10 files changed, 0 insertions, 256 deletions
diff --git a/biology/nab/files/config.h b/biology/nab/files/config.h
deleted file mode 100644
index a3e4889166b3..000000000000
--- a/biology/nab/files/config.h
+++ /dev/null
@@ -1,74 +0,0 @@
-#  NAB configuration file, created with: ./configure -p4 -static gcc
-
-###############################################################################
-
-# (1)  You need to define the symbol NABHOME in your environment
-
-#    NABHOME should be an absolute path to the top-level NAB directory;
-#    files are installed to the following directories:
-
-BINDIR=$(NABHOME)/bin
-LIBDIR=$(NABHOME)/lib
-INCDIR=$(NABHOME)/include
-
-###############################################################################
-
-
-#  (2) If you want to search additional libraries by default, add them
-#      to the FLIBS variable here.  (External libraries can also be linked into
-#      NAB programs simply by including them on the command line; libraries
-#      included in FLIBS are always searched.)
-
-FLIBS= $(LIBDIR)/libsym.a $(LIBDIR)/lapack.a $(LIBDIR)/blas.a $(LIBDIR)/f2c.a -static   
-
-###############################################################################
-
-#  (3)  Modify any of the following if you need to change, e.g. to use gcc
-#        rather than cc, etc.
-
-SHELL=/bin/sh
-
-#  Set the C compiler, etc. 
-
-#          For GNU:  CC-->gcc; LEX-->flex; YACC-->bison -y -t;
-#          Note: If your lexer is "really" flex, you need to set
-#          LEX=flex below.  For example, on many linux distributions,
-#          /usr/bin/lex is really just a pointer to /usr/bin/flex,
-#          so LEX=flex is necessary.  In general, gcc seems to need
-#          flex.
-
-NABFLAGS=
-
-LEX=    flex
-YACC=   yacc
-AR=     ar
-RANLIB= ranlib
-
-#  Set the C-preprocessor.  Code for a small preprocessor is in
-#    uccp-1.3;  it gets installed as $(NABHOME)/bin/ucpp;
-#    this can generally be used (maybe not on 64-bit machines like altix).
-
-CPP=    /usr/local/bin/ucpp -l
-
-#  If you are going to link in Fortran routines, you need
-#  to set the compiler information here.  (Also, add the appropriate entries
-#  to the FLIBS variable, above.)
-#
-#FC=f77
-#FFLAGS?=$(FFLAGS)
-#FOPTFLAGS?=$(FFLAGS)
-FREEFORMAT_FLAG=-ffree-form
-
-#  These variables control whether we will use compiled versions of BLAS
-#  and LAPACK (which are generally slower), or whether those libraries are
-#  already available (presumably in an optimized form).
-
-LAPACK=install
-BLAS=install
-F2C=install
-UCPP=
-
-#  For Windows/cygwin, set SFX to ".exe"; for Unix/Linux leave it empty:
-
-SFX=
-
diff --git a/biology/nab/files/patch-Makefile b/biology/nab/files/patch-Makefile
deleted file mode 100644
index 3fe19a6cd21f..000000000000
--- a/biology/nab/files/patch-Makefile
+++ /dev/null
@@ -1,70 +0,0 @@
---- Makefile.orig	Mon Aug 21 11:16:05 2006
-+++ Makefile	Fri Dec 15 16:06:57 2006
-@@ -2,31 +2,32 @@
- 
- include config.h
- 
-+all: install
-+
- install:
- 	-mkdir $(BINDIR) $(LIBDIR) $(INCDIR)
--	(cd ucpp-1.3; make $(UCPP) )
--	(cd byacc; make install )
--
--#   here are the Fortran versions:
--#	(cd lapack; make $(LAPACK) )
--#	(cd blas; make $(BLAS) )
--
--#   here are the C versions:
--	(cd clapack; make $(LAPACK) )
--	(cd cblas; make $(BLAS) )
--	(cd f2c;  make $(F2C)  )
--
--	(cd cifparse; make install )
--	(cd src; make install )
--	(cd nss; make install )
--	(cd tleap; make install )
-+	(cd clapack; env NABHOME=.. make $(LAPACK) )
-+	(cd cblas; env NABHOME=.. make $(BLAS) )
-+	(cd f2c; env NABHOME=.. make $(F2C) )
-+	(cd cifparse; env NABHOME=.. make install )
-+	(cd src; env NABHOME=.. make install )
-+	(cd nss; env NABHOME=.. make install )
-+	(cd tleap; env NABHOME=.. make install )
-+#	(cd peptide && \
-+#		env NABHOME=.. ../bin/nab $(CFLAGS) -o peptide peptide.nab )
-+#	cp -p peptide/README doc/README-peptide
-+#	mv peptide/peptide bin
-+#	@echo
-+#	@echo "Ignore conflicting types warnings"
-+#	@echo
-+#	(cd suppose; env NABHOME=.. make all )
-+#	cp -p suppose/suppose.1 doc
-+#	mv suppose/suppose suppose/PCA_suppose bin
- 	@echo
--	@echo "completed installation of NAB version 5"
-+	@echo "completed installation of NAB version 5.1"
- 	@echo
- 
- clean:
--	(cd ucpp-1.3; make clean )
--	(cd byacc; make clean )
- 	(cd cifparse; make clean )
- 	(cd src; make clean )
- 	(cd nss; make clean )
-@@ -34,10 +35,12 @@
- 	(cd cblas; make clean )
- 	(cd clapack; make clean )
- 	(cd f2c; make clean )
--	
-+	(cd suppose; make clean )
-+	(cd peptide && rm -f peptide.c peptide )
-+
- #   note:  "make test" needs to follow "make", since it is very hard to
- #          tell if the compiler is completely "made" or not.
- 
- test::
--	(cd test; make test)
--	(cd nss; make test)
-+	(cd test; env NABHOME=.. make test)
-+	(cd nss; env NABHOME=.. make test)
diff --git a/biology/nab/files/patch-configure b/biology/nab/files/patch-configure
deleted file mode 100644
index 412974c8fcfa..000000000000
--- a/biology/nab/files/patch-configure
+++ /dev/null
@@ -1,11 +0,0 @@
---- configure.orig	Mon Aug 21 11:18:10 2006
-+++ configure	Fri Aug 25 22:30:10 2006
-@@ -61,7 +61,7 @@
- p4='no'
- gotolib='no'
- compiler='gcc'
--processor=`/bin/uname -p`
-+processor=`/usr/bin/uname -p`
- static='no'
- 
- while [ $# -gt 0 ]; do
diff --git a/biology/nab/files/patch-reslib:conf.lib b/biology/nab/files/patch-reslib:conf.lib
deleted file mode 100644
index 088afbf29321..000000000000
--- a/biology/nab/files/patch-reslib:conf.lib
+++ /dev/null
@@ -1,14 +0,0 @@
-*** reslib/conf.lib.orig	Wed Mar 10 19:00:11 1999
---- reslib/conf.lib	Tue Dec 23 15:34:07 2003
-***************
-*** 13,18 ****
---- 13,21 ----
-  PI 1 		pi helix
-  phi    -57.0 psi    -70.0 omega  180.0
-  
-+ PPII 1 		polyproline II helix
-+ phi    -75.0 psi    145.0 omega  180.0
-+ 
-  EXTENDED 1 	extended  conformation
-  phi    180.0 psi    180.0 omega  180.0
-  
diff --git a/biology/nab/files/patch-src:wc_helix.nab b/biology/nab/files/patch-src:wc_helix.nab
deleted file mode 100644
index 960c76b2341e..000000000000
--- a/biology/nab/files/patch-src:wc_helix.nab
+++ /dev/null
@@ -1,11 +0,0 @@
---- src/wc_helix.nab.orig	Thu Apr  7 20:17:27 2005
-+++ src/wc_helix.nab	Fri Sep 15 09:22:13 2006
-@@ -25,6 +25,8 @@
- 
- 	loup["g"] = "G"; loup["a"] = "A";
- 	loup["t"] = "T"; loup["c"] = "C";
-+	loup["G"] = "G"; loup["A"] = "A";
-+	loup["T"] = "T"; loup["C"] = "C";
- 
- 	has_s = 1; has_a = 1;
- 	if( sreslib == "" ) sreslib_use = "all_nucleic94.lib";
diff --git a/biology/nab/files/patch-src_Makefile b/biology/nab/files/patch-src_Makefile
deleted file mode 100644
index 70f7c1b799f1..000000000000
--- a/biology/nab/files/patch-src_Makefile
+++ /dev/null
@@ -1,17 +0,0 @@
---- src/Makefile.orig	Fri Aug 11 17:38:10 2006
-+++ src/Makefile	Fri Dec 15 17:01:39 2006
-@@ -189,6 +189,14 @@
- 	cp defreal.h $(INCDIR)
- 	cp nab.h $(INCDIR)
- 
-+beforerealinstall:
-+	$(CC) -DBINDIR='"$(PREFIX)/bin"' \
-+		-DINCDIR='"$(PREFIX)/include"' \
-+		-DLIBDIR='"$(PREFIX)/share/nab/lib"' \
-+		$(CFLAGS) -DCC='"$(CC)"' -DCPP='"$(CPP)"' \
-+		-DFLIBS='"$(PREFIX)/share/nab/lib/libsym.a $(PREFIX)/share/nab/lib/lapack.a $(PREFIX)/share/nab/lib/blas.a $(PREFIX)/share/nab/lib/f2c.a"' \
-+		-static -o ../bin/nab${SFX} nab.c
-+
- uninstall: clean
- 	-rm -f \
-         $(BINDIR)/nab2c$(SFX) $(BINDIR)/nab$(SFX) $(INCDIR)/nabcode.h \
diff --git a/biology/nab/files/patch-src_cgen.c b/biology/nab/files/patch-src_cgen.c
deleted file mode 100644
index c6538200406e..000000000000
--- a/biology/nab/files/patch-src_cgen.c
+++ /dev/null
@@ -1,21 +0,0 @@
---- src/cgen.c.orig	Thu Apr  7 20:17:27 2005
-+++ src/cgen.c	Sun Apr 17 20:21:22 2005
-@@ -102,6 +102,7 @@
- void	CG_genpids( NODE_T * );
- void	CG_genpdecl( NODE_T * );
- char	*CG_gentemp( int );
-+void	CG_gennull( void );
- 
- static	int	getdims( NODE_T *, int, int, int *, NODE_T *[] );
- static	NODE_T	*mk_arraysize( int, NODE_T *[], int );
-@@ -115,6 +116,10 @@
- static	void	CG_debug( char [], NODE_T *, int );
- 
- FILE	*tmpfile();
-+
-+void	CG_gennull( )
-+{
-+}
- 
- int	CG_init( char cfname[], int aopt )
- {
diff --git a/biology/nab/files/patch-src_nabgrm.y b/biology/nab/files/patch-src_nabgrm.y
deleted file mode 100644
index 348e3a157d8b..000000000000
--- a/biology/nab/files/patch-src_nabgrm.y
+++ /dev/null
@@ -1,20 +0,0 @@
---- src/nabgrm.y.orig	Thu Apr  7 20:17:27 2005
-+++ src/nabgrm.y	Sun Apr 17 20:21:36 2005
-@@ -41,6 +41,8 @@
- 
- # define YYSTYPE_IS_DECLARED 1
- 
-+#define YYSTYPE_IS_DECLARED 1
-+
- %}
- 
- %token	<ival>	SYM_ADDRESS
-@@ -299,7 +301,7 @@
- 		  f_stmtpart SYM_RBRACE
- 				{ CG_genestmts( TRUE );
- 				  CG_genop( NULL, SYM_RBRACE ); }
--		  SYM_SEMICOLON ;
-+		  SYM_SEMICOLON { CG_gennull ( ); } ;
- f_defpart	: lv_decls 
- 		| 		{ $$ = NULL; } ;
- lv_decls	: var_decl
diff --git a/biology/nab/files/patch-suppose_Makefile b/biology/nab/files/patch-suppose_Makefile
deleted file mode 100644
index 9317b951a30c..000000000000
--- a/biology/nab/files/patch-suppose_Makefile
+++ /dev/null
@@ -1,10 +0,0 @@
---- suppose/Makefile.orig	Thu Apr  7 20:18:34 2005
-+++ suppose/Makefile	Sat Aug 26 08:49:50 2006
-@@ -1,5 +1,7 @@
- include ../config.h
- 
-+all: suppose$(SFX) PCA_suppose$(SFX)
-+
- suppose$(SFX): suppose.nab
- 	nab -o suppose$(SFX) suppose.nab
- 
diff --git a/biology/nab/files/pkg-message.in b/biology/nab/files/pkg-message.in
deleted file mode 100644
index e89f4516b02e..000000000000
--- a/biology/nab/files/pkg-message.in
+++ /dev/null
@@ -1,8 +0,0 @@
--------------------------------------------------------------------------------
-You must set the environment variable NABHOME to
-
-  %%DATADIR%%
-
-before nab is used. This is needed so that nab can find its residue and
-structure databases.
--------------------------------------------------------------------------------