ports/184242: commit references a PR

[dfilter service]

The following reply was made to PR ports/184242; it has been noted by GNATS.

From: dfilter at FreeBSD.ORG (dfilter service)
To: bug-followup at FreeBSD.org
Cc:  
Subject: Re: ports/184242: commit references a PR
Date: Wed, 27 Nov 2013 16:07:59 +0000 (UTC)

 Author: jadawin
 Date: Wed Nov 27 16:07:51 2013
 New Revision: 335028
 URL: http://svnweb.freebsd.org/changeset/ports/335028
 
 Log:
   - Fix build with clang
   - Support STAGEDIR
   
   PR:		ports/184242
   Submitted by:	KATO Tsuguru <tkato432 at yahoo.com>
 
 Added:
   head/biology/avida/files/patch-avida-core__source__main__cGenomeUtil.cc   (contents, props changed)
   head/biology/avida/files/patch-libs__tcmalloc-1.4__src__malloc_extension.cc   (contents, props changed)
 Deleted:
   head/biology/avida/files/patch-libs_apto_include_apto_core_Functor.h
   head/biology/avida/files/patch-libs_apto_utils_unittest_googletest_include_gtest_internal_gtest-port.h
 Modified:
   head/biology/avida/Makefile
 
 Modified: head/biology/avida/Makefile
 ==============================================================================
 --- head/biology/avida/Makefile	Wed Nov 27 15:57:39 2013	(r335027)
 +++ head/biology/avida/Makefile	Wed Nov 27 16:07:51 2013	(r335028)
 @@ -8,13 +8,14 @@ CATEGORIES=	biology
  MASTER_SITES=	SF/${PORTNAME}/${PORTNAME}-stable/${PORTVERSION}
  
  MAINTAINER=	ports at FreeBSD.org
 -COMMENT=	An auto-adaptive genetic system designed for ALife research
 +COMMENT=	Auto-adaptive genetic system designed for ALife research
  
  LICENSE=	GPLv3
  
  OPTIONS_DEFINE=	DOCS
  
  USES=		cmake:outsource ncurses
 +CMAKE_ARGS=	-DAPTO_UNIT_TESTS:BOOL=OFF -DAVD_UNIT_TESTS:BOOL=OFF
  
  PORTDOCS=	*
  PLIST_FILES=	${BIN_FILES:S|^|bin/|} \
 @@ -30,7 +31,6 @@ DATA_FILES=	analyze.cfg avida.cfg defaul
  		instset-heads-sex.cfg instset-heads.cfg instset-smt.cfg \
  		instset-transsmt.cfg
  
 -NO_STAGE=	yes
  .include <bsd.port.pre.mk>
  
  .if ${ARCH} == "ia64" || ${ARCH} == "powerpc" || ${ARCH} == "sparc64"
 @@ -41,7 +41,7 @@ post-patch:
  	@${FIND} ${WRKSRC} -name "CMakeLists.txt" | ${XARGS} \
  		${REINPLACE_CMD} -e \
  		's|-O[0-9]|| ; \
 -		 s| pthread| ${PTHREAD_LIBS}|'
 +		 s| pthread| -pthread|'
  	@${REINPLACE_CMD} -e '/long long int/s|std::abs|llabs|' \
  		${WRKSRC}/avida-core/source/main/cPopulationInterface.cc
  
 @@ -52,20 +52,22 @@ pre-build:
  .endfor
  
  do-install:
 -	@${MKDIR} ${PREFIX}/lib/${PORTNAME}
 +	@${MKDIR} ${STAGEDIR}${PREFIX}/lib/${PORTNAME}
  .for exec in ${BIN_FILES}
 -	(cd ${WRKSRC} \
 -		&& ${INSTALL_SCRIPT} ${exec}.sh ${PREFIX}/bin/${exec})
 -	(cd ${BUILD_WRKSRC}/bin \
 -		&& ${INSTALL_PROGRAM} ${exec} ${PREFIX}/lib/${PORTNAME})
 +	(cd ${WRKSRC} && ${INSTALL_SCRIPT} ${exec}.sh \
 +		${STAGEDIR}${PREFIX}/bin/${exec})
 +	(cd ${BUILD_WRKSRC}/bin && ${INSTALL_PROGRAM} ${exec} \
 +		${STAGEDIR}${PREFIX}/lib/${PORTNAME})
  .endfor
 -	(cd ${WRKSRC}/avida-core/support/config \
 -		&& ${INSTALL_DATA} *.cfg ${PREFIX}/lib/${PORTNAME} \
 -		&& ${INSTALL_DATA} *.org ${PREFIX}/lib/${PORTNAME})
 +	(cd ${WRKSRC}/avida-core/support/config && ${INSTALL_DATA} *.cfg \
 +		${STAGEDIR}${PREFIX}/lib/${PORTNAME})
 +	(cd ${WRKSRC}/avida-core/support/config && ${INSTALL_DATA} *.org \
 +		${STAGEDIR}${PREFIX}/lib/${PORTNAME})
 +
  .if ${PORT_OPTIONS:MDOCS}
 -	@${MKDIR} ${DOCSDIR}
 -	@(cd ${WRKSRC}/avida-core/documentation \
 -		&& ${COPYTREE_SHARE} . ${DOCSDIR})
 +	@${MKDIR} ${STAGEDIR}${DOCSDIR}
 +	@(cd ${WRKSRC}/avida-core/documentation && ${COPYTREE_SHARE} . \
 +		${STAGEDIR}${DOCSDIR})
  .endif
  
  .include <bsd.port.post.mk>
 
 Added: head/biology/avida/files/patch-avida-core__source__main__cGenomeUtil.cc
 ==============================================================================
 --- /dev/null	00:00:00 1970	(empty, because file is newly added)
 +++ head/biology/avida/files/patch-avida-core__source__main__cGenomeUtil.cc	Wed Nov 27 16:07:51 2013	(r335028)
 @@ -0,0 +1,18 @@
 +--- avida-core/source/main/cGenomeUtil.cc.orig
 ++++ avida-core/source/main/cGenomeUtil.cc
 +@@ -214,7 +214,14 @@
 +  */
 + void cGenomeUtil::RandomShuffle(cAvidaContext& ctx, Sequence& genome) {
 + 	std::vector<int> idx(static_cast<std::size_t>(genome.GetSize()));
 +-	std::iota(idx.begin(), idx.end(), 0);
 ++
 ++	std::vector<int>::iterator idx_it = idx.begin();
 ++	int value = 0;
 ++	while (idx_it != idx.end()) {
 ++		*idx_it++ = value;
 ++		++value;
 ++	}
 ++
 + 	cRandomStdAdaptor rng(ctx.GetRandom());
 + 	std::random_shuffle(idx.begin(), idx.end(), rng);
 + 	Sequence shuffled(genome.GetSize());
 
 Added: head/biology/avida/files/patch-libs__tcmalloc-1.4__src__malloc_extension.cc
 ==============================================================================
 --- /dev/null	00:00:00 1970	(empty, because file is newly added)
 +++ head/biology/avida/files/patch-libs__tcmalloc-1.4__src__malloc_extension.cc	Wed Nov 27 16:07:51 2013	(r335028)
 @@ -0,0 +1,10 @@
 +--- libs/tcmalloc-1.4/src/malloc_extension.cc.orig
 ++++ libs/tcmalloc-1.4/src/malloc_extension.cc
 +@@ -57,6 +57,7 @@
 + #include <string.h>
 + #include <stdio.h>
 + #include <stdlib.h>
 ++#include <pthread.h>
 + #if defined HAVE_STDINT_H
 + #include <stdint.h>
 + #elif defined HAVE_INTTYPES_H
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