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Date: Wed, 18 Dec 2013 18:28:27 +0100 (CET)
From: Tijl Coosemans <tijl@FreeBSD.org>
Reply-To: Tijl Coosemans <tijl@FreeBSD.org>
To: FreeBSD-gnats-submit@freebsd.org
Cc:
Subject: [patch] biology/clustalw: fix build with clang/libc++
X-Send-Pr-Version: 3.114
X-GNATS-Notify:

>Number:         184974
>Category:       ports
>Synopsis:       [patch] biology/clustalw: fix build with clang/libc++
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    wen
>State:          closed
>Quarter:        
>Keywords:       
>Date-Required:  
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Wed Dec 18 17:30:00 UTC 2013
>Closed-Date:    Fri Dec 20 15:29:56 UTC 2013
>Last-Modified:  Fri Dec 20 16:10:01 UTC 2013
>Originator:     Tijl Coosemans
>Release:        FreeBSD 11.0-CURRENT i386
>Organization:
>Environment:
>Description:
- Fix build with clang/libc++.
- Support staging.
>How-To-Repeat:
>Fix:

--- clustalw.patch begins here ---
Index: biology/clustalw/Makefile
===================================================================
--- biology/clustalw/Makefile	(revision 336709)
+++ biology/clustalw/Makefile	(working copy)
@@ -10,7 +10,7 @@ MASTER_SITES=	ftp://ftp.ebi.ac.uk/pub/so
 MASTER_SITE_SUBDIR=	${PORTVERSION}
 
 MAINTAINER=	wen@FreeBSD.org
-COMMENT=	A multiple alignment program for DNA or proteins
+COMMENT=	Multiple alignment program for DNA or proteins
 
 RESTRICTED=	No commercial use.
 
@@ -20,8 +20,7 @@ GNU_CONFIGURE=	yes
 
 PLIST_FILES=	bin/clustalw bin/clustalw2
 
-NO_STAGE=	yes
 post-install:
-	${LN} -sf clustalw2 ${PREFIX}/bin/clustalw
+	${LN} -sf clustalw2 ${STAGEDIR}${PREFIX}/bin/clustalw
 
 .include <bsd.port.mk>
Index: biology/clustalw/files/patch-src-general-VectorOutOfRange.h
===================================================================
--- biology/clustalw/files/patch-src-general-VectorOutOfRange.h	(revision 0)
+++ biology/clustalw/files/patch-src-general-VectorOutOfRange.h	(working copy)
@@ -0,0 +1,10 @@
+--- src/general/VectorOutOfRange.h.orig	2013-12-18 18:06:35.000000000 +0100
++++ src/general/VectorOutOfRange.h	2013-12-18 18:07:03.000000000 +0100
+@@ -5,6 +5,7 @@
+  */
+ #include <stdexcept>
+ #include <exception>
++#include <string>
+ namespace clustalw
+ {
+ 

Property changes on: biology/clustalw/files/patch-src-general-VectorOutOfRange.h
___________________________________________________________________
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
--- clustalw.patch ends here ---

>Release-Note:
>Audit-Trail:
Responsible-Changed-From-To: freebsd-ports-bugs->wen 
Responsible-Changed-By: edwin 
Responsible-Changed-When: Wed Dec 18 17:30:08 UTC 2013 
Responsible-Changed-Why:  
Over to maintainer (via the GNATS Auto Assign Tool) 

http://www.freebsd.org/cgi/query-pr.cgi?pr=184974 
State-Changed-From-To: open->closed 
State-Changed-By: wen 
State-Changed-When: Fri Dec 20 15:29:55 UTC 2013 
State-Changed-Why:  
Committed. Thanks! 

http://www.freebsd.org/cgi/query-pr.cgi?pr=184974 

From: dfilter@FreeBSD.ORG (dfilter service)
To: bug-followup@FreeBSD.org
Cc:  
Subject: Re: ports/184974: commit references a PR
Date: Fri, 20 Dec 2013 15:29:15 +0000 (UTC)

 Author: wen
 Date: Fri Dec 20 15:29:07 2013
 New Revision: 337026
 URL: http://svnweb.freebsd.org/changeset/ports/337026
 
 Log:
   - Fix build with clang/libc++.
   - Support staging.
   
   PR:		184974
   Submitted by:	tijl@
 
 Added:
   head/biology/clustalw/files/
   head/biology/clustalw/files/patch-src-general-VectorOutOfRange.h   (contents, props changed)
 Modified:
   head/biology/clustalw/Makefile
 
 Modified: head/biology/clustalw/Makefile
 ==============================================================================
 --- head/biology/clustalw/Makefile	Fri Dec 20 15:27:26 2013	(r337025)
 +++ head/biology/clustalw/Makefile	Fri Dec 20 15:29:07 2013	(r337026)
 @@ -10,7 +10,7 @@ MASTER_SITES=	ftp://ftp.ebi.ac.uk/pub/so
  MASTER_SITE_SUBDIR=	${PORTVERSION}
  
  MAINTAINER=	wen@FreeBSD.org
 -COMMENT=	A multiple alignment program for DNA or proteins
 +COMMENT=	Multiple alignment program for DNA or proteins
  
  RESTRICTED=	No commercial use.
  
 @@ -20,8 +20,7 @@ GNU_CONFIGURE=	yes
  
  PLIST_FILES=	bin/clustalw bin/clustalw2
  
 -NO_STAGE=	yes
  post-install:
 -	${LN} -sf clustalw2 ${PREFIX}/bin/clustalw
 +	${LN} -sf clustalw2 ${STAGEDIR}${PREFIX}/bin/clustalw
  
  .include <bsd.port.mk>
 
 Added: head/biology/clustalw/files/patch-src-general-VectorOutOfRange.h
 ==============================================================================
 --- /dev/null	00:00:00 1970	(empty, because file is newly added)
 +++ head/biology/clustalw/files/patch-src-general-VectorOutOfRange.h	Fri Dec 20 15:29:07 2013	(r337026)
 @@ -0,0 +1,10 @@
 +--- src/general/VectorOutOfRange.h.orig	2013-12-20 23:16:13.000000000 +0800
 ++++ src/general/VectorOutOfRange.h	2013-12-20 23:16:37.000000000 +0800
 +@@ -5,6 +5,7 @@
 +  */
 + #include <stdexcept>
 + #include <exception>
 ++#include <string>
 + namespace clustalw
 + {
 + 
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From: dfilter@FreeBSD.ORG (dfilter service)
To: bug-followup@FreeBSD.org
Cc:  
Subject: Re: ports/184974: commit references a PR
Date: Fri, 20 Dec 2013 16:01:46 +0000 (UTC)

 Author: mat
 Date: Fri Dec 20 16:01:38 2013
 New Revision: 337027
 URL: http://svnweb.freebsd.org/changeset/ports/337027
 
 Log:
   MFH: r337026
   
   - Fix build with clang/libc++.
   - Support staging.
   
   PR:		184974
   Submitted by:	tijl@
   Approved by:	portmgr (implicit)
 
 Added:
   branches/2014Q1/biology/clustalw/files/
      - copied from r337026, head/biology/clustalw/files/
 Modified:
   branches/2014Q1/biology/clustalw/Makefile
 Directory Properties:
   branches/2014Q1/   (props changed)
 
 Modified: branches/2014Q1/biology/clustalw/Makefile
 ==============================================================================
 --- branches/2014Q1/biology/clustalw/Makefile	Fri Dec 20 15:29:07 2013	(r337026)
 +++ branches/2014Q1/biology/clustalw/Makefile	Fri Dec 20 16:01:38 2013	(r337027)
 @@ -10,7 +10,7 @@ MASTER_SITES=	ftp://ftp.ebi.ac.uk/pub/so
  MASTER_SITE_SUBDIR=	${PORTVERSION}
  
  MAINTAINER=	wen@FreeBSD.org
 -COMMENT=	A multiple alignment program for DNA or proteins
 +COMMENT=	Multiple alignment program for DNA or proteins
  
  RESTRICTED=	No commercial use.
  
 @@ -20,8 +20,7 @@ GNU_CONFIGURE=	yes
  
  PLIST_FILES=	bin/clustalw bin/clustalw2
  
 -NO_STAGE=	yes
  post-install:
 -	${LN} -sf clustalw2 ${PREFIX}/bin/clustalw
 +	${LN} -sf clustalw2 ${STAGEDIR}${PREFIX}/bin/clustalw
  
  .include <bsd.port.mk>
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 http://lists.freebsd.org/mailman/listinfo/svn-ports-all
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>Unformatted:
