Update MCSim to version 5.4.0

Changes are unknown, changelog is unavailable.

10 files changed, 110 insertions, 488 deletions

diff --git a/math/mcsim/Makefile b/math/mcsim/Makefile
index 0d0f1fceef1..3dc6f5b4631 100644
--- a/math/mcsim/Makefile
+++ b/math/mcsim/Makefile
@@ -1,33 +1,23 @@
-# $NetBSD: Makefile,v 1.19 2008/03/04 18:12:59 jlam Exp $
+# $NetBSD: Makefile,v 1.20 2011/05/09 20:59:10 asau Exp $
 
-DISTNAME=	mcsim-4.2.0
+DISTNAME=	mcsim-5.4.0
 CATEGORIES=	math
 MASTER_SITES=	${MASTER_SITE_GNU:=mcsim/}
 
 MAINTAINER=	pkgsrc-users@NetBSD.org
+HOMEPAGE=	http://www.gnu.org/software/mcsim
 COMMENT=	Monte Carlo Simulation software
 
 PKG_DESTDIR_SUPPORT=	user-destdir
 
+GNU_CONFIGURE=	yes
+USE_LIBTOOL=	yes
 USE_TOOLS+=	makeinfo
 INFO_FILES=	# PLIST
-WRKSRC=		${WRKDIR}/mcsim
 
-INSTALLATION_DIRS=	bin ${PKGINFODIR} share/doc/mcsim share/doc/html/mcsim
+REPLACE_SH=	sim/makemcsim.in sim/makemcsimd.in sim/makemcsims.in
 
-post-build:
-	cd ${WRKSRC}/doc && makeinfo mcsim.texinfo
-
-do-install:
-	${INSTALL_PROGRAM} ${WRKSRC}/mod/mod ${DESTDIR}${PREFIX}/bin
-	${INSTALL_PROGRAM} ${WRKSRC}/sim/mcsim ${DESTDIR}${PREFIX}/bin
-	${INSTALL_DATA} ${WRKSRC}/doc/*.txt ${WRKSRC}/doc/MCSim*	\
-		${WRKSRC}/doc/mcsim.dvi ${DESTDIR}${PREFIX}/share/doc/mcsim/
-	${INSTALL_DATA} ${WRKSRC}/doc/mcsim.html			\
-		${DESTDIR}${PREFIX}/share/doc/html/mcsim
-	cd ${WRKSRC}/doc; for f in mcsim mcsim-[0-9]*; do		\
-		${TEST} ! -f "$$f" ||					\
-		${INSTALL_DATA} "$$f" ${DESTDIR}${PREFIX}/${PKGINFODIR};\
-	done
+TEST_TARGET=	check
 
+.include "../../math/gsl/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/math/mcsim/PLIST b/math/mcsim/PLIST
index 21ab5c7feb0..d77c7fbac59 100644
--- a/math/mcsim/PLIST
+++ b/math/mcsim/PLIST
@@ -1,13 +1,85 @@
-@comment $NetBSD: PLIST,v 1.6 2009/06/14 18:05:45 joerg Exp $
-bin/mcsim
+@comment $NetBSD: PLIST,v 1.7 2011/05/09 20:59:10 asau Exp $
+bin/makemcsim
+bin/makemcsimd
+bin/makemcsims
 bin/mod
-info/mcsim
-share/doc/html/mcsim/mcsim.html
-share/doc/mcsim/About-Datasets.txt
-share/doc/mcsim/About-Doc.txt
-share/doc/mcsim/About-MCSim.txt
-share/doc/mcsim/MCSim-changelog
-share/doc/mcsim/MCSim-to-do
-share/doc/mcsim/Manual-Update.txt
-share/doc/mcsim/Programming-notes.txt
-share/doc/mcsim/mcsim.dvi
+include/config.h
+include/hungtype.h
+include/lex.h
+include/lexfn.h
+include/list.h
+include/matutil.h
+include/modelu.h
+include/modiface.h
+include/random.h
+include/sim.h
+include/yourcode.h
+info/mcsim.info
+lib/libmcsim.la
+lib/libmodelu.la
+share/mcsim/doc/mcsim.pdf
+share/mcsim/doc/mcsim.ps
+share/mcsim/mod/getopt.c
+share/mcsim/mod/getopt.h
+share/mcsim/mod/hungtype.h
+share/mcsim/mod/lex.c
+share/mcsim/mod/lex.h
+share/mcsim/mod/lexerr.c
+share/mcsim/mod/lexerr.h
+share/mcsim/mod/lexfn.c
+share/mcsim/mod/lexfn.h
+share/mcsim/mod/mod.c
+share/mcsim/mod/mod.h
+share/mcsim/mod/modd.c
+share/mcsim/mod/modd.h
+share/mcsim/mod/modi.c
+share/mcsim/mod/modi.h
+share/mcsim/mod/modiSBML.c
+share/mcsim/mod/modiSBML.h
+share/mcsim/mod/modiSBML2.c
+share/mcsim/mod/modiface.h
+share/mcsim/mod/modo.c
+share/mcsim/mod/modo.h
+share/mcsim/mod/strutil.c
+share/mcsim/mod/strutil.h
+share/mcsim/sim/getopt.c
+share/mcsim/sim/getopt.h
+share/mcsim/sim/hungtype.h
+share/mcsim/sim/lex.c
+share/mcsim/sim/lex.h
+share/mcsim/sim/lexerr.c
+share/mcsim/sim/lexerr.h
+share/mcsim/sim/lexfn.c
+share/mcsim/sim/lexfn.h
+share/mcsim/sim/list.c
+share/mcsim/sim/list.h
+share/mcsim/sim/lsodes.h
+share/mcsim/sim/lsodes1.c
+share/mcsim/sim/lsodes2.c
+share/mcsim/sim/matutil.c
+share/mcsim/sim/matutil.h
+share/mcsim/sim/matutilo.c
+share/mcsim/sim/matutilo.h
+share/mcsim/sim/mh.c
+share/mcsim/sim/mh.h
+share/mcsim/sim/modelu.c
+share/mcsim/sim/modelu.h
+share/mcsim/sim/modiface.h
+share/mcsim/sim/optdsign.c
+share/mcsim/sim/optdsign.h
+share/mcsim/sim/random.c
+share/mcsim/sim/random.h
+share/mcsim/sim/sim.c
+share/mcsim/sim/sim.h
+share/mcsim/sim/simi.c
+share/mcsim/sim/simi.h
+share/mcsim/sim/siminit.c
+share/mcsim/sim/siminit.h
+share/mcsim/sim/simmonte.c
+share/mcsim/sim/simmonte.h
+share/mcsim/sim/simo.c
+share/mcsim/sim/simo.h
+share/mcsim/sim/strutil.c
+share/mcsim/sim/strutil.h
+share/mcsim/sim/yourcode.c
+share/mcsim/sim/yourcode.h
diff --git a/math/mcsim/distinfo b/math/mcsim/distinfo
index 3a75254a1a6..305b7e5bef8 100644
--- a/math/mcsim/distinfo
+++ b/math/mcsim/distinfo
@@ -1,11 +1,6 @@
-$NetBSD: distinfo,v 1.3 2005/02/23 12:06:56 agc Exp $
+$NetBSD: distinfo,v 1.4 2011/05/09 20:59:10 asau Exp $
 
-SHA1 (mcsim-4.2.0.tar.gz) = 2ad29254cf40bb4ddadfc915e23e5d0eec90e2af
-RMD160 (mcsim-4.2.0.tar.gz) = 258884ed23500b1ee05c82012375595acf2e7e49
-Size (mcsim-4.2.0.tar.gz) = 521646 bytes
-SHA1 (patch-aa) = 993abbc45444214bf626eb2d41939860ae365e6c
-SHA1 (patch-ab) = 4d4d73af09fc96373c2255ff4a6a47bc3e556f27
-SHA1 (patch-ac) = a43fc2826a5b818579a536f5155b799001d180f8
-SHA1 (patch-ad) = 98e453e77d6b403464e3dfabfa84a4fa5992b3ad
-SHA1 (patch-ae) = 819a304489151e2f4c92f70e9425cd85da936daf
-SHA1 (patch-af) = cd2990081687b81e21af53379a8f682040ada0dd
+SHA1 (mcsim-5.4.0.tar.gz) = 63a9b9fd22869f49bb92dbbf5e90e8320571b8a1
+RMD160 (mcsim-5.4.0.tar.gz) = 7294cdac918fef2e0e52b4e0c226492af7423fd2
+Size (mcsim-5.4.0.tar.gz) = 1840057 bytes
+SHA1 (patch-Makefile.in) = 9d4e0a8b716d41a6e9c046909bc69ec8ff2a9749
diff --git a/math/mcsim/patches/patch-Makefile.in b/math/mcsim/patches/patch-Makefile.in
new file mode 100644
index 00000000000..43604d8f4b7
--- /dev/null
+++ b/math/mcsim/patches/patch-Makefile.in
@@ -0,0 +1,13 @@
+$NetBSD: patch-Makefile.in,v 1.1 2011/05/09 20:59:10 asau Exp $
+
+--- Makefile.in.orig	2011-01-29 15:52:31.000000000 +0000
++++ Makefile.in
+@@ -481,7 +481,7 @@ check-TESTS: $(TESTS)
+ 	    if test -f ./$$tst; then dir=./; \
+ 	    elif test -f $$tst; then dir=; \
+ 	    else dir="$(srcdir)/"; fi; \
+-	    if $(TESTS_ENVIRONMENT) $${dir}$$tst; then \
++	    if $(TESTS_ENVIRONMENT) $(SHELL) $${dir}$$tst; then \
+ 	      all=`expr $$all + 1`; \
+ 	      case " $(XFAIL_TESTS) " in \
+ 	      *[\ \	]$$tst[\ \	]*) \
diff --git a/math/mcsim/patches/patch-aa b/math/mcsim/patches/patch-aa
deleted file mode 100644
index ac1dbf1b05f..00000000000
--- a/math/mcsim/patches/patch-aa
+++ /dev/null
@@ -1,20 +0,0 @@
-$NetBSD: patch-aa,v 1.1.1.1 2000/11/26 23:02:38 jtb Exp $
-
---- doc/mcsim.texinfo.orig	Sat Nov 15 02:14:40 1997
-+++ doc/mcsim.texinfo
-@@ -1,10 +1,14 @@
- \input texinfo @c -*-texinfo-*-
- @comment %**start of header (This is for running Texinfo on a region.)
--@setfilename mcsimdoc
-+@setfilename mcsim
- @settitle MCSim User' Manual
- @setchapternewpage odd
- @comment %**end of header (This is for running Texinfo on a region.)
- 
-+@dircategory Monte Carlo Simulation
-+@direntry
-+* MCSim: (mcsim).		A Monte Carlo Simulation Program.
-+@end direntry
- 
- @comment  the following is just for the texinfo file
- @ifinfo
diff --git a/math/mcsim/patches/patch-ab b/math/mcsim/patches/patch-ab
deleted file mode 100644
index c6e521ffdfe..00000000000
--- a/math/mcsim/patches/patch-ab
+++ /dev/null
@@ -1,70 +0,0 @@
-$NetBSD: patch-ab,v 1.2 2001/02/25 22:14:20 jtb Exp $
-
---- mod/Makefile.orig	Thu Mar  6 16:14:37 1997
-+++ mod/Makefile
-@@ -77,16 +77,16 @@
- #		`realclean' removes other stuff not distributed
- #
- 
--
-+all:	mod
- 
- #---------- System Calls ----------
- #
- #>>>>  Define any system dependent calls here
- 
--ECHO = echo
--COPY = cp
--DEL = rm
--MKDIR = mkdir
-+ECHO ?= echo
-+COPY ?= cp
-+DEL ?= rm -f
-+MKDIR ?= mkdir
- ARC  = tar
- ARCFLAGS = cvf
- MOD = mod
-@@ -97,8 +97,8 @@
- #
- #>>>>  Define the COMPILER name and LINKER name here only.
- 
--CC = gcc
--LINK = gcc
-+#CC =
-+LINK = $(CC)
- 
- #>>>>  Define PATHS
- #	The include path should be a directory containing header
-@@ -137,27 +137,27 @@
- #>>>> To compile with OPTIMIZATION uncomment the following lines
- #
- DEBUG_SYMBOLS = -DNDEBUG
--C_OPTIM_FLAG = -O
-+C_OPTIM_FLAG =
- L_OPTIM_FLAG =
- 
- #
- #>>>> Include any special warning flags 
- #
--WARNINGS = -Wall
-+WARNINGS = -ansi
- 
- #--------------------
- #****  You shouldn't need to change these lines.  They are dependent
- #****  only on the above setup.
- 
--CFLAGS = $(C_OPTIM_FLAG) $(C_DEBUG_FLAG) $(DEBUG_SYMBOLS) \
-+CFLAGS += $(C_OPTIM_FLAG) $(C_DEBUG_FLAG) $(DEBUG_SYMBOLS) \
- 	-I $(INCPATH) $(WARNINGS) -DMODGEN
--CLFLAGS = $(L_OPTIM_FLAG) $(L_DEBUG_FLAG)
-+CLFLAGS += $(L_OPTIM_FLAG) $(L_DEBUG_FLAG)
- 
- 
- #
- #>>>> Extra link flags.  Include libraries here
- #
--LFLAGS = -lm
-+LFLAGS += -lm
- 
- 
- 
diff --git a/math/mcsim/patches/patch-ac b/math/mcsim/patches/patch-ac
deleted file mode 100644
index 94ea1a5f307..00000000000
--- a/math/mcsim/patches/patch-ac
+++ /dev/null
@@ -1,69 +0,0 @@
-$NetBSD: patch-ac,v 1.2 2001/02/25 22:14:20 jtb Exp $
-
---- sim/Makefile.orig	Fri Nov 14 15:45:53 1997
-+++ sim/Makefile
-@@ -46,14 +46,16 @@
- #       LFLAGS :  any flags specific to the linker.
- #
- 
-+all:	mcsim
-+
- #---------- System Calls ----------
- #
- #>>>>  Define any system dependent calls here
- 
--ECHO = echo
--COPY = cp
--DEL = rm
--MKDIR = mkdir
-+ECHO ?= echo
-+COPY ?= cp
-+DEL ?= rm
-+MKDIR ?= mkdir
- MOD = mod
- 
- 
-@@ -62,8 +64,8 @@
- #
- #>>>>  Define the COMPILER name and LINKER name here only.
- 
--CC = gcc
--LINK = gcc
-+#CC = gcc
-+LINK = $(CC)
- 
- #>>>>  Define PATHS
- #	The include path should be a directory containing header
-@@ -101,27 +103,27 @@
- #>>>> To compile with OPTIMIZATION uncomment the following lines
- #
- DEBUG_SYMBOLS = -DNDEBUG
--C_OPTIM_FLAG = -O
-+C_OPTIM_FLAG =
- L_OPTIM_FLAG =
- 
- #
- #>>>> Include any special warning flags 
- #
--WARNINGS = -Wall -ansi
-+WARNINGS = -ansi
- 
- #--------------------
- #****  You shouldn't need to change the next 2 lines.  They are dependent
- #****  only on the above setup.
- 
--CFLAGS = $(C_OPTIM_FLAG) $(C_DEBUG_FLAG) $(DEBUG_SYMBOLS) \
-+CFLAGS += $(C_OPTIM_FLAG) $(C_DEBUG_FLAG) $(DEBUG_SYMBOLS) \
- 	-I $(INCPATH) $(WARNINGS)
--CLFLAGS = $(L_OPTIM_FLAG) $(L_DEBUG_FLAG)
-+CLFLAGS += $(L_OPTIM_FLAG) $(L_DEBUG_FLAG)
- 
- 
- #
- #>>>> Extra link flags.  Include libraries here
- #
--LFLAGS = -lm
-+LFLAGS += -lm
- 
- 
- 
diff --git a/math/mcsim/patches/patch-ad b/math/mcsim/patches/patch-ad
deleted file mode 100644
index 57462315c28..00000000000
--- a/math/mcsim/patches/patch-ad
+++ /dev/null
@@ -1,22 +0,0 @@
-$NetBSD: patch-ad,v 1.2 2001/02/25 22:14:20 jtb Exp $
-
---- sim/sim.c.orig	Wed Nov 22 22:45:45 2000
-+++ sim/sim.c
-@@ -653,7 +653,7 @@
-   scanf ("%[^:\f\r\v\n]", *pszFileIn);
-   getchar();
- #else
--  gets (*pszFileIn);
-+  fgets (*pszFileIn, sizeof(*pszFileIn), stdin);
-   *pszFileIn = strtok (*pszFileIn, " \t");
- #endif
- 
-@@ -665,7 +665,7 @@
- #ifdef _MACOSLEVEL1_
-     scanf ("%[^:\f\r\v\n]", *pszFileOut);
- #else
--    gets (*pszFileOut);
-+    fgets (*pszFileOut, sizeof(*pszFileOut), stdin);
-     *pszFileOut = strtok (*pszFileOut, " \t");
- #endif
-   }
diff --git a/math/mcsim/patches/patch-ae b/math/mcsim/patches/patch-ae
deleted file mode 100644
index 8aa82a6ce26..00000000000
--- a/math/mcsim/patches/patch-ae
+++ /dev/null
@@ -1,259 +0,0 @@
-$NetBSD: patch-ae,v 1.1.1.1 2000/11/26 23:02:41 jtb Exp $
-
---- sim/Test_mcsim.orig	Fri Nov 14 15:45:56 1997
-+++ sim/Test_mcsim
-@@ -1,147 +1,147 @@
- # Run diagnostic tests on several features of the program.
- # results are compared to prepared files.
--one:	
--	@echo
--	@echo ----------
--	@echo
--	@echo '* Testing MCSim: this could take a few minutes.'
--	@echo '* Creating logfile mcsim.log'
--	@touch mcsim.log
--	@date >> mcsim.log
--#
--	@echo
--	@echo ----------
--	@echo
--	@echo Testing with the tetrachloroethylene model
--	@mod perc.model
--	@gcc -I . -Wall -ansi -c model.c -o model.o  > /dev/null
--	@gcc -o mcsim *.o -lm
--	@echo
-+#one:	
-+	echo
-+	echo ----------
-+	echo
-+	echo '* Testing MCSim: this could take a few minutes.'
-+	echo '* Creating logfile mcsim.log'
-+	touch mcsim.log
-+	date >> mcsim.log
-+#
-+	echo
-+	echo ----------
-+	echo
-+	echo Testing with the tetrachloroethylene model
-+	../mod/mod perc.model
-+	cc -I . -Wall -ansi -c model.c -o model.o  > /dev/null
-+	cc -o mcsim *.o -lm
-+	echo
- #
- # perc.lsodes.in    
--	@echo Testing Lsodes with perc.lsodes.in ...
--	@chmod -w perc.lsodes.in perc.lsodes.out 
--	@mcsim perc.lsodes.in sim.out >> mcsim.log
--	@(diff sim.out perc.lsodes.out > .tmp) && echo '-PASSED-'
-+	echo Testing Lsodes with perc.lsodes.in ...
-+	chmod -w perc.lsodes.in perc.lsodes.out 
-+	./mcsim perc.lsodes.in sim.out >> mcsim.log
-+	(diff sim.out perc.lsodes.out > .tmp) && echo '-PASSED-'
- #
- # perc.ndoses.in
--	@echo Testing NDoses with perc.ndoses.in ...
--	@chmod -w perc.ndoses.in perc.ndoses.out 
--	@mcsim perc.ndoses.in sim.out >> mcsim.log
--	@(diff sim.out perc.ndoses.out > .tmp) && echo '-PASSED-'
-+	echo Testing NDoses with perc.ndoses.in ...
-+	chmod -w perc.ndoses.in perc.ndoses.out 
-+	./mcsim perc.ndoses.in sim.out >> mcsim.log
-+	(diff sim.out perc.ndoses.out > .tmp) && echo '-PASSED-'
- #
- # perc.mtc.in
--	@echo Testing Monte Carlo with perc.mtc.in ...
--	@chmod -w perc.mtc.in perc.mtc.out 
--	@mcsim perc.mtc.in sim.out >> mcsim.log
--	@(diff sim.out perc.mtc.out > .tmp) && echo '-PASSED-'
-+	echo Testing Monte Carlo with perc.mtc.in ...
-+	chmod -w perc.mtc.in perc.mtc.out 
-+	./mcsim perc.mtc.in sim.out >> mcsim.log
-+	(diff sim.out perc.mtc.out > .tmp) && echo '-PASSED-'
- #
- # perc.setpoint.in
--	@echo Testing Set Point run with perc.setpoint.in ...
--	@chmod -w perc.setpoint.dat perc.setpoint.in perc.setpoint.out 
--	@mcsim perc.setpoint.in sim.out >> mcsim.log
--	@(diff sim.out perc.setpoint.out > .tmp) && echo '-PASSED-'
--#
--	@echo
--	@echo ----------
--	@echo
--	@echo Testing with the 1 compartment model
--	@mod 1cpt.model
--	@gcc -I . -Wall -ansi -c model.c -o model.o  > /dev/null
--	@gcc -o mcsim *.o -lm
--	@echo
-+	echo Testing Set Point run with perc.setpoint.in ...
-+	chmod -w perc.setpoint.dat perc.setpoint.in perc.setpoint.out 
-+	./mcsim perc.setpoint.in sim.out >> mcsim.log
-+	(diff sim.out perc.setpoint.out > .tmp) && echo '-PASSED-'
-+#
-+	echo
-+	echo ----------
-+	echo
-+	echo Testing with the 1 compartment model
-+	../mod/mod 1cpt.model
-+	cc -I . -Wall -ansi -c model.c -o model.o  > /dev/null
-+	cc -o mcsim *.o -lm
-+	echo
- #
- # 1cpt_no_noise.in
--	@echo Testing Lsodes non random output with 1cpt_no_noise.in ...
--	@chmod -w 1cpt_no_noise.in 1cpt_no_noise.out
--	@mcsim 1cpt_no_noise.in sim.out >> mcsim.log
--	@(diff sim.out 1cpt_no_noise.out > .tmp) && echo '-PASSED-'
-+	echo Testing Lsodes non random output with 1cpt_no_noise.in ...
-+	chmod -w 1cpt_no_noise.in 1cpt_no_noise.out
-+	./mcsim 1cpt_no_noise.in sim.out >> mcsim.log
-+	(diff sim.out 1cpt_no_noise.out > .tmp) && echo '-PASSED-'
- #
- # 1cpt_w._noise.in
--	@echo Testing Lsodes randomized output with 1cpt_w._noise.in ...
--	@chmod -w 1cpt_w._noise.in 1cpt_w._noise.out
--	@mcsim 1cpt_w._noise.in sim.out >> mcsim.log
--	@(diff sim.out 1cpt_w._noise.out > .tmp) && echo '-PASSED-'
-+	echo Testing Lsodes randomized output with 1cpt_w._noise.in ...
-+	chmod -w 1cpt_w._noise.in 1cpt_w._noise.out
-+	./mcsim 1cpt_w._noise.in sim.out >> mcsim.log
-+	(diff sim.out 1cpt_w._noise.out > .tmp) && echo '-PASSED-'
- #
- # 1cpt.MCMC1.in
--	@echo Testing MCMC set uncertainties with 1cpt.MCMC1.in ...
--	@chmod -w 1cpt.MCMC1.in 1cpt.MCMC1.out
--	@mcsim 1cpt.MCMC1.in sim.out >> mcsim.log
--	@(diff sim.out 1cpt.MCMC1.out > .tmp) && echo '-PASSED-'
-+	echo Testing MCMC set uncertainties with 1cpt.MCMC1.in ...
-+	chmod -w 1cpt.MCMC1.in 1cpt.MCMC1.out
-+	./mcsim 1cpt.MCMC1.in sim.out >> mcsim.log
-+	(diff sim.out 1cpt.MCMC1.out > .tmp) && echo '-PASSED-'
- #
- # 1cpt.MCMC2.in
--	@echo Testing MCMC estimated uncertainties with 1cpt.MCMC2.in ...
--	@chmod -w 1cpt.MCMC2.in 1cpt.MCMC2.out
--	@mcsim 1cpt.MCMC2.in sim.out >> mcsim.log
--	@(diff sim.out 1cpt.MCMC2.out > .tmp) && echo '-PASSED-'
-+	echo Testing MCMC estimated uncertainties with 1cpt.MCMC2.in ...
-+	chmod -w 1cpt.MCMC2.in 1cpt.MCMC2.out
-+	./mcsim 1cpt.MCMC2.in sim.out >> mcsim.log
-+	(diff sim.out 1cpt.MCMC2.out > .tmp) && echo '-PASSED-'
- #
- # 1cpt.MCMC3.in
--	@echo Testing MCMC print every 2 iterations with 1cpt.MCMC3.in ...
--	@chmod -w 1cpt.MCMC3.in 1cpt.MCMC3.out
--	@mcsim 1cpt.MCMC3.in sim.out >> mcsim.log
--	@(diff sim.out 1cpt.MCMC3.out > .tmp) && echo '-PASSED-'
-+	echo Testing MCMC print every 2 iterations with 1cpt.MCMC3.in ...
-+	chmod -w 1cpt.MCMC3.in 1cpt.MCMC3.out
-+	./mcsim 1cpt.MCMC3.in sim.out >> mcsim.log
-+	(diff sim.out 1cpt.MCMC3.out > .tmp) && echo '-PASSED-'
- #
- # 1cpt.MCMC4.in
--	@echo Testing MCMC estimated bounds on F with 1cpt.MCMC4.in ...
--	@chmod -w 1cpt.MCMC4.in 1cpt.MCMC4.out
--	@mcsim 1cpt.MCMC4.in sim.out >> mcsim.log
--	@(diff sim.out 1cpt.MCMC4.out > .tmp) && echo '-PASSED-'
-+	echo Testing MCMC estimated bounds on F with 1cpt.MCMC4.in ...
-+	chmod -w 1cpt.MCMC4.in 1cpt.MCMC4.out
-+	./mcsim 1cpt.MCMC4.in sim.out >> mcsim.log
-+	(diff sim.out 1cpt.MCMC4.out > .tmp) && echo '-PASSED-'
- #
- # 1cpt.MCMC5.in
--	@echo Testing MCMC model-computed SDs with 1cpt.MCMC5.in ...
--	@chmod -w 1cpt.MCMC5.in 1cpt.MCMC5.out
--	@mcsim 1cpt.MCMC5.in sim.out >> mcsim.log
--	@(diff sim.out 1cpt.MCMC5.out > .tmp) && echo '-PASSED-'
--#
--	@echo
--	@echo ----------
--	@echo
--	@echo Testing with the linear model
--	@mod linear.model
--	@gcc -I . -Wall -ansi -c model.c -o model.o  > /dev/null
--	@gcc -o mcsim *.o -lm
--	@echo
-+	echo Testing MCMC model-computed SDs with 1cpt.MCMC5.in ...
-+	chmod -w 1cpt.MCMC5.in 1cpt.MCMC5.out
-+	./mcsim 1cpt.MCMC5.in sim.out >> mcsim.log
-+	(diff sim.out 1cpt.MCMC5.out > .tmp) && echo '-PASSED-'
-+#
-+	echo
-+	echo ----------
-+	echo
-+	echo Testing with the linear model
-+	../mod/mod linear.model
-+	cc -I . -Wall -ansi -c model.c -o model.o  > /dev/null
-+	cc -o mcsim *.o -lm
-+	echo
- #
- # linear.in
--	@echo Testing Lsodes with linear.in ...
--	@chmod -w linear.in linear.out 
--	@mcsim linear.in sim.out >> mcsim.log
--	@(diff sim.out linear.out > .tmp) && echo '-PASSED-'
-+	echo Testing Lsodes with linear.in ...
-+	chmod -w linear.in linear.out 
-+	./mcsim linear.in sim.out >> mcsim.log
-+	(diff sim.out linear.out > .tmp) && echo '-PASSED-'
- #
- # linear.MCMC1.in
--	@echo Testing MCMC 1 experiment with linear.MCMC1.in ...
--	@chmod -w linear.MCMC1.in linear.MCMC1.out 
--	@mcsim linear.MCMC1.in sim.out >> mcsim.log
--	@(diff sim.out linear.MCMC1.out > .tmp) && echo '-PASSED-'
-+	echo Testing MCMC 1 experiment with linear.MCMC1.in ...
-+	chmod -w linear.MCMC1.in linear.MCMC1.out 
-+	./mcsim linear.MCMC1.in sim.out >> mcsim.log
-+	(diff sim.out linear.MCMC1.out > .tmp) && echo '-PASSED-'
- #
- # linear.MCMC2.in
--	@echo Testing MCMC 1 repeated experiment with linear.MCMC2.in ...
--	@chmod -w linear.MCMC2.in linear.MCMC2.out 
--	@mcsim linear.MCMC2.in sim.out >> mcsim.log
--	@(diff sim.out linear.MCMC2.out > .tmp) && echo '-PASSED-'
-+	echo Testing MCMC 1 repeated experiment with linear.MCMC2.in ...
-+	chmod -w linear.MCMC2.in linear.MCMC2.out 
-+	./mcsim linear.MCMC2.in sim.out >> mcsim.log
-+	(diff sim.out linear.MCMC2.out > .tmp) && echo '-PASSED-'
- #
- # linear.H.MCMC1.in
--	@echo Testing MCMC hierarchical linear model, 10 exps with \
-+	echo Testing MCMC hierarchical linear model, 10 exps with \
-          linear.H.MCMC1.in ...
--	@chmod -w linear.H.MCMC1.in linear.H.MCMC1.out 
--	@mcsim linear.H.MCMC1.in sim.out >> mcsim.log
--	@(diff sim.out linear.H.MCMC1.out > .tmp) && echo '-PASSED-'
-+	chmod -w linear.H.MCMC1.in linear.H.MCMC1.out 
-+	./mcsim linear.H.MCMC1.in sim.out >> mcsim.log
-+	(diff sim.out linear.H.MCMC1.out > .tmp) && echo '-PASSED-'
- #
- # linear.H.MCMC2.in
--	@echo Testing MCMC hierarchical linear model, B1.1 set with \
-+	echo Testing MCMC hierarchical linear model, B1.1 set with \
-          linear.H.MCMC2.in
--	@chmod -w linear.H.MCMC2.in linear.H.MCMC2.out 
--	@mcsim linear.H.MCMC2.in sim.out >> mcsim.log
--	@(diff sim.out linear.H.MCMC2.out > .tmp) && echo '-PASSED-'
-+	chmod -w linear.H.MCMC2.in linear.H.MCMC2.out 
-+	./mcsim linear.H.MCMC2.in sim.out >> mcsim.log
-+	(diff sim.out linear.H.MCMC2.out > .tmp) && echo '-PASSED-'
- #
- # linear.H.MCMC3.in
--	@echo Testing MCMC hierarchical model, restart file with \
-+	echo Testing MCMC hierarchical model, restart file with \
-          linear.H.MCMC3.in
--	@chmod -w linear.H.MCMC3.in linear.H.MCMC3.out 
--	@mcsim linear.H.MCMC3.in sim.out >> mcsim.log
--	@(diff sim.out linear.H.MCMC3.out > .tmp) && echo '-PASSED-'
--#
--	@echo
--	@echo Hourra!
--	@echo MCSim passed all tests.
-+	chmod -w linear.H.MCMC3.in linear.H.MCMC3.out 
-+	./mcsim linear.H.MCMC3.in sim.out >> mcsim.log
-+	(diff sim.out linear.H.MCMC3.out > .tmp) && echo '-PASSED-'
-+#
-+	echo
-+	echo Hourra!
-+	echo MCSim passed all tests.
- 
diff --git a/math/mcsim/patches/patch-af b/math/mcsim/patches/patch-af
deleted file mode 100644
index 24b0bb50ebb..00000000000
--- a/math/mcsim/patches/patch-af
+++ /dev/null
@@ -1,8 +0,0 @@
-$NetBSD: patch-af,v 1.1 2001/02/25 22:14:20 jtb Exp $
-
---- /dev/null	Sun Feb 25 21:54:22 2001
-+++ Makefile
-@@ -0,0 +1,3 @@
-+SUBDIR = mod sim
-+
-+.include <bsd.subdir.mk>