From owner-freebsd-ports-bugs@FreeBSD.ORG Tue Oct 29 21:20:00 2013 Return-Path: Delivered-To: freebsd-ports-bugs@smarthost.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) (using TLSv1 with cipher ADH-AES256-SHA (256/256 bits)) (No client certificate requested) by hub.freebsd.org (Postfix) with ESMTP id B83A7413 for ; Tue, 29 Oct 2013 21:20:00 +0000 (UTC) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (freefall.freebsd.org [IPv6:2001:1900:2254:206c::16:87]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by mx1.freebsd.org (Postfix) with ESMTPS id 96B0B289F for ; Tue, 29 Oct 2013 21:20:00 +0000 (UTC) Received: from freefall.freebsd.org (localhost [127.0.0.1]) by freefall.freebsd.org (8.14.7/8.14.7) with ESMTP id r9TLK0TB069025 for ; Tue, 29 Oct 2013 21:20:00 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.14.7/8.14.7/Submit) id r9TLK0WB069024; Tue, 29 Oct 2013 21:20:00 GMT (envelope-from gnats) Resent-Date: Tue, 29 Oct 2013 21:20:00 GMT Resent-Message-Id: <201310292120.r9TLK0WB069024@freefall.freebsd.org> Resent-From: FreeBSD-gnats-submit@FreeBSD.org (GNATS Filer) Resent-To: freebsd-ports-bugs@FreeBSD.org Resent-Reply-To: FreeBSD-gnats-submit@FreeBSD.org, Jason Bacon Received: from mx1.freebsd.org (mx1.freebsd.org [8.8.178.115]) (using TLSv1 with cipher ADH-AES256-SHA (256/256 bits)) (No client certificate requested) by hub.freebsd.org (Postfix) with ESMTP id 4DF1CF7B for ; Tue, 29 Oct 2013 21:12:59 +0000 (UTC) (envelope-from nobody@FreeBSD.org) Received: from oldred.freebsd.org (oldred.freebsd.org [8.8.178.121]) (using TLSv1 with cipher DHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by mx1.freebsd.org (Postfix) with ESMTPS id 2B33C281A for ; Tue, 29 Oct 2013 21:12:59 +0000 (UTC) Received: from oldred.freebsd.org ([127.0.1.6]) by oldred.freebsd.org (8.14.5/8.14.7) with ESMTP id r9TLCw1g028829 for ; Tue, 29 Oct 2013 21:12:58 GMT (envelope-from nobody@oldred.freebsd.org) Received: (from nobody@localhost) by oldred.freebsd.org (8.14.5/8.14.5/Submit) id r9TLCwNa028826; Tue, 29 Oct 2013 21:12:58 GMT (envelope-from nobody) Message-Id: <201310292112.r9TLCwNa028826@oldred.freebsd.org> Date: Tue, 29 Oct 2013 21:12:58 GMT From: Jason Bacon To: freebsd-gnats-submit@FreeBSD.org X-Send-Pr-Version: www-3.1 Subject: ports/183454: maintainer update: science/nifticlib X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.14 Precedence: list List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 29 Oct 2013 21:20:00 -0000 >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 +# Created by: Jason W. Bacon # $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 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: