Update to v2.0.0 and patch for clang.

PR:		ports/183454
Submitted by:	Jason Bacon <jwbacon (at) tds.net> (maintainer)

7 files changed, 86 insertions, 124 deletions

diff --git a/science/nifticlib/Makefile b/science/nifticlib/Makefile
index 02ebc5a..bbc3af2 100644
--- a/science/nifticlib/Makefile
+++ b/science/nifticlib/Makefile
@@ -1,28 +1,27 @@
-# Created by: Jason Bacon <bacon@smithers.neuro.mcw.edu>
+# Created by: Jason W. Bacon <jwbacon@tds.net>
 # $FreeBSD$
 
 PORTNAME=	nifticlib
-PORTVERSION=	1.1.0
+PORTVERSION=	2.0.0
 CATEGORIES=	science graphics
-MASTER_SITES=	SF/niftilib/${PORTNAME}/${PORTNAME}-${PORTVERSION}
+MASTER_SITES=	SF/niftilib/nifticlib/nifticlib_2_0_0
 
 MAINTAINER=	jwbacon@tds.net
 COMMENT=	Neuroimaging Informatics Technology Initiative data format
 
-USES=		gmake
+# LICENSE=	public domain
 
-MAN1=		nifticlib.1
+USES=		gmake
+MAKE_JOBS_UNSAFE=yes
 
-NO_STAGE=	yes
-post-patch:
-	@${REINPLACE_CMD} -e 's/include depend.mk/-&/' \
-		${WRKSRC}/fsliolib/Makefile ${WRKSRC}/nifticdf/Makefile \
-		${WRKSRC}/niftilib/Makefile ${WRKSRC}/znzlib/Makefile
+# AFNI currently has nifti embedded in the distfile and installs the
+# nifti bins by itself.
+CONFLICTS=	afni-[0-9]* dbh-[0-9]*
 
 do-install:
-	${INSTALL_PROGRAM} ${WRKSRC}/bin/* ${PREFIX}/bin
-	${INSTALL_DATA} ${WRKSRC}/lib/* ${PREFIX}/lib
-	${INSTALL_DATA} ${WRKSRC}/include/* ${PREFIX}/include
-	${INSTALL_MAN} ${FILESDIR}/nifticlib.1 ${MANPREFIX}/man/man1
+	${INSTALL_PROGRAM} ${WRKSRC}/bin/* ${STAGEDIR}${PREFIX}/bin
+	${INSTALL_DATA} ${WRKSRC}/lib/*.a ${STAGEDIR}${PREFIX}/lib
+	${INSTALL_DATA} ${WRKSRC}/include/*.h ${STAGEDIR}${PREFIX}/include
+	${INSTALL_MAN} ${FILESDIR}/nifticlib.1 ${STAGEDIR}${PREFIX}/man/man1
 
 .include <bsd.port.mk>
diff --git a/science/nifticlib/distinfo b/science/nifticlib/distinfo
index e43b2b4..a1e25af 100644
--- a/science/nifticlib/distinfo
+++ b/science/nifticlib/distinfo
@@ -1,2 +1,2 @@
-SHA256 (nifticlib-1.1.0.tar.gz) = 8997ade09c3b86806cccaf4e030f278dc91706ffafdda6043dca1c2f126cd018
-SIZE (nifticlib-1.1.0.tar.gz) = 251180
+SHA256 (nifticlib-2.0.0.tar.gz) = a3e988e6a32ec57833056f6b09f940c69e79829028da121ff2c5c6f7f94a7f88
+SIZE (nifticlib-2.0.0.tar.gz) = 258491
diff --git a/science/nifticlib/files/patch-Makefile b/science/nifticlib/files/patch-Makefile
index 4004521..ef3b199 100644
--- a/science/nifticlib/files/patch-Makefile
+++ b/science/nifticlib/files/patch-Makefile
@@ -1,106 +1,49 @@
---- Makefile.orig	2013-07-28 02:33:14.000000000 +0800
-+++ Makefile	2013-07-28 02:38:08.000000000 +0800
-@@ -115,34 +115,33 @@
- 
- 
- znz:
--	echo "arch is $(ARCH)"
--	(cd $(ZNZ); $(MAKE) depend; $(MAKE) lib;)
-+	$(MAKE) -C $(ZNZ) depend lib
- 	@echo " ----------- $(ZNZ) build completed."
- 	@echo ""
- 
- nifti:	znz
--	(cd $(NIFTI); $(MAKE) depend; $(MAKE) lib;)
-+	$(MAKE) -C $(NIFTI) depend lib
- 	@echo " ----------- $(NIFTI) build completed."
- 	@echo ""
- 
- nifticdf:nifti
--	(cd $(NIFTICDF); $(MAKE) depend; $(MAKE) lib;)
-+	$(MAKE) -C $(NIFTICDF) depend lib
- 	@echo " ----------- $(NIFTICDF) build completed."
- 	@echo ""
- 
- fslio:	nifti
--	(cd $(FSLIO); $(MAKE) depend; $(MAKE) lib;)
-+	$(MAKE) -C $(FSLIO) depend lib
- 	@echo " ----------  $(FSLIO) build completed."
- 	@echo ""
- 
- example:nifti
--	(cd $(EXAMPLES); $(MAKE) all;)
-+	$(MAKE) -C $(EXAMPLES) all
- 	@echo Example programs built.
- 	@echo ""
- 
- 
- utils:  nifti nifticdf
--	(cd $(UTILS); $(MAKE) all;)
-+	$(MAKE) -C $(UTILS) all
- 	@echo Utility programs built.
- 	@echo ""
- 
-@@ -152,7 +151,7 @@
- 	@echo ""
- 
- regress_data:
--	(cd $(TESTING); $(MAKE) regress_data 'RM=$(RM)' 'TAR=$(TAR)'; )
-+	$(MAKE) -C $(TESTING) regress_data 'RM=$(RM)' 'TAR=$(TAR)'
- 	@echo ""
- 	@echo Regression testing data installed.
- 	@echo See Testing/README_regress for details.
-@@ -167,25 +166,25 @@
- $(INSTALL_LIB_DIR):
- 	mkdir -p $@
- 
--znz_install: $(INSTALL_INC_DIR) $(INSTALL_LIB_DIR)
-+znz_install: znz $(INSTALL_INC_DIR) $(INSTALL_LIB_DIR)
- 	($(CP) $(ZNZ)/*.a $(INSTALL_LIB_DIR); $(CP) $(ZNZ)/*.h $(INSTALL_INC_DIR);)
- 	$(RANLIB) $(INSTALL_LIB_DIR)/*.a
- 	@echo " $(ZNZ) installed."
- 	@echo ""
- 
--nifti_install: $(INSTALL_INC_DIR) $(INSTALL_LIB_DIR)
-+nifti_install: nifti $(INSTALL_INC_DIR) $(INSTALL_LIB_DIR)
- 	($(CP) $(NIFTI)/*.a $(INSTALL_LIB_DIR); $(CP) $(NIFTI)/*.h $(INSTALL_INC_DIR);)
- 	$(RANLIB) $(INSTALL_LIB_DIR)/*.a
- 	@echo " $(NIFTI) installed."
- 	@echo ""
- 
--nifticdf_install: $(INSTALL_INC_DIR) $(INSTALL_LIB_DIR)
-+nifticdf_install: nifticdf $(INSTALL_INC_DIR) $(INSTALL_LIB_DIR)
- 	($(CP) $(NIFTICDF)/*.a $(INSTALL_LIB_DIR); $(CP) $(NIFTICDF)/*.h $(INSTALL_INC_DIR);)
- 	$(RANLIB) $(INSTALL_LIB_DIR)/*.a
- 	@echo " $(NIFTI) installed."
- 	@echo ""
- 
--fslio_install: $(INSTALL_INC_DIR) $(INSTALL_LIB_DIR)
-+fslio_install: fslio $(INSTALL_INC_DIR) $(INSTALL_LIB_DIR)
- 	($(CP) $(FSLIO)/*.a $(INSTALL_LIB_DIR); $(CP) $(FSLIO)/*.h $(INSTALL_INC_DIR);)
- 	$(RANLIB) $(INSTALL_LIB_DIR)/*.a
- 	@echo " $(FSLIO) installed."
-@@ -212,19 +211,19 @@
- 	(cd $(FSLIO); $(RM) -f *.o *.a core; $(RM) -f depend.mk;)
- 
- examples_clean:
--	(cd $(EXAMPLES); $(MAKE) clean;)
-+	$(MAKE) -C $(EXAMPLES) clean
- 
- utils_clean:
--	(cd $(UTILS); $(MAKE) clean;)
-+	$(MAKE) -C $(UTILS) clean
- 
- doc_clean:
- 	($(RM) -fr docs/html;)
- 
- regress_clean:
--	(cd $(TESTING); $(MAKE) regress_clean; )
-+	$(MAKE) -C $(TESTING) regress_clean
- 
- regress_clean_all:
--	(cd $(TESTING); $(MAKE) regress_clean_all; )
-+	$(MAKE) -C $(TESTING) regress_clean_all
- 
- tar:
- 	(cd .. ; ln -s $(THIS_DIR) ${TARFILE_NAME} ; \
+--- Makefile.orig	2010-07-20 12:18:58.000000000 -0500
++++ Makefile	2013-10-29 15:55:12.000000000 -0500
+@@ -17,21 +17,21 @@
+ 
+ 
+ ## Compiler  defines
+-cc		=	gcc
+-CC		=	gcc
+-AR		=	ar
+-RANLIB  = ranlib
+-DEPENDFLAGS	=	-MM
+-GNU_ANSI_FLAGS	= 	-Wall -ansi -pedantic
+-ANSI_FLAGS	= 	${GNU_ANSI_FLAGS}
+-CFLAGS		=	$(ANSI_FLAGS)
++cc		?=	gcc
++CC		?=	gcc
++AR		?=	ar
++RANLIB  	?=	ranlib
++DEPENDFLAGS	?=	-MM
++GNU_ANSI_FLAGS	?= 	-Wall -ansi -pedantic
++ANSI_FLAGS	+= 	${GNU_ANSI_FLAGS}
++CFLAGS		+=	$(ANSI_FLAGS)
+ 
+ ## Command defines
+ ## gmake does not work on MacOSX or some versions of linux MAKE  = gmake 
+-RM		=	rm
+-MV		=	mv
+-CP		=	cp
+-TAR		=	tar
++RM		?=	rm
++MV		?=	mv
++CP		?=	cp
++TAR		?=	tar
+ 
+ 
+ ## Installation
+@@ -41,9 +41,9 @@
+ 
+ 
+ ## Zlib defines
+-ZLIB_INC	=	-I/usr/include
+-ZLIB_PATH	=	-L/usr/lib
+-ZLIB_LIBS 	= 	$(ZLIB_PATH) -lm -lz 
++ZLIB_INC	?=	-I/usr/include
++ZLIB_PATH	?=	-L/usr/lib
++ZLIB_LIBS 	?= 	$(ZLIB_PATH) -lm -lz 
+ 
+ ##############################################################
+ # platform specific redefines (to use, set ARCH appropriately)
diff --git a/science/nifticlib/files/patch-examples-Makefile b/science/nifticlib/files/patch-examples-Makefile
new file mode 100644
index 0000000..a60095c
--- /dev/null
+++ b/science/nifticlib/files/patch-examples-Makefile
@@ -0,0 +1,8 @@
+--- examples/Makefile.orig	2013-10-29 15:56:43.000000000 -0500
++++ examples/Makefile	2013-10-29 15:56:48.000000000 -0500
+@@ -1,4 +1,4 @@
+-CC	=	gcc
++CC	?=	gcc
+ CFLAGS	=	-ansi -pedantic
+ 
+ FSLIO_INCS	=	-I../include
diff --git a/science/nifticlib/files/patch-utils-Makefile b/science/nifticlib/files/patch-utils-Makefile
new file mode 100644
index 0000000..49ca2d2
--- /dev/null
+++ b/science/nifticlib/files/patch-utils-Makefile
@@ -0,0 +1,10 @@
+--- utils/Makefile.orig	2007-05-17 15:18:44.000000000 -0500
++++ utils/Makefile	2013-10-29 15:55:12.000000000 -0500
+@@ -1,5 +1,5 @@
+-CC	=	gcc
+-CFLAGS	=	-ansi -pedantic
++CC	?=	gcc
++CFLAGS	?=	-ansi -pedantic
+ 
+ FSLIO_INCS	=	-I../include
+ NIFTI_INCS	=	-I../include
diff --git a/science/nifticlib/pkg-descr b/science/nifticlib/pkg-descr
index 46111ff..eee3225 100644
--- a/science/nifticlib/pkg-descr
+++ b/science/nifticlib/pkg-descr
@@ -1,4 +1,4 @@
-NIfTI-1 is a new Analyze-style data format, proposed by the NIfTI DFWG
+NIfTI-1 is an Analyze-style data format, proposed by the NIfTI DFWG
 as a short-term measure to facilitate inter-operation of functional MRI
 data analysis software packages.
 
diff --git a/science/nifticlib/pkg-plist b/science/nifticlib/pkg-plist
index add9be6..8a147fd 100644
--- a/science/nifticlib/pkg-plist
+++ b/science/nifticlib/pkg-plist
@@ -1,13 +1,15 @@
+@comment Generated by sysutils/genplist
 bin/nifti1_test
 bin/nifti_stats
 bin/nifti_tool
 include/dbh.h
 include/fslio.h
 include/nifti1.h
-include/nifticdf.h
 include/nifti1_io.h
+include/nifticdf.h
 include/znzlib.h
 lib/libfslio.a
 lib/libnifticdf.a
 lib/libniftiio.a
 lib/libznz.a
+man/man1/nifticlib.1.gz