install:
  .for exe in ${EXECUTABLES}
 -	${INSTALL_PROGRAM} ${WRKSRC}/bin/${ARCH}/${exe} ${PREFIX}/bin
 +	(cd ${WRKSRC}/bin/${ARCH} && ${INSTALL_PROGRAM} ${exe} \
 +		${STAGEDIR}${PREFIX}/bin)
  .endfor
 -	@${MKDIR} ${DATADIR}/webBlat
 -	${INSTALL_PROGRAM} ${WRKSRC}/webBlat/webBlat ${DATADIR}/webBlat
 -	${INSTALL_DATA} ${WRKSRC}/webBlat/install.txt ${DATADIR}/webBlat
 -.if ${PORT_OPTIONS:MDOCS}
 -	@${MKDIR} ${DOCSDIR}
 -	${INSTALL_DATA} ${WRKSRC}/README ${DOCSDIR}
 -.endif
 -
 -post-install:
 -	@${ECHO_MSG}
 -	@${CAT} ${PKGMESSAGE}
 -	@${ECHO_MSG}
 +	@${MKDIR} ${STAGEDIR}${PREFIX}/lib/blat/webBlat
 +	(cd ${WRKSRC}/webBlat && ${INSTALL_PROGRAM} webBlat \
 +		${STAGEDIR}${PREFIX}/lib/blat/webBlat)
 +	(cd ${WRKSRC}/webBlat && ${INSTALL_DATA} install.txt \
 +		${STAGEDIR}${PREFIX}/lib/blat/webBlat)
 +	@${MKDIR} ${STAGEDIR}${DOCSDIR}
 +	(cd ${WRKSRC} && ${INSTALL_DATA} README ${STAGEDIR}${DOCSDIR})
  
  .include <bsd.port.mk>
 diff -urN /usr/ports/biology/blat/distinfo biology/blat/distinfo
 --- /usr/ports/biology/blat/distinfo	2013-06-21 03:53:41.000000000 +0900
 +++ biology/blat/distinfo	2013-11-01 00:00:00.000000000 +0900
 @@ -1,2 +1,2 @@
 -SHA256 (blatSrc34.zip) = b764828fdf8ef4c9994ae4b6148340a776493475edb573b6adf63ae7ca9b2629
 -SIZE (blatSrc34.zip) = 2142975
 +SHA256 (blatSrc35.zip) = 2fb53c9489f9bd95f4119a526e6911f107a759eeb228ccc53b3bebb3aa6e50ab
 +SIZE (blatSrc35.zip) = 1887567
 diff -urN /usr/ports/biology/blat/files/pkg-message.in biology/blat/files/pkg-message.in
 --- /usr/ports/biology/blat/files/pkg-message.in	2013-06-21 03:53:41.000000000 +0900
 +++ biology/blat/files/pkg-message.in	2013-11-01 00:00:00.000000000 +0900
 @@ -3,6 +3,6 @@
   A CGI script (webBlat) and instructions on how to set up a BLAT web server
   have been installed in 
   
 - %%DATADIR%%
 + %%PREFIX%%/lib/blat
  
  ===============================================================================
 diff -urN /usr/ports/biology/blat/pkg-descr biology/blat/pkg-descr
 --- /usr/ports/biology/blat/pkg-descr	2013-06-21 03:53:41.000000000 +0900
 +++ biology/blat/pkg-descr	2013-11-01 00:00:00.000000000 +0900
 @@ -1,9 +1,9 @@
 -BLAT is a bioinformatics software tool which performs rapid mRNA/DNA
 -and cross-species protein alignments. BLAT is more accurate and 500
 -times faster than popular existing tools for mRNA/DNA alignments and 50
 -times faster for protein alignments at sensitivity settings typically
 -used when comparing vertebrate sequences. (Source: Kent, W.J. 2002. BLAT
 --- The BLAST-Like Alignment Tool. Genome Research 4: 656-664.
 +BLAT is a bioinformatics software tool which performs rapid mRNA/DNA and
 +cross-species protein alignments. BLAT is more accurate and 500 times
 +faster than popular existing tools for mRNA/DNA alignments and 50 times
 +faster for protein alignments at sensitivity settings typically used
 +when comparing vertebrate sequences. (Source: Kent, W.J. 2002. BLAT --
 +The BLAST-Like Alignment Tool. Genome Research 4: 656-664.
  http://dx.doi.org/10.1101/gr.229202)
  
  BLAT is not BLAST. DNA BLAT works by keeping an index of the entire
 @@ -11,4 +11,4 @@
  bit less than a gigabyte of RAM, BLAT can deliver high performance on a
  reasonably priced Linux box.
  
 -WWW: http://www.genomeblat.com
 +WWW: http://users.soe.ucsc.edu/~kent/
 
 --Multipart=_Fri__1_Nov_2013_04_25_33_+0900_fsq_ImQqfDQNdKuY--

From: KATO Tsuguru <tkato432@yahoo.com>
To: bug-followup@FreeBSD.org
Cc:  
Subject: Re: ports/172496: biology/blat: Update to version 35
Date: Thu, 14 Nov 2013 03:00:00 +0900

 This is a multi-part message in MIME format.
 
 --Multipart=_Thu__14_Nov_2013_03_00_00_+0900_dixb.PG4H+LErrY3
 Content-Type: text/plain; charset=US-ASCII
 Content-Transfer-Encoding: 7bit
 
 Remake of the patch against current tree.
 
 --Multipart=_Thu__14_Nov_2013_03_00_00_+0900_dixb.PG4H+LErrY3
 Content-Type: text/x-diff;
  name="biology_blat.diff"
 Content-Disposition: attachment;
  filename="biology_blat.diff"
 Content-Transfer-Encoding: 7bit
 
 diff -urN /usr/ports/biology/blat/Makefile biology/blat/Makefile
 --- /usr/ports/biology/blat/Makefile	2013-11-13 17:50:18.000000000 +0900
 +++ biology/blat/Makefile	2013-11-14 00:00:00.000000000 +0900
 @@ -2,45 +2,68 @@
  # $FreeBSD: head/biology/blat/Makefile 333628 2013-11-12 22:02:02Z bapt $
  
  PORTNAME=	blat
 -PORTVERSION=	34
 +PORTVERSION=	35
  CATEGORIES=	biology
 -MASTER_SITES=	http://www.soe.ucsc.edu/~kent/src/
 +MASTER_SITES=	http://hgwdev.cse.ucsc.edu/~kent/src/
  DISTNAME=	${PORTNAME}Src${PORTVERSION}
 +EXTRACT_SUFX=	.zip
  
  MAINTAINER=	ports@FreeBSD.org
  COMMENT=	Fast tool for local sequence similarity searches
  
 +LIB_DEPENDS=	libpng15.so:${PORTSDIR}/graphics/png
 +
 +OPTIONS_DEFINE=	DOCS
 +
 +WRKSRC=		${WRKDIR}/${PORTNAME}Src
 +
  USES=		gmake
 -EXTRACT_SUFX=	.zip
 +USE_OPENSSL=	yes
  MAKEFILE=	makefile
 -WRKSRC=		${WRKDIR}/${PORTNAME}Src
 -MAKE_ENV+=	HOME="${WRKSRC}/${BINDIR}" MACHTYPE="${ARCH}"
 +MAKE_ENV=	MACHTYPE="${ARCH}" SSLDIR="${OPENSSLBASE}/include/openssl" \
 +		PNGLIB="${LDFLAGS}" PNGINCL="${CPPFLAGS}" \
 +		HOME="${WRKSRC}/${BINDIR}" STRIP="${TRUE}"
 +
 +CPPFLAGS+=	$$(libpng-config --I_opts)
 +LDFLAGS+=	$$(libpng-config --ldflags)
  
  SUB_FILES=	pkg-message
  
 +PORTDOCS=	README
 +PLIST_FILES=	${EXECUTABLES:S,^,bin/,} \
 +		lib/blat/webBlat/webBlat \
 +		lib/blat/webBlat/install.txt
 +PLIST_DIRS=	lib/blat/webBlat \
 +		lib/blat
 +
  EXECUTABLES=	blat faToNib faToTwoBit gfClient gfServer nibFrag \
  		pslPretty pslReps pslSort twoBitInfo twoBitToFa
  
 -PLIST_FILES+=	${EXECUTABLES:S,^,bin/,}
 -PORTDOCS=	README
 -PORTDATA=	*
 -
 -OPTIONS_DEFINE=	DOCS
 +.include <bsd.port.options.mk>
  
  post-patch:
  	@${MKDIR} ${WRKSRC}/bin/${ARCH}
  	@${MKDIR} ${WRKSRC}/lib/${ARCH}
 -	@${REINPLACE_CMD} -E 's,^(CC|CFLAGS)=,\1 ?=,g;s,-Werror,,g' \
 -		${WRKSRC}/inc/common.mk
 +	@${FIND} ${WRKSRC} -name "makefile" | ${XARGS} ${REINPLACE_CMD} -e \
 +		's|$${DESTDIR}||g'
 +	@${REINPLACE_CMD} -e \
 +		's|cd |$$(MAKE) -C | ; \
 +		 s| &&.*||' ${WRKSRC}/makefile
 +	@${REINPLACE_CMD} -e \
 +		's|^CC=|CC?=| ; \
 +		 s|COPT=.*|COPT=|' ${WRKSRC}/inc/common.mk
  
  do-install:
  .for exe in ${EXECUTABLES}
 -	${INSTALL_PROGRAM} ${WRKSRC}/bin/${ARCH}/${exe} ${STAGEDIR}${PREFIX}/bin
 +	(cd ${WRKSRC}/bin/${ARCH} && ${INSTALL_PROGRAM} ${exe} \
 +		${STAGEDIR}${PREFIX}/bin)
  .endfor
 -	@${MKDIR} ${STAGEDIR}${DATADIR}/webBlat
 -	${INSTALL_PROGRAM} ${WRKSRC}/webBlat/webBlat ${STAGEDIR}${DATADIR}/webBlat
 -	${INSTALL_DATA} ${WRKSRC}/webBlat/install.txt ${STAGEDIR}${DATADIR}/webBlat
 +	@${MKDIR} ${STAGEDIR}${PREFIX}/lib/blat/webBlat
 +	(cd ${WRKSRC}/webBlat && ${INSTALL_PROGRAM} webBlat \
 +		${STAGEDIR}${PREFIX}/lib/blat/webBlat)
 +	(cd ${WRKSRC}/webBlat && ${INSTALL_DATA} install.txt \
 +		${STAGEDIR}${PREFIX}/lib/blat/webBlat)
  	@${MKDIR} ${STAGEDIR}${DOCSDIR}
 -	${INSTALL_DATA} ${WRKSRC}/README ${STAGEDIR}${DOCSDIR}
 +	(cd ${WRKSRC} && ${INSTALL_DATA} README ${STAGEDIR}${DOCSDIR})
  
  .include <bsd.port.mk>
 diff -urN /usr/ports/biology/blat/distinfo biology/blat/distinfo
 --- /usr/ports/biology/blat/distinfo	2013-11-06 22:05:44.000000000 +0900
 +++ biology/blat/distinfo	2013-11-14 00:00:00.000000000 +0900
 @@ -1,2 +1,2 @@
 -SHA256 (blatSrc34.zip) = b764828fdf8ef4c9994ae4b6148340a776493475edb573b6adf63ae7ca9b2629
 -SIZE (blatSrc34.zip) = 2142975
 +SHA256 (blatSrc35.zip) = 2fb53c9489f9bd95f4119a526e6911f107a759eeb228ccc53b3bebb3aa6e50ab
 +SIZE (blatSrc35.zip) = 1887567
 diff -urN /usr/ports/biology/blat/files/pkg-message.in biology/blat/files/pkg-message.in
 --- /usr/ports/biology/blat/files/pkg-message.in	2013-11-06 22:05:44.000000000 +0900
 +++ biology/blat/files/pkg-message.in	2013-11-14 00:00:00.000000000 +0900
 @@ -3,6 +3,6 @@
   A CGI script (webBlat) and instructions on how to set up a BLAT web server
   have been installed in 
   
 - %%DATADIR%%
 + %%PREFIX%%/lib/blat
  
  ===============================================================================
 diff -urN /usr/ports/biology/blat/pkg-descr biology/blat/pkg-descr
 --- /usr/ports/biology/blat/pkg-descr	2013-11-06 22:05:44.000000000 +0900
 +++ biology/blat/pkg-descr	2013-11-14 00:00:00.000000000 +0900
 @@ -1,9 +1,9 @@
 -BLAT is a bioinformatics software tool which performs rapid mRNA/DNA
 -and cross-species protein alignments. BLAT is more accurate and 500
 -times faster than popular existing tools for mRNA/DNA alignments and 50
 -times faster for protein alignments at sensitivity settings typically
 -used when comparing vertebrate sequences. (Source: Kent, W.J. 2002. BLAT
 --- The BLAST-Like Alignment Tool. Genome Research 4: 656-664.
 +BLAT is a bioinformatics software tool which performs rapid mRNA/DNA and
 +cross-species protein alignments. BLAT is more accurate and 500 times
 +faster than popular existing tools for mRNA/DNA alignments and 50 times
 +faster for protein alignments at sensitivity settings typically used
 +when comparing vertebrate sequences. (Source: Kent, W.J. 2002. BLAT --
 +The BLAST-Like Alignment Tool. Genome Research 4: 656-664.
  http://dx.doi.org/10.1101/gr.229202)
  
  BLAT is not BLAST. DNA BLAT works by keeping an index of the entire
 @@ -11,4 +11,4 @@
  bit less than a gigabyte of RAM, BLAT can deliver high performance on a
  reasonably priced Linux box.
  
 -WWW: http://www.genomeblat.com
 +WWW: http://users.soe.ucsc.edu/~kent/
 
 --Multipart=_Thu__14_Nov_2013_03_00_00_+0900_dixb.PG4H+LErrY3--
State-Changed-From-To: open->closed 
State-Changed-By: jadawin 
State-Changed-When: Wed Nov 20 15:34:13 UTC 2013 
State-Changed-Why:  
fetch: http://hgwdev.cse.ucsc.edu/~kent/src/blatSrc35.zip: size 
mismatch: expected 1887567, actual 1886214 

http://www.freebsd.org/cgi/query-pr.cgi?pr=172496 
>Unformatted:
