- Fix build with clang

- Support STAGEDIR

PR:		ports/184242
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>

5 files changed, 44 insertions, 34 deletions

diff --git a/biology/avida/Makefile b/biology/avida/Makefile
index 4d283832b17e..79ba36776c62 100644
--- a/biology/avida/Makefile
+++ b/biology/avida/Makefile
@@ -8,13 +8,14 @@ CATEGORIES=	biology
 MASTER_SITES=	SF/${PORTNAME}/${PORTNAME}-stable/${PORTVERSION}
 
 MAINTAINER=	ports@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 default-gx.org \
 		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>
diff --git a/biology/avida/files/patch-avida-core__source__main__cGenomeUtil.cc b/biology/avida/files/patch-avida-core__source__main__cGenomeUtil.cc
new file mode 100644
index 000000000000..0aef270a88ce
--- /dev/null
+++ b/biology/avida/files/patch-avida-core__source__main__cGenomeUtil.cc
@@ -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());
diff --git a/biology/avida/files/patch-libs__tcmalloc-1.4__src__malloc_extension.cc b/biology/avida/files/patch-libs__tcmalloc-1.4__src__malloc_extension.cc
new file mode 100644
index 000000000000..7134dc16aea3
--- /dev/null
+++ b/biology/avida/files/patch-libs__tcmalloc-1.4__src__malloc_extension.cc
@@ -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
diff --git a/biology/avida/files/patch-libs_apto_include_apto_core_Functor.h b/biology/avida/files/patch-libs_apto_include_apto_core_Functor.h
deleted file mode 100644
index ae59b88cbf53..000000000000
--- a/biology/avida/files/patch-libs_apto_include_apto_core_Functor.h
+++ /dev/null
@@ -1,10 +0,0 @@
---- libs/apto/include/apto/core/Functor.h.orig	2012-09-29 03:33:38.000000000 +0000
-+++ libs/apto/include/apto/core/Functor.h
-@@ -38,6 +38,7 @@
- 
- #include "apto/platform/Visibility.h"
- 
-+#include <typeinfo>
- #include <cassert>
- 
- 
diff --git a/biology/avida/files/patch-libs_apto_utils_unittest_googletest_include_gtest_internal_gtest-port.h b/biology/avida/files/patch-libs_apto_utils_unittest_googletest_include_gtest_internal_gtest-port.h
deleted file mode 100644
index 83dd715504b6..000000000000
--- a/biology/avida/files/patch-libs_apto_utils_unittest_googletest_include_gtest_internal_gtest-port.h
+++ /dev/null
@@ -1,10 +0,0 @@
---- libs/apto/utils/unittest/googletest/include/gtest/internal/gtest-port.h.orig	2012-09-29 03:33:39.000000000 +0000
-+++ libs/apto/utils/unittest/googletest/include/gtest/internal/gtest-port.h
-@@ -173,6 +173,7 @@
- #include <stdlib.h>
- #include <stdio.h>
- #include <string.h>
-+#include <unistd.h>
- #ifndef _WIN32_WCE
- #include <sys/stat.h>
- #endif  // !_WIN32_WCE