Remove expired ports:

2018-06-06 biology/ssaha: Broken for more than 6 months
2018-06-06 biology/crux: Broken for more than 6 months
2018-06-06 biology/ariadne: Broken for more than 6 months
2018-06-06 cad/sceptre: Broken for more than 6 months
2018-06-06 cad/cider: Broken for more than 6 months
2018-06-06 chinese/scim-array: Broken for more than 6 months
2018-06-06 chinese/xpdf: Broken for more than 6 months
2018-06-06 chinese/telnet: Broken for more than 6 months
2018-06-06 comms/java-commapi-freebsd: Depends on BROKEN and expiring comms/java-commapi
2018-06-06 comms/soundmodem: Broken for more than 6 months
2018-06-06 comms/jsdr: Broken for more than 6 months
2018-06-06 comms/java-commapi: Broken for more than 6 months
2018-06-06 converters/pdf2djvu: Broken for more than 6 months
2018-06-06 databases/rdb: Broken for more than 6 months
2018-06-06 databases/animenfo-client: Broken for more than 6 months
2018-06-06 databases/ruby-mysql: Broken for more than 6 months
2018-06-06 databases/riak: Broken for more than 6 months
2018-06-06 databases/animenfo-client-gtk: Broken for more than 6 months
2018-06-06 databases/rdfdb: Broken for more than 6 months
2018-06-06 databases/riak2: Broken for more than 6 months
2018-06-06 devel/subversion-static: Broken for more than 6 months
2018-06-06 japanese/xgate: Broken for more than 6 months
2018-06-06 textproc/opengrm-ngram: Broken for more than 6 months
2018-06-06 textproc/ocaml-tyxml: Depends on BROKEN and expiring www/ocaml-net
2018-06-06 www/ocaml-net: Broken for more than 6 months
2018-06-06 audio/linux-genpuid: Broken for more than 6 months
2018-06-06 x11/enventor: Broken for more than 6 months
2018-06-06 audio/xmms-timidity: Broken for more than 6 months
2018-06-06 audio/kaudiocreator: Broken for more than 6 months
2018-06-06 audio/jxm: Depends on BROKEN and expiring comms/java-commapi
2018-06-06 audio/deforaos-mixer: Broken for more than 6 months
2018-06-06 audio/gkrellmss2: Broken for more than 6 months
2018-06-06 audio/ogg2mp3: Broken for more than 6 months
2018-06-06 audio/abcmidi: Broken for more than 6 months
2018-06-06 benchmarks/netpipe: Broken for more than 6 months
2018-06-06 biology/plink: Broken for more than 6 months

7 files changed, 0 insertions, 152 deletions

diff --git a/biology/plink/Makefile b/biology/plink/Makefile
deleted file mode 100644
index b77e97515548..000000000000
--- a/biology/plink/Makefile
+++ /dev/null
@@ -1,30 +0,0 @@
-# $FreeBSD$
-
-PORTNAME=	plink
-PORTVERSION=	1.07
-PORTREVISION=	8
-CATEGORIES=	biology science
-MASTER_SITES=	http://pngu.mgh.harvard.edu/~purcell/plink/dist/
-DISTNAME=	${PORTNAME}-${PORTVERSION}-src
-
-MAINTAINER=	jwb@FreeBSD.org
-COMMENT=	Whole genome association analysis toolset
-
-BROKEN=		no public distfiles
-DEPRECATED=	Broken for more than 6 months
-EXPIRATION_DATE=	2018-06-06
-
-LICENSE=	GPLv2
-
-LIB_DEPENDS=	liblapack.so:math/lapack
-
-# We need Fortran LDFLAGS to link with Lapack.
-USES=		fortran gmake zip
-
-PLIST_FILES=	bin/plink
-
-do-install:
-	${MKDIR} ${STAGEDIR}${PREFIX}/bin
-	${INSTALL_PROGRAM} ${WRKSRC}/plink ${STAGEDIR}${PREFIX}/bin
-
-.include <bsd.port.mk>
diff --git a/biology/plink/distinfo b/biology/plink/distinfo
deleted file mode 100644
index 0e6de032e915..000000000000
--- a/biology/plink/distinfo
+++ /dev/null
@@ -1,2 +0,0 @@
-SHA256 (plink-1.07-src.zip) = 4af56348443d0c6a1db64950a071b1fcb49cc74154875a7b43cccb4b6a7f482b
-SIZE (plink-1.07-src.zip) = 2257297
diff --git a/biology/plink/files/patch-Makefile b/biology/plink/files/patch-Makefile
deleted file mode 100644
index e98b69aa6559..000000000000
--- a/biology/plink/files/patch-Makefile
+++ /dev/null
@@ -1,53 +0,0 @@
---- Makefile.orig	2009-10-10 11:00:20.000000000 -0500
-+++ Makefile	2012-09-07 08:24:26.000000000 -0500
-@@ -26,25 +26,25 @@
- WITH_WEBCHECK = 1
- FORCE_32BIT = 
- WITH_ZLIB = 1
--WITH_LAPACK = 
--FORCE_DYNAMIC = 
-+WITH_LAPACK = 1
-+FORCE_DYNAMIC = 1
- 
- # Put C++ compiler here; Windows has it's own specific version
- CXX_UNIX = g++
- CXX_WIN = c:\bin\mingw\bin\mingw32-g++.exe
- 
- # Any other compiler flags here ( -Wall, -g, etc)
--CXXFLAGS = 
-+# CXXFLAGS = 
- 
- # Misc
--LIB_LAPACK = /usr/lib/liblapack.so.3
-+LIB_LAPACK = ${LDFLAGS} -L${LOCALBASE}/lib -llapack -lblas
- 
- 
- # --------------------------------------------------------------------
- # Do not edit below this line
- # --------------------------------------------------------------------
- 
--CXXFLAGS += -O3 -I.
-+CXXFLAGS += -I.
- OUTPUT = plink
- 
- # Some system specific flags
-@@ -58,8 +58,8 @@
- endif
- 
- ifeq ($(SYS),UNIX)
-- CXXFLAGS += -DUNIX
-- CXX = $(CXX_UNIX)
-+ CXXFLAGS += -DUNIX -Dfopen64=fopen
-+ CXX ?= $(CXX_UNIX)
-  ifndef FORCE_DYNAMIC
-   CXXFLAGS += -static
-  endif
-@@ -128,7 +128,7 @@
- LIB += -ldl
- endif
- ifeq ($(SYS),UNIX)
--LIB += -ldl -lcrypt
-+LIB += -lcrypt
- endif
- endif
- 
diff --git a/biology/plink/files/patch-elf.cpp b/biology/plink/files/patch-elf.cpp
deleted file mode 100644
index 0cc22cb84e6a..000000000000
--- a/biology/plink/files/patch-elf.cpp
+++ /dev/null
@@ -1,25 +0,0 @@
---- elf.cpp.orig	2013-11-16 17:09:56.000000000 +0100
-+++ elf.cpp	2013-11-16 17:10:24.000000000 +0100
-@@ -1175,10 +1175,10 @@
- 	  << setw(8) << gcnt << " "
- 	  << setw(8) << (double)cnt / (double)gcnt << "\n";
- 
--      map<int,int>::iterator i = chr_cnt.begin();
--      while ( i != chr_cnt.end() )
-+      map<int,int>::iterator ichr = chr_cnt.begin();
-+      while ( ichr != chr_cnt.end() )
- 	{
--	  int c = i->first;
-+	  int c = ichr->first;
- 	  int x = chr_cnt.find( c )->second;
- 	  int y = chr_gcnt.find( c )->second;
- 	  
-@@ -1189,7 +1189,7 @@
- 	      << setw(8) << y << " "
- 	      << setw(8) << (double)x / (double)y << "\n";
- 	  
--	  ++i;
-+	  ++ichr;
- 	}
-       
-     }
diff --git a/biology/plink/files/patch-idhelp.cpp b/biology/plink/files/patch-idhelp.cpp
deleted file mode 100644
index c0026984f854..000000000000
--- a/biology/plink/files/patch-idhelp.cpp
+++ /dev/null
@@ -1,19 +0,0 @@
---- idhelp.cpp.orig	2013-11-16 17:11:42.000000000 +0100
-+++ idhelp.cpp	2013-11-16 17:12:53.000000000 +0100
-@@ -772,12 +772,12 @@
-       for (int j = 0 ; j < jointField.size(); j++ )
- 	{
- 	  set<IDField*> & jf = jointField[j];
--	  set<IDField*>::iterator j = jf.begin();
-+	  set<IDField*>::iterator jfit = jf.begin();
- 	  PP->printLOG(" { ");
--	  while ( j != jf.end() )
-+	  while ( jfit != jf.end() )
- 	    {
--	      PP->printLOG( (*j)->name + " " );
--	      ++j;
-+	      PP->printLOG( (*jfit)->name + " " );
-+	      ++jfit;
- 	    }
- 	  PP->printLOG(" }");
- 	}
diff --git a/biology/plink/files/patch-sets.cpp b/biology/plink/files/patch-sets.cpp
deleted file mode 100644
index 4d773fb36db2..000000000000
--- a/biology/plink/files/patch-sets.cpp
+++ /dev/null
@@ -1,18 +0,0 @@
---- sets.cpp.orig	2013-11-16 17:06:29.000000000 +0100
-+++ sets.cpp	2013-11-16 17:07:12.000000000 +0100
-@@ -768,11 +768,11 @@
-       //////////////////////////////////////////////
-       // Reset original missing status
- 
--      vector<Individual*>::iterator i = PP->sample.begin();
--      while ( i != PP->sample.end() )
-+      vector<Individual*>::iterator ipp = PP->sample.begin();
-+      while ( ipp != PP->sample.end() )
- 	{
--	  (*i)->missing = (*i)->flag;
--	  ++i;
-+	  (*ipp)->missing = (*ipp)->flag;
-+	  ++ipp;
- 	}
- 
-       ////////////////////////////////////////////////
diff --git a/biology/plink/pkg-descr b/biology/plink/pkg-descr
deleted file mode 100644
index cc38aca9112e..000000000000
--- a/biology/plink/pkg-descr
+++ /dev/null
@@ -1,5 +0,0 @@
-PLINK is a free, open-source whole genome association analysis toolset,
-designed to perform a range of basic, large-scale analyses in a
-computationally efficient manner.
-
-WWW: http://pngu.mgh.harvard.edu/~purcell/plink/