Bug 184974 - [patch] biology/clustalw: fix build with clang/libc++
Summary: [patch] biology/clustalw: fix build with clang/libc++
Status: Closed FIXED
Alias: None
Product: Ports & Packages
Classification: Unclassified
Component: Individual Port(s) (show other bugs)
Version: Latest
Hardware: Any Any
: Normal Affects Only Me
Assignee: Wen Heping
URL:
Keywords:
Depends on:
Blocks:
 
Reported: 2013-12-18 17:30 UTC by Tijl Coosemans
Modified: 2013-12-20 16:10 UTC (History)
0 users

See Also:

Attachments
clustalw.patch (1.62 KB, patch)
2013-12-18 17:30 UTC, Tijl Coosemans 		no flags Details | Diff
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Description Tijl Coosemans freebsd_committer freebsd_triage 2013-12-18 17:30:00 UTC 
- Fix build with clang/libc++.
- Support staging.
Comment 1 Edwin Groothuis freebsd_committer freebsd_triage 2013-12-18 17:30:08 UTC 
Responsible Changed
From-To: freebsd-ports-bugs->wen

Over to maintainer (via the GNATS Auto Assign Tool)
Comment 2 dfilter service freebsd_committer freebsd_triage 2013-12-20 15:29:15 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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Comment 3 Wen Heping freebsd_committer freebsd_triage 2013-12-20 15:29:55 UTC 
State Changed
From-To: open->closed

Committed. Thanks!
Comment 4 dfilter service freebsd_committer freebsd_triage 2013-12-20 16:01:46 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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