Date: Tue, 29 Oct 2013 21:12:58 GMT From: Jason Bacon <jwbacon@tds.net> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/183454: maintainer update: science/nifticlib Message-ID: <201310292112.r9TLCwNa028826@oldred.freebsd.org> Resent-Message-ID: <201310292120.r9TLK0WB069024@freefall.freebsd.org>
next in thread | raw e-mail | index | archive | help
>Number: 183454
>Category: ports
>Synopsis: maintainer update: science/nifticlib
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: maintainer-update
>Submitter-Id: current-users
>Arrival-Date: Tue Oct 29 21:20:00 UTC 2013
>Closed-Date:
>Last-Modified:
>Originator: Jason Bacon
>Release: 10.0-BETA1
>Organization:
Acadix Consulting, LLC
>Environment:
FreeBSD freebsd10.local 10.0-BETA1 FreeBSD 10.0-BETA1 #0 r256420: Sun Oct 13 01:43:07 UTC 2013 root@snap.freebsd.org:/usr/obj/usr/src/sys/GENERIC amd64
>Description:
Update to v2.0.0 and patch for clang on 10.0-BETA1.
>How-To-Repeat:
Try to build science/nifticlib on 10.0.
>Fix:
Attached.
Patch attached with submission follows:
diff -ruN --exclude=CVS /usr/ports/science/nifticlib/Makefile /usr/wip/science/nifticlib/Makefile
--- /usr/ports/science/nifticlib/Makefile 2013-09-20 17:48:30.000000000 -0500
+++ /usr/wip/science/nifticlib/Makefile 2013-10-29 16:08:27.000000000 -0500
@@ -1,28 +1,28 @@
-# Created by: Jason Bacon <bacon@smithers.neuro.mcw.edu>
+# Created by: Jason W. Bacon <jwbacon@tds.net>
# $FreeBSD: science/nifticlib/Makefile 327767 2013-09-20 22:48:30Z bapt $
PORTNAME= nifticlib
-PORTVERSION= 1.1.0
+PORTVERSION= 2.0.0
CATEGORIES= science graphics
-MASTER_SITES= SF/niftilib/${PORTNAME}/${PORTNAME}-${PORTVERSION}
+MASTER_SITES= SF/niftilib/nifticlib/nifticlib_2_0_0
MAINTAINER= jwbacon@tds.net
-COMMENT= Neuroimaging Informatics Technology Initiative data format
+COMMENT= Neuroimaging Infoirmatics Technology Initiative data format
+
+# LICENSE= public domain
USES= gmake
-MAN1= nifticlib.1
+# AFNI currently has nifti embedded in the distfile and installs the
+# nifti bins by itself.
+CONFLICTS= afni-[0-9]* dbh-[0-9]*
-NO_STAGE= yes
-post-patch:
- @${REINPLACE_CMD} -e 's/include depend.mk/-&/' \
- ${WRKSRC}/fsliolib/Makefile ${WRKSRC}/nifticdf/Makefile \
- ${WRKSRC}/niftilib/Makefile ${WRKSRC}/znzlib/Makefile
+MAN1= nifticlib.1
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 -ruN --exclude=CVS /usr/ports/science/nifticlib/distinfo /usr/wip/science/nifticlib/distinfo
--- /usr/ports/science/nifticlib/distinfo 2012-07-14 09:29:18.000000000 -0500
+++ /usr/wip/science/nifticlib/distinfo 2013-10-29 16:08:27.000000000 -0500
@@ -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 -ruN --exclude=CVS /usr/ports/science/nifticlib/files/patch-Makefile /usr/wip/science/nifticlib/files/patch-Makefile
--- /usr/ports/science/nifticlib/files/patch-Makefile 2013-07-28 03:32:18.000000000 -0500
+++ /usr/wip/science/nifticlib/files/patch-Makefile 2013-10-29 16:08:27.000000000 -0500
@@ -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
+--- 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
- tar:
- (cd .. ; ln -s $(THIS_DIR) ${TARFILE_NAME} ; \
+ ##############################################################
+ # platform specific redefines (to use, set ARCH appropriately)
diff -ruN --exclude=CVS /usr/ports/science/nifticlib/files/patch-examples-Makefile /usr/wip/science/nifticlib/files/patch-examples-Makefile
--- /usr/ports/science/nifticlib/files/patch-examples-Makefile 1969-12-31 18:00:00.000000000 -0600
+++ /usr/wip/science/nifticlib/files/patch-examples-Makefile 2013-10-29 16:08:27.000000000 -0500
@@ -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 -ruN --exclude=CVS /usr/ports/science/nifticlib/files/patch-utils-Makefile /usr/wip/science/nifticlib/files/patch-utils-Makefile
--- /usr/ports/science/nifticlib/files/patch-utils-Makefile 1969-12-31 18:00:00.000000000 -0600
+++ /usr/wip/science/nifticlib/files/patch-utils-Makefile 2013-10-29 16:08:27.000000000 -0500
@@ -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 -ruN --exclude=CVS /usr/ports/science/nifticlib/patch-Makefile /usr/wip/science/nifticlib/patch-Makefile
--- /usr/ports/science/nifticlib/patch-Makefile 1969-12-31 18:00:00.000000000 -0600
+++ /usr/wip/science/nifticlib/patch-Makefile 2013-10-29 16:08:27.000000000 -0500
@@ -0,0 +1,49 @@
+--- Makefile.orig Thu Dec 6 15:32:47 2007
++++ Makefile Mon Dec 31 17:09:05 2007
+@@ -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 = /usr/local/pkg/gnu/bin/tar
++RM ?= rm
++MV ?= mv
++CP ?= cp
++TAR ?= /usr/bin/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 -ruN --exclude=CVS /usr/ports/science/nifticlib/pkg-descr /usr/wip/science/nifticlib/pkg-descr
--- /usr/ports/science/nifticlib/pkg-descr 2013-07-28 03:32:18.000000000 -0500
+++ /usr/wip/science/nifticlib/pkg-descr 2013-10-29 16:08:27.000000000 -0500
@@ -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 -ruN --exclude=CVS /usr/ports/science/nifticlib/pkg-plist /usr/wip/science/nifticlib/pkg-plist
--- /usr/ports/science/nifticlib/pkg-plist 2012-07-14 09:29:18.000000000 -0500
+++ /usr/wip/science/nifticlib/pkg-plist 2013-10-29 16:08:27.000000000 -0500
@@ -1,11 +1,12 @@
+@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
>Release-Note:
>Audit-Trail:
>Unformatted:
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?201310292112.r9TLCwNa028826>