17 files changed, 0 insertions, 462 deletions

diff --git a/biology/Makefile b/biology/Makefile
index f5958aff4c2e..ea5b43a5df38 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -10,11 +10,9 @@
     SUBDIR += babel
     SUBDIR += biojava
     SUBDIR += blast
-    SUBDIR += chemeq
     SUBDIR += clustalw
     SUBDIR += coalesce
     SUBDIR += crimap
-    SUBDIR += deft
     SUBDIR += distribfold
     SUBDIR += dna-qc
     SUBDIR += embassy
@@ -23,7 +21,6 @@
     SUBDIR += fasta3
     SUBDIR += fastdnaml
     SUBDIR += finchtv
-    SUBDIR += flip
     SUBDIR += fluctuate
     SUBDIR += garlic
     SUBDIR += genpak
diff --git a/biology/chemeq/Makefile b/biology/chemeq/Makefile
deleted file mode 100644
index 2ef8290434ae..000000000000
--- a/biology/chemeq/Makefile
+++ /dev/null
@@ -1,43 +0,0 @@
-# New ports collection makefile for:	chemeq
-# Date created:				31 May 2000
-# Whom:					rmiya
-#
-# $FreeBSD$
-
-PORTNAME=	chemeq
-PORTVERSION=	1.10
-PORTREVISION=	2
-CATEGORIES=	biology textproc
-MASTER_SITES=	ftp://boltz.univ-littoral.fr/pub/chemeq/
-DISTNAME=	chemeq-V110-1
-
-MAINTAINER=	rmiya@cc.hirosaki-u.ac.jp
-COMMENT=	Outputs LaTeX code for chemical reaction
-
-DEPRECATED=	"mastersite disappeared, no longer maintained by author"
-EXPIRATION_DATE=	2005-12-31
-
-WRKSRC=		${WRKDIR}/${PORTNAME}
-
-USE_BISON=	yes
-
-MAN1=		chemeq.1
-
-do-install:
-	${INSTALL_PROGRAM} ${WRKSRC}/src/chemeq ${PREFIX}/bin
-	${INSTALL_MAN}	${WRKSRC}/chemeq.1 ${MAN1PREFIX}/man/man1
-.if !defined(NOPORTDOCS)
-	${MKDIR} ${DOCSDIR}
-	${MKDIR} ${EXAMPLESDIR}
-	${INSTALL_DATA} ${WRKSRC}/COPYING ${DOCSDIR}
-	${INSTALL_DATA} ${WRKSRC}/LISEZMOI ${DOCSDIR}
-	${INSTALL_DATA} ${WRKSRC}/README ${DOCSDIR}
-	${INSTALL_DATA} ${WRKSRC}/src/TODO ${EXAMPLESDIR}
-	${INSTALL_DATA} ${WRKSRC}/src/test.1 ${EXAMPLESDIR}
-	${INSTALL_SCRIPT} ${WRKSRC}/src/chemreport ${EXAMPLESDIR}
-	${INSTALL_SCRIPT} ${WRKSRC}/src/chemreport.pl ${EXAMPLESDIR}
-	${INSTALL_SCRIPT} ${WRKSRC}/src/chemtest ${EXAMPLESDIR}
-	${INSTALL_SCRIPT} ${WRKSRC}/src/chemtest.pl ${EXAMPLESDIR}
-.endif
-
-.include <bsd.port.mk>
diff --git a/biology/chemeq/distinfo b/biology/chemeq/distinfo
deleted file mode 100644
index c784c4302dac..000000000000
--- a/biology/chemeq/distinfo
+++ /dev/null
@@ -1,2 +0,0 @@
-MD5 (chemeq-V110-1.tar.gz) = bfe0008317e248110bea7cb38d202be6
-SIZE (chemeq-V110-1.tar.gz) = 20372
diff --git a/biology/chemeq/files/patch-src_Makefile b/biology/chemeq/files/patch-src_Makefile
deleted file mode 100644
index 13a3ee3c2f02..000000000000
--- a/biology/chemeq/files/patch-src_Makefile
+++ /dev/null
@@ -1,24 +0,0 @@
-
-$FreeBSD$
-
---- src/Makefile.orig	Sat Mar  8 21:56:02 2003
-+++ src/Makefile	Sat Mar  8 21:56:33 2003
-@@ -1,14 +1,14 @@
- #CXXFLAGS= -g
--CXXFLAGS= -O1
-+#CXXFLAGS= -O1
- 
- chemeq : chemeq.o chemparser.o
--	g++ $(CXXFLAGS) -o chemeq chemeq.o chemparser.o -lfl
-+	$(CXX) $(CXXFLAGS) -o chemeq chemeq.o chemparser.o -lfl
- 
- chemeq.o : chemeq.cc chemeq.h
--	g++ $(CXXFLAGS) -c chemeq.cc
-+	$(CXX) $(CXXFLAGS) -c chemeq.cc
- 
- chemparser.o : chemparser.cc chemeq.h
--	g++ $(CXXFLAGS) -c chemparser.cc
-+	$(CXX) $(CXXFLAGS) -c chemparser.cc
- 
- chemparser.cc : chemlex.cc chemeq.y chemeq.h
- 	bison  --verbose -o chemparser.cc chemeq.y
diff --git a/biology/chemeq/files/patch-src_chemeq.cc b/biology/chemeq/files/patch-src_chemeq.cc
deleted file mode 100644
index 8762460854f3..000000000000
--- a/biology/chemeq/files/patch-src_chemeq.cc
+++ /dev/null
@@ -1,31 +0,0 @@
-
-$FreeBSD$
-
---- src/chemeq.cc.orig	Thu May 10 19:10:19 2001
-+++ src/chemeq.cc	Sun Jan 25 20:56:21 2004
-@@ -1,6 +1,6 @@
- #include "chemeq.h"
- #include <math.h>
--#include <strstream.h>
-+#include <strstream>
- atome lesatomes[] ={
- {-1, "e"},
- {1, "H"},
-@@ -150,7 +150,7 @@
-   if (suiv) suiv->compte(c,mult);
- };
- 
--void AtomeListe::numerote(int n=0){
-+void AtomeListe::numerote(int n){
-   if(Zed!=0){ /* cas oł ce n'est pas un groupe */
-     no = n;
-   }
-@@ -245,7 +245,7 @@
-   nb.simplifie();
- }
- 
--bool Molec::printNernst(ostream & o, char * prefix =""){
-+bool Molec::printNernst(ostream & o, char * prefix){
-   switch(t){
-   case sol : return 0;
-   case aqueous :
diff --git a/biology/chemeq/files/patch-src_chemeq.h b/biology/chemeq/files/patch-src_chemeq.h
deleted file mode 100644
index 95649ead65f7..000000000000
--- a/biology/chemeq/files/patch-src_chemeq.h
+++ /dev/null
@@ -1,19 +0,0 @@
-
-$FreeBSD$
-
---- src/chemeq.h.orig	Sat Mar  8 21:48:53 2003
-+++ src/chemeq.h	Sat Mar  8 21:50:34 2003
-@@ -2,10 +2,12 @@
- #define CHEMEQ_H
- 
- #include <string.h>
--#include <stdiostream.h>
-+#include <iostream>
- #include <vector>
- #include <string>
- #include <map>
-+
-+using namespace std;
- 
- typedef struct {
-   int Zed;
diff --git a/biology/chemeq/pkg-descr b/biology/chemeq/pkg-descr
deleted file mode 100644
index 14ba1b63bcf6..000000000000
--- a/biology/chemeq/pkg-descr
+++ /dev/null
@@ -1,8 +0,0 @@
-`chemeq' outputs code, and checks the equilibrium of a chemical
-reaction. For example, 
-
-  IN: 2H2 + O2 ---> 2 H2O
-  OUT: 2\,H_{2}\,+\,O_{2}\,\rightarrow\,2\,H_{2}O
-
---
-rmiya
diff --git a/biology/chemeq/pkg-plist b/biology/chemeq/pkg-plist
deleted file mode 100644
index 5740162378c5..000000000000
--- a/biology/chemeq/pkg-plist
+++ /dev/null
@@ -1,13 +0,0 @@
-@comment $FreeBSD$
-bin/chemeq
-%%PORTDOCS%%%%DOCSDIR%%/COPYING
-%%PORTDOCS%%%%DOCSDIR%%/LISEZMOI
-%%PORTDOCS%%%%DOCSDIR%%/README
-%%PORTDOCS%%%%EXAMPLESDIR%%/TODO
-%%PORTDOCS%%%%EXAMPLESDIR%%/test.1
-%%PORTDOCS%%%%EXAMPLESDIR%%/chemreport
-%%PORTDOCS%%%%EXAMPLESDIR%%/chemreport.pl
-%%PORTDOCS%%%%EXAMPLESDIR%%/chemtest
-%%PORTDOCS%%%%EXAMPLESDIR%%/chemtest.pl
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
-%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%
diff --git a/biology/deft/Makefile b/biology/deft/Makefile
deleted file mode 100644
index 5c066f53fea2..000000000000
--- a/biology/deft/Makefile
+++ /dev/null
@@ -1,81 +0,0 @@
-# New ports collection makefile for:	DeFT
-# Date created:				1999-01-11
-# Whom:					Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
-#
-# $FreeBSD$
-#
-
-PORTNAME=	deft
-PORTVERSION=	2.2
-PORTREVISION=	2
-CATEGORIES=	biology
-MASTER_SITES=	http://www.dq.ufscar.br/download/chem/dft/
-DISTNAME=	DeFT_${PORTVERSION}
-EXTRACT_SUFX=	.tar.Z
-
-MAINTAINER=	rmiya@cc.hirosaki-u.ac.jp
-COMMENT=	Density functional molecular orbital calculation
-
-DEPRECATED=	"mastersite disappeared, no longer maintained by author"
-EXPIRATION_DATE=	2005-12-31
-
-WRKSRC=		${WRKDIR}/${DISTNAME}/source
-USE_REINPLACE=	yes
-
-.include <bsd.port.pre.mk>
-
-.if ${OSVERSION} >= 502126
-BROKEN=		"Does not install on FreeBSD >= 5.x"
-.endif
-
-.if ${OSVERSION} >= 400005
-# Using g77 is troublesome, then it is better to use f2c/cc.
-BUILD_DEPENDS=	ftn77:${PORTSDIR}/lang/f77
-.endif
-.if defined(USEMPICH) && ${USEMPICH} == yes
-BUILD_DEPENDS+=	mpif77:${PORTSDIR}/net/mpich
-FFLAGS+=	-I/usr/local/mpich/include
-FC=		/usr/local/mpich/bin/mpif77
-LFLAGS+=	-L/usr/local/mpich/lib -lmpich
-.endif
-
-post-patch:
-	@${REINPLACE_CMD} -e "s|%%PREFIX%%|${PREFIX}|g"\
-		${WRKDIR}/${DISTNAME}/examples/DeFT
-.if !defined(USEMPICH)
-	@echo "******************************"
-	@echo "If you want to use MPI library, set 'USEMPICH=yes'."
-	@echo "******************************"
-.endif
-
-post-configure:
-	${CP} ${FILESDIR}/Makefile.deft ${WRKSRC}/Makefile
-.if defined(USEMPICH) && ${USEMPICH} == yes
-	${MV} ${WRKSRC}/mpi.f ${WRKSRC}/mpi.f.notuse
-.endif
-
-do-install:
-	${INSTALL_PROGRAM} ${WRKSRC}/DeFT.exec ${PREFIX}/bin/
-	${INSTALL_SCRIPT} ${WRKDIR}/${DISTNAME}/examples/DeFT ${PREFIX}/bin/
-	${MKDIR} ${PREFIX}/share/DeFT
-	${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/bases ${PREFIX}/share/DeFT/
-
-post-install:
-.if !defined(NOPORTDOCS)
-	${MKDIR} ${PREFIX}/share/doc/DeFT
-	${MKDIR} ${PREFIX}/share/examples/DeFT
-	${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/README_Liability \
-		${PREFIX}/share/doc/DeFT/
-	${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/input.* \
-		${PREFIX}/share/doc/DeFT/
-	${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/install.* \
-		${PREFIX}/share/doc/DeFT/
-	${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/examples/README \
-		${PREFIX}/share/examples/DeFT
-	${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/examples/*.dft \
-		${PREFIX}/share/examples/DeFT
-	${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/examples/*.out \
-		${PREFIX}/share/examples/DeFT
-.endif
-
-.include <bsd.port.post.mk>
diff --git a/biology/deft/distinfo b/biology/deft/distinfo
deleted file mode 100644
index 4b7b2787b087..000000000000
--- a/biology/deft/distinfo
+++ /dev/null
@@ -1,2 +0,0 @@
-MD5 (DeFT_2.2.tar.Z) = be72e0ee373cb9f650daa3a550ed9132
-SIZE (DeFT_2.2.tar.Z) = 1327225
diff --git a/biology/deft/files/Makefile.deft b/biology/deft/files/Makefile.deft
deleted file mode 100644
index 18e8684be2e5..000000000000
--- a/biology/deft/files/Makefile.deft
+++ /dev/null
@@ -1,40 +0,0 @@
-#
-# Makefile for DeFT
-#
-TARGET = DeFT.exec
-FFLAGS += -w -O3
-CFLAGS += -w -O3
-.if ${MACHINE_ARCH} == "i386"
-FFLAGS += -malign-double
-CFLAGS += -malign-double
-.endif
-F2C = f2c
-F2CFLAGS += -w -Nn802
-.if ${OSVERSION} >= 400005
-FC = ftn77
-#FC = fc
-CFLAGS += -I${PREFIX}/include
-.endif
-LFLAGS = 
-SRCS:sh = ls *.f
-OBJS = $(SRCS:.f=.o)
-.if defined(USEMPICH) && ${USEMPICH} == yes
-FFLAGS+=	-I/usr/local/mpich/include
-FC=		/usr/local/mpich/bin/mpif77
-LFLAGS+=	-L/usr/local/mpich/lib -lmpich
-.endif
-
-all: ${TARGET}
-
-${TARGET}: ${OBJS}
-	${FC} ${LFLAGS} ${OBJS} -o $@
-
-.if ${FC} == ftn77
-cdgrxx.o: cdgrxx.f
-	${F2C} ${F2CFLAGS} cdgrxx.f
-	${CC} ${CFLAGS} -c cdgrxx.c
-.endif
-
-clean:
-	rm -f ${OBJS} ${TARGET}
-
diff --git a/biology/deft/files/patch-aa b/biology/deft/files/patch-aa
deleted file mode 100644
index 7164a838b73c..000000000000
--- a/biology/deft/files/patch-aa
+++ /dev/null
@@ -1,32 +0,0 @@
---- ../examples/DeFT.orig	Thu Aug 27 16:35:41 1998
-+++ ../examples/DeFT	Wed May 31 18:40:28 2000
-@@ -1,10 +1,14 @@
-+#!/bin/csh -f
- #
--# here is the shell for running DeFT
-+# running DeFT
- #
- 
--setenv my_directory $HOME/DeFT_2.2/examples
--setenv DeFT_directory $HOME/DeFT_2.2
--setenv temp_directory /scratch/tmp$$
-+setenv my_directory $2
-+if (null$my_directory == null) then
-+    setenv my_directory `echo $PWD`
-+endif
-+setenv DeFT_directory %%PREFIX%%/share/DeFT
-+setenv temp_directory /usr/tmp/tmp$$
- 
- mkdir $temp_directory
- cd $temp_directory
-@@ -19,9 +23,7 @@
- 
- chmod u+w $temp_directory/*
- 
--cp $DeFT_directory/source/DeFT             DeFT
--
--time DeFT < input >& $my_directory/$1.out
-+time DeFT.exec < input >& $my_directory/$1.out
- 
- cp new_restart $my_directory/$1.rst
- cp espf        $my_directory/$1.espf
diff --git a/biology/deft/pkg-descr b/biology/deft/pkg-descr
deleted file mode 100644
index 0d0cf60112c9..000000000000
--- a/biology/deft/pkg-descr
+++ /dev/null
@@ -1,16 +0,0 @@
-DeFT is a density functional moleculat orbital calculation program, 
-which was made by Alain St-Amant at Univ. Ottawa. 
-If you are interested in DeFT, please try to contact him.
-
-URL:http://www.chem.uottawa.ca/st-amant/st-amant_en.html
-
-DeFT_2.2 may be run with MPI, but I did not try it.
-
-
-Potring to 4.0-CURRENT (__FreeBSD_version == 400005) and later versions 
-have been assisted greatly by Glenn Johnson <gjohnson@nola.srrc.usda.gov>, 
-thanks a lot !
-He found a couple of troublesome in optimization using g77 at FreeBSD 4,
-then it is recommended to use f2c/cc.
---
-rmiya
diff --git a/biology/deft/pkg-plist b/biology/deft/pkg-plist
deleted file mode 100644
index c866751201e4..000000000000
--- a/biology/deft/pkg-plist
+++ /dev/null
@@ -1,110 +0,0 @@
-bin/DeFT.exec
-bin/DeFT
-share/DeFT/bases
-%%PORTDOCS%%share/doc/DeFT/README_Liability
-%%PORTDOCS%%share/doc/DeFT/input.dvi
-%%PORTDOCS%%share/doc/DeFT/input.ps
-%%PORTDOCS%%share/doc/DeFT/input.tex
-%%PORTDOCS%%share/doc/DeFT/install.dvi
-%%PORTDOCS%%share/doc/DeFT/install.ps
-%%PORTDOCS%%share/doc/DeFT/install.tex
-%%PORTDOCS%%share/examples/DeFT/1,3-difluorobenzene.dft
-%%PORTDOCS%%share/examples/DeFT/1,3-difluorobenzene.out
-%%PORTDOCS%%share/examples/DeFT/2-hydroxybicyclopentane.dft
-%%PORTDOCS%%share/examples/DeFT/2-hydroxybicyclopentane.out
-%%PORTDOCS%%share/examples/DeFT/README
-%%PORTDOCS%%share/examples/DeFT/acetone.dft
-%%PORTDOCS%%share/examples/DeFT/acetone.out
-%%PORTDOCS%%share/examples/DeFT/acetone_a.dft
-%%PORTDOCS%%share/examples/DeFT/acetone_a.out
-%%PORTDOCS%%share/examples/DeFT/acetone_b.dft
-%%PORTDOCS%%share/examples/DeFT/acetone_b.out
-%%PORTDOCS%%share/examples/DeFT/acetylene.dft
-%%PORTDOCS%%share/examples/DeFT/acetylene.out
-%%PORTDOCS%%share/examples/DeFT/allene.dft
-%%PORTDOCS%%share/examples/DeFT/allene.out
-%%PORTDOCS%%share/examples/DeFT/ammonia.dft
-%%PORTDOCS%%share/examples/DeFT/ammonia.out
-%%PORTDOCS%%share/examples/DeFT/benzaldehyde.dft
-%%PORTDOCS%%share/examples/DeFT/benzaldehyde.out
-%%PORTDOCS%%share/examples/DeFT/benzene.dft
-%%PORTDOCS%%share/examples/DeFT/benzene.out
-%%PORTDOCS%%share/examples/DeFT/bh4-.dft
-%%PORTDOCS%%share/examples/DeFT/bh4-.out
-%%PORTDOCS%%share/examples/DeFT/c_atom.dft
-%%PORTDOCS%%share/examples/DeFT/c_atom.out
-%%PORTDOCS%%share/examples/DeFT/ch2.dft
-%%PORTDOCS%%share/examples/DeFT/ch2.out
-%%PORTDOCS%%share/examples/DeFT/disilyl_ether.dft
-%%PORTDOCS%%share/examples/DeFT/disilyl_ether.out
-%%PORTDOCS%%share/examples/DeFT/ethane.dft
-%%PORTDOCS%%share/examples/DeFT/ethane.out
-%%PORTDOCS%%share/examples/DeFT/ethanol.dft
-%%PORTDOCS%%share/examples/DeFT/ethanol.out
-%%PORTDOCS%%share/examples/DeFT/ethylene_a.dft
-%%PORTDOCS%%share/examples/DeFT/ethylene_a.out
-%%PORTDOCS%%share/examples/DeFT/ethylene_b.dft
-%%PORTDOCS%%share/examples/DeFT/ethylene_b.out
-%%PORTDOCS%%share/examples/DeFT/f_atom.dft
-%%PORTDOCS%%share/examples/DeFT/f_atom.out
-%%PORTDOCS%%share/examples/DeFT/formaldehyde_a.dft
-%%PORTDOCS%%share/examples/DeFT/formaldehyde_a.out
-%%PORTDOCS%%share/examples/DeFT/formaldehyde_b.dft
-%%PORTDOCS%%share/examples/DeFT/formaldehyde_b.out
-%%PORTDOCS%%share/examples/DeFT/furan.dft
-%%PORTDOCS%%share/examples/DeFT/furan.out
-%%PORTDOCS%%share/examples/DeFT/hcn_a.dft
-%%PORTDOCS%%share/examples/DeFT/hcn_a.out
-%%PORTDOCS%%share/examples/DeFT/hcn_b.dft
-%%PORTDOCS%%share/examples/DeFT/hcn_b.out
-%%PORTDOCS%%share/examples/DeFT/hydroxide_a.dft
-%%PORTDOCS%%share/examples/DeFT/hydroxide_a.out
-%%PORTDOCS%%share/examples/DeFT/hydroxide_b.dft
-%%PORTDOCS%%share/examples/DeFT/hydroxide_b.out
-%%PORTDOCS%%share/examples/DeFT/hydroxide_c.dft
-%%PORTDOCS%%share/examples/DeFT/hydroxide_c.out
-%%PORTDOCS%%share/examples/DeFT/hydroxysulphane.dft
-%%PORTDOCS%%share/examples/DeFT/hydroxysulphane.out
-%%PORTDOCS%%share/examples/DeFT/malonaldehyde_a.dft
-%%PORTDOCS%%share/examples/DeFT/malonaldehyde_a.out
-%%PORTDOCS%%share/examples/DeFT/malonaldehyde_b.dft
-%%PORTDOCS%%share/examples/DeFT/malonaldehyde_b.out
-%%PORTDOCS%%share/examples/DeFT/malonaldehyde_c.dft
-%%PORTDOCS%%share/examples/DeFT/malonaldehyde_c.out
-%%PORTDOCS%%share/examples/DeFT/malonaldehyde_d.dft
-%%PORTDOCS%%share/examples/DeFT/malonaldehyde_d.out
-%%PORTDOCS%%share/examples/DeFT/malonaldehyde_e.dft
-%%PORTDOCS%%share/examples/DeFT/malonaldehyde_e.out
-%%PORTDOCS%%share/examples/DeFT/malonaldehyde_f.dft
-%%PORTDOCS%%share/examples/DeFT/malonaldehyde_f.out
-%%PORTDOCS%%share/examples/DeFT/malonaldehyde_g.dft
-%%PORTDOCS%%share/examples/DeFT/malonaldehyde_g.out
-%%PORTDOCS%%share/examples/DeFT/malonaldehyde_h.dft
-%%PORTDOCS%%share/examples/DeFT/malonaldehyde_h.out
-%%PORTDOCS%%share/examples/DeFT/malonaldehyde_i.dft
-%%PORTDOCS%%share/examples/DeFT/malonaldehyde_i.out
-%%PORTDOCS%%share/examples/DeFT/methanol.dft
-%%PORTDOCS%%share/examples/DeFT/methanol.out
-%%PORTDOCS%%share/examples/DeFT/methylamine.dft
-%%PORTDOCS%%share/examples/DeFT/methylamine.out
-%%PORTDOCS%%share/examples/DeFT/neopentane.dft
-%%PORTDOCS%%share/examples/DeFT/neopentane.out
-%%PORTDOCS%%share/examples/DeFT/nh4+.dft
-%%PORTDOCS%%share/examples/DeFT/nh4+.out
-%%PORTDOCS%%share/examples/DeFT/o2.dft
-%%PORTDOCS%%share/examples/DeFT/o2.out
-%%PORTDOCS%%share/examples/DeFT/peroxide_a.dft
-%%PORTDOCS%%share/examples/DeFT/peroxide_a.out
-%%PORTDOCS%%share/examples/DeFT/peroxide_b.dft
-%%PORTDOCS%%share/examples/DeFT/peroxide_b.out
-%%PORTDOCS%%share/examples/DeFT/peroxide_c.dft
-%%PORTDOCS%%share/examples/DeFT/peroxide_c.out
-%%PORTDOCS%%share/examples/DeFT/peroxide_d.dft
-%%PORTDOCS%%share/examples/DeFT/peroxide_d.out
-%%PORTDOCS%%share/examples/DeFT/peroxide_e.dft
-%%PORTDOCS%%share/examples/DeFT/peroxide_e.out
-%%PORTDOCS%%share/examples/DeFT/water.dft
-%%PORTDOCS%%share/examples/DeFT/water.out
-%%PORTDOCS%%@dirrm share/doc/DeFT
-%%PORTDOCS%%@dirrm share/examples/DeFT
-@dirrm share/DeFT
diff --git a/biology/flip/Makefile b/biology/flip/Makefile
deleted file mode 100644
index 84fda67243e7..000000000000
--- a/biology/flip/Makefile
+++ /dev/null
@@ -1,33 +0,0 @@
-# New ports collection makefile for:	flip
-# Date created:				26 February 2002
-# Whom:					Tony Maher <tonym@biolateral.com.au>
-#
-# $FreeBSD$
-#
-
-PORTNAME=	flip
-PORTVERSION=	2.0.2
-CATEGORIES=	biology
-MASTER_SITES=	ftp://megasun.bch.umontreal.ca/pub/flip/
-
-MAINTAINER=	tonymaher@optusnet.com.au
-COMMENT=	Flip is used to find/translate orfs
-
-DEPRECATED=	mastersite disappeared, no longer maintained by author
-EXPIRATION_DATE=	2005-12-31
-
-USE_REINPLACE=	yes
-
-MAN1=		flip.1
-PLIST_FILES=	bin/flip
-
-# make it respect CFLAGS
-
-post-configure:
-	@${REINPLACE_CMD} -e 's/CFLAGS=//' ${WRKSRC}/${MAKEFILE}
-
-do-install:
-	${INSTALL_PROGRAM} ${WRKSRC}/flip ${PREFIX}/bin
-	${INSTALL_MAN} ${WRKSRC}/${MAN1} ${PREFIX}/man/man1
-
-.include <bsd.port.mk>
diff --git a/biology/flip/distinfo b/biology/flip/distinfo
deleted file mode 100644
index 3eadb349103a..000000000000
--- a/biology/flip/distinfo
+++ /dev/null
@@ -1,2 +0,0 @@
-MD5 (flip-2.0.2.tar.gz) = a579fcb268ddf7ba39a5355ea73da0a6
-SIZE (flip-2.0.2.tar.gz) = 48440
diff --git a/biology/flip/pkg-descr b/biology/flip/pkg-descr
deleted file mode 100644
index 70a55439190c..000000000000
--- a/biology/flip/pkg-descr
+++ /dev/null
@@ -1,3 +0,0 @@
-Flip is used to find/translate orfs.
-
-WWW: ftp://megasun.bch.umontreal.ca/pub/flip/