Attachment 140418 Details for Bug 186988 – file.diff

[patch] file.diff

file.diff (text/plain), 27.40 KB, created by Jason W. Bacon on 2014-02-23 20:20:00 UTC

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Creator: Jason W. Bacon

Created: 2014-02-23 20:20:00 UTC

Size: 27.40 KB

patch

obsolete

>diff -ruN --exclude=CVS --exclude=.svn /usr/ports/science/afni/Makefile /usr/wip/science/afni/Makefile
>--- /usr/ports/science/afni/Makefile	2014-02-23 09:54:40.000000000 -0600
>+++ /usr/wip/science/afni/Makefile	2014-02-23 11:33:36.000000000 -0600
>@@ -23,18 +23,29 @@
> MAINTAINER=	jwbacon@tds.net
> COMMENT=	Advanced Functional Neuro Imaging
> 
>-LIB_DEPENDS=	R:${PORTSDIR}/math/R \
>-		gsl:${PORTSDIR}/math/gsl
>+LICENSE=	GPLv2
>+
>+LIB_DEPENDS=	Xm:${PORTSDIR}/x11-toolkits/open-motif \
>+		R:${PORTSDIR}/math/R \
>+		gsl:${PORTSDIR}/math/gsl \
>+		netcdf:${PORTSDIR}/science/netcdf-ftn
> RUN_DEPENDS=	cjpeg:${PORTSDIR}/graphics/jpeg \
> 		mpeg_encode:${PORTSDIR}/multimedia/mpeg_encode \
> 		whirlgif:${PORTSDIR}/graphics/whirlgif \
> 		ppmtogif:${PORTSDIR}/graphics/netpbm \
>-		endian:${PORTSDIR}/sysutils/endian
>+		endian:${PORTSDIR}/sysutils/endian \
>+		qhull:${PORTSDIR}/math/qhull5
>+
>+CONFLICTS=	im-[0-9]* \
>+		nifticlib-[0-9]* \
>+		open-usp-tukubai-[0-9]*
> 
> USES=		gettext iconv gmake motif
> 
>-NO_STAGE=	yes
>-# BROKEN=	R_io.so fails to build with R-3.0.2
>+# Some prereqs use gcc anyway
>+USE_GCC=	yes
>+
>+# NO_STAGE=	yes
> 
> .include <bsd.port.pre.mk>
> 
>@@ -53,12 +64,10 @@
> ###########################################################################
> # Install parameters
> 
>-MAN1=		afni.1
>-
> SUB_FILES=	pkg-message afni.cshrc afni.profile
> 
> INSTALL_WRKSRC=	${WRKSRC}/BSD
>-STAGE=		${WRKSRC}/stage
>+PRESTAGE=	${WRKSRC}/prestage
> 
> X11R6_FILES=	coxplot/Makefile \
> 		coxplot/Makefile.f2c \
>@@ -83,49 +92,50 @@
> 	@${REINPLACE_CMD} "s|%%PREFIX%%|${PREFIX}|g" ${WRKDIR}/afni.1
> 
> post-build:
>-	${MKDIR} ${STAGE}/bin \
>-		${STAGE}/scripts \
>-		${STAGE}/lib \
>-		${STAGE}/include \
>-		${STAGE}/trash \
>-		${STAGE}/doc \
>-		${STAGE}/share
>+	${MKDIR} ${PRESTAGE}/bin \
>+		${PRESTAGE}/scripts \
>+		${PRESTAGE}/lib \
>+		${PRESTAGE}/include \
>+		${PRESTAGE}/trash \
>+		${PRESTAGE}/doc \
>+		${PRESTAGE}/share
> 	${MV}	${INSTALL_WRKSRC}/libf2c.a \
>-		${STAGE}/trash
>+		${PRESTAGE}/trash
> 	${MV}	${INSTALL_WRKSRC}/*.a \
> 		${INSTALL_WRKSRC}/*.so \
>-		${STAGE}/lib
>+		${PRESTAGE}/lib
> 	${MV}	${INSTALL_WRKSRC}/funstuff \
> 		${INSTALL_WRKSRC}/AFNI.*rc \
> 		${INSTALL_WRKSRC}/afnigui* \
>-		${STAGE}/share
>+		${PRESTAGE}/share
> 	${MV}	${INSTALL_WRKSRC}/*.h \
>-		${STAGE}/include
>+		${PRESTAGE}/include
> 	${MV}	${INSTALL_WRKSRC}/README* \
>-		${STAGE}/doc
>+		${PRESTAGE}/doc
> 	${MV}	${INSTALL_WRKSRC}/abut ${INSTALL_WRKSRC}/afni_abut
>-	${MV}	${INSTALL_WRKSRC}/qhull ${INSTALL_WRKSRC}/afni_qhull
> 	for binary in `${FILE} ${INSTALL_WRKSRC}/* | fgrep 'ELF' | ${AWK} -F ':' ' { print $$1 }'` ; do \
>-		${MV} $${binary} ${STAGE}/bin ; \
>+		${MV} $${binary} ${PRESTAGE}/bin ; \
> 	done
> 	${MV}	${INSTALL_WRKSRC}/* \
>-		${STAGE}/scripts
>+		${PRESTAGE}/scripts
> 
> do-install:
>-	${MKDIR} ${DATADIR} ${PREFIX}/lib/afni ${PREFIX}/include/afni
>-	${INSTALL_DATA} ${STAGE}/lib/* ${PREFIX}/lib/afni
>-	${INSTALL_DATA} ${STAGE}/include/* ${PREFIX}/include/afni
>-	${CP} -R ${STAGE}/share/* ${DATADIR}
>-	${INSTALL_PROGRAM} ${STAGE}/bin/* ${PREFIX}/bin
>-	${INSTALL_SCRIPT} ${STAGE}/scripts/* ${PREFIX}/bin
>-	${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/TTatlas* ${DATADIR}
>-	${INSTALL_DATA} ${WRKDIR}/CA_EZ_v1.5-July3107/* ${DATADIR}
>-	${INSTALL_MAN} ${WRKDIR}/afni.1 ${MAN1PREFIX}/man/man1
>+	${MKDIR} ${STAGEDIR}${DATADIR} \
>+		${STAGEDIR}${PREFIX}/lib/afni \
>+		${STAGEDIR}${PREFIX}/include/afni
>+	${INSTALL_DATA} ${PRESTAGE}/lib/* ${STAGEDIR}${PREFIX}/lib/afni
>+	${INSTALL_DATA} ${PRESTAGE}/include/* ${STAGEDIR}${PREFIX}/include/afni
>+	${CP} -R ${PRESTAGE}/share/* ${STAGEDIR}${DATADIR}
>+	${INSTALL_PROGRAM} ${PRESTAGE}/bin/* ${STAGEDIR}${PREFIX}/bin
>+	${INSTALL_SCRIPT} ${PRESTAGE}/scripts/* ${STAGEDIR}${PREFIX}/bin
>+	${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/TTatlas* ${STAGEDIR}${DATADIR}
>+	${INSTALL_DATA} ${WRKDIR}/CA_EZ_v1.5-July3107/* ${STAGEDIR}${DATADIR}
>+	${INSTALL_MAN} ${WRKDIR}/afni.1 ${STAGEDIR}${MAN1PREFIX}/man/man1
> .if !defined(NOPORTDOCS)
>-	${MKDIR} ${DOCSDIR} ${PREFIX}/etc/mri
>-	${INSTALL_DATA} ${STAGE}/doc/* ${DOCSDIR}
>+	${MKDIR} ${STAGEDIR}${DOCSDIR} ${STAGEDIR}${PREFIX}/etc/mri
>+	${INSTALL_DATA} ${PRESTAGE}/doc/* ${STAGEDIR}${DOCSDIR}
> 	${INSTALL_SCRIPT} ${WRKDIR}/afni.cshrc ${WRKDIR}/afni.profile \
>-		${PREFIX}/etc/mri
>+		${STAGEDIR}${PREFIX}/etc/mri
> .endif
> 
> post-install:
>diff -ruN --exclude=CVS --exclude=.svn /usr/ports/science/afni/files/Makefile.FreeBSD_PORT /usr/wip/science/afni/files/Makefile.FreeBSD_PORT
>--- /usr/ports/science/afni/files/Makefile.FreeBSD_PORT	2014-02-23 10:05:19.000000000 -0600
>+++ /usr/wip/science/afni/files/Makefile.FreeBSD_PORT	2014-02-13 16:39:00.000000000 -0600
>@@ -45,7 +45,7 @@
> LD?     = ${CC}
> 
> CCDEBS = -DAFNI_DEBUG -DIMSEQ_DEBUG -DDISPLAY_DEBUG -DTHD_DEBUG
>-CEXTRA = -DFreeBSD -DNO_GAMMA -DUSE_TRACING -DHAVE_XDBE -DSUMA_MOTIF_GLXAREA -Wno-return-type
>+CEXTRA = -DFreeBSD -DNO_GAMMA -DUSE_TRACING -DHAVE_XDBE -DSUMA_MOTIF_GLXAREA
> ifeq (${ARCH}, amd64)
> CEXTRA += -DPIC -fPIC
> endif
>@@ -53,7 +53,7 @@
> CEXTRA += -DPIC -fPIC
> endif
> 
>-CFLAGS += ${CEXTRA}
>+CFLAGS += -Wno-return-type -Wno-switch ${CEXTRA}
> CC     += ${CFLAGS}
> 
> CCVOL  = ${CC}
>@@ -67,6 +67,9 @@
> LFLAGS = -s -L. -L${LOCALBASE}/lib
> 
> MAKE   = gmake
>+# Some build scripts pick up the wrong make, so Makefile.INCLUDE is edited
>+# to use GMAKE
>+GMAKE  = gmake
> 
> PLUGIN_SUFFIX = so
> PLUGIN_LFLAGS = -shared
>diff -ruN --exclude=CVS --exclude=.svn /usr/ports/science/afni/files/patch-Makefile.INCLUDE /usr/wip/science/afni/files/patch-Makefile.INCLUDE
>--- /usr/ports/science/afni/files/patch-Makefile.INCLUDE	2014-01-22 11:40:44.000000000 -0600
>+++ /usr/wip/science/afni/files/patch-Makefile.INCLUDE	2014-02-13 16:39:00.000000000 -0600
>@@ -1,5 +1,5 @@
> --- Makefile.INCLUDE.orig	2012-04-17 15:56:21.000000000 -0500
>-+++ Makefile.INCLUDE	2012-04-18 13:39:29.000000000 -0500
>++++ Makefile.INCLUDE	2013-10-30 08:19:45.000000000 -0500
> @@ -48,7 +48,7 @@
>  ## AFNI package, but included because they are useful.  Some of
>  ## them are Open Source programs, not from the AFNI group at all.
>@@ -9,6 +9,51 @@
>  
>  # mpegtoppm in above list
>  
>+@@ -58,7 +58,7 @@
>+ PROGRAMS = afni to3d from3d abut 3dclust nsize 3dinfo 3dproject 3dmerge count   \
>+            sfim tfim ftosh 3dttest 3ddup imrotate imreg imstat 3dnvals          \
>+            fim2 imand FD2 sqwave immask imdump imaver 3dhistog 3dfim 3daxialize \
>+-               cdf 2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta   \
>++               2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta       \
>+            waver 3dnewid 3dcalc ccalc imcalc 1dmatcalc 3drefit 3dbucket         \
>+            3dNLfim 3dTSgen AlphaSim 3dFWHM plugout_tt 3dnoise plugout_ijk       \
>+            3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna         \
>+@@ -70,7 +70,7 @@
>+            3dWavelets 3dfim+ imcutup imcat 3dWinsor 3dZeropad 3dTagalign        \
>+            3dMean 3dAttribute cat_matvec 3dOverlap 3dClipLevel 3dZregrid        \
>+            3dEntropy 3ddelay ent16 3dRowFillin 1dgrayplot 3dToutcount 1dsum     \
>+-           3dExtrema qhull strblast 3dConvolve 3dZcutup 3dZcat 3dTqual 3dGetrow \
>++           3dExtrema strblast 3dConvolve 3dZcutup 3dZcat 3dTqual 3dGetrow       \
>+            3dTcorrelate 3dAnatNudge 3dcopy Vecwarp 3dMINCtoAFNI 3dCM fdrval     \
>+            3dAFNItoANALYZE siemens_vision ge_header mayo_analyze 3dAFNItoNIFTI  \
>+            3dAutoTcorrelate 3dFDR rtfeedme 3dAutomask 3dAFNItoMINC 3dBrickStat  \
>+@@ -89,7 +89,7 @@
>+            3dBlurInMask 3dRank 3dFFT 1dgenARMA11 3dPeriodogram 1dAstrip         \
>+            3dLocalPV 3dBandpass 3dSetupGroupInCorr 3dGroupInCorr 3dTcorr1D      \
>+            3dClustSim 3dRetinoPhase 3dMaskToASCII 3dttest++ 3dDTtoDWI           \
>+-           niccc rbox qdelaunay 3dkmeans 3dXYZcat 3dPolyfit 3dNwarpApply        \
>++           niccc 3dkmeans 3dXYZcat 3dPolyfit 3dNwarpApply                       \
>+            1dCorrelate 3dCountSpikes 3dNwarpCalc dicom_hinfo apsearch 1dBport   \
>+            3dNormalityTest                                                      \
>+            $(EXTRAS)
>+@@ -97,7 +97,7 @@
>+ PROGRAMS_NOPLUG = afni to3d from3d abut 3dclust nsize 3dinfo 3dproject 3dmerge      \
>+                   sfim tfim ftosh 3dttest 3ddup imrotate imreg imstat 3dnoise count \
>+                   fim2 imand FD2 sqwave immask imdump imaver 3dhistog 3dfim imupsam \
>+-                      cdf 2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 3drefit    \
>++                      2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 3drefit        \
>+                   waver 3dnewid 3dcalc ccalc imcalc 2dImReg 3dmaskave adwarp fdrval \
>+                   3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna      \
>+                   imstack byteorder 3dDeconvolve 3dTcat 3drotate 3dvolreg 1dplot    \
>+@@ -133,7 +133,7 @@
>+ PROGRAMS_EXE = afni.exe to3d from3d abut 3dclust nsize 3dinfo 3dproject 3dmerge   \
>+                sfim tfim ftosh 3dttest 3ddup imrotate imreg imstat 3dnvals count  \
>+                fim2 imand FD2 sqwave immask imdump imaver 3dhistog 3dfim 3dGetrow \
>+-                   cdf 2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta \
>++                   2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta     \
>+                waver 3dnewid 3dcalc ccalc imcalc 1dmatcalc 3drefit 3dbucket       \
>+                3dAFNItoNIML    AlphaSim 3dFWHM plugout_tt 3dnoise plugout_ijk     \
>+                3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna       \
> @@ -282,6 +282,9 @@
>  3dbuc2fim:3dbuc2fim.o
>  	$(CC) -o 3dbuc2fim 3dbuc2fim.o $(LFLAGS) $(LLIBS)
>@@ -19,3 +64,378 @@
>  mritopgm:mritopgm.c
>  	$(CC) -o mritopgm mritopgm.c $(INFLAGS) $(LFLAGS) $(LLIBS)
>  
>+@@ -2038,7 +2041,7 @@
>+ # remake netcdf objects with PIC
>+ shared_netcdf_attr:
>+ 	$(RM) netcdf_attr.o
>+-	$(MAKE) netcdf_attr.o CCMIN="${CCMIN} -fPIC"
>++	$(GMAKE) netcdf_attr.o CCMIN="${CCMIN} -fPIC"
>+ 
>+ # same as .a, but build as a shared object
>+ libmrix.a:$(IMOBJS) imseq.h display.h xim.h bbox.h xutil.h
>+@@ -2228,13 +2231,13 @@
>+ 
>+ f2c:
>+ 	( cd f2cdir ;                                                         \
>+-	  $(MAKE) f2c clean 'RM=$(RM)' 'CC=$(CC)' 'AR=$(AR)' 'CCMIN=$(CCMIN)' \
>++	  $(GMAKE) f2c clean 'RM=$(RM)' 'CC=$(CC)' 'AR=$(AR)' 'CCMIN=$(CCMIN)' \
>+ 	        'RANLIB=$(RANLIB)' 'LDFLAGS=$(LDFLAGS)' 'IFLAGS=$(ISFLAGS)' ;  \
>+ 	  $(MV) f2c .. ; )
>+ 
>+ libf2c.a:
>+ 	( cd f2cdir ;                                                        \
>+-	  $(MAKE) libf2c.a clean 'RM=$(RM)' 'CC=$(CC)' 'AR=$(AR)'            \
>++	  $(GMAKE) libf2c.a clean 'RM=$(RM)' 'CC=$(CC)' 'AR=$(AR)'            \
>+ 	        'RANLIB=$(RANLIB)' 'LDFLAGS=$(LDFLAGS)' 'IFLAGS=$(ISFLAGS)' ; \
>+ 	  $(MV) libf2c.a .. ; )
>+ 
>+@@ -2249,7 +2252,7 @@
>+ 
>+ libdl.a:dlcompat/dlfcn.h dlcompat/dlopen.c
>+ 	( cd dlcompat ;              \
>+-	  $(MAKE) libdl.a ;          \
>++	  $(GMAKE) libdl.a ;          \
>+ 	  $(CP) libdl.a dlfcn.h .. ; \
>+           cd .. ;                    \
>+ 	  $(RANLIB) libdl.a ;     )
>+@@ -2259,7 +2262,7 @@
>+ 
>+ libcoxplot.a:coxplot.h
>+ 	( cd coxplot ;                                                       \
>+-	  $(MAKE) libcoxplot.a clean 'RM=$(RM)' 'CC=$(CC)' 'AR=$(AR)'        \
>++	  $(GMAKE) libcoxplot.a clean 'RM=$(RM)' 'CC=$(CC)' 'AR=$(AR)'        \
>+ 	        'RANLIB=$(RANLIB)' 'LDFLAGS=$(LDFLAGS)' 'IFLAGS=$(ISFLAGS)' ; \
>+ 	  $(MV) libcoxplot.a .. ; )
>+ 
>+@@ -2305,26 +2308,26 @@
>+ 
>+ file_tool: ge4_header.o
>+ 	( cd rickr ;                                                    \
>+-	$(MAKE) file_tool 'RM=$(RM)' 'CC=$(CC)' 'IFLAGS=$(ISFLAGS)'      \
>++	$(GMAKE) file_tool 'RM=$(RM)' 'CC=$(CC)' 'IFLAGS=$(ISFLAGS)'      \
>+ 			'LFLAGS=$(LFLAGS)' 'LLIBS=$(LLIBS)' ;           \
>+ 	$(MV) file_tool .. ; )
>+ 
>+ Dimon: rickr/Dimon.c rickr/Imon.h rickr/realtime.c rickr/realtime.h
>+ 	( cd rickr ; 							\
>+-	$(MAKE) Dimon 'RM=$(RM)' 'CC=$(CC)' 'IFLAGS=$(ISFLAGS)'        	\
>++	$(GMAKE) Dimon 'RM=$(RM)' 'CC=$(CC)' 'IFLAGS=$(ISFLAGS)'        	\
>+ 		  'LFLAGS=$(LFLAGS)' 'EXTRA_LIBS_2=$(EXTRA_LIBS_2)'	\
>+ 		  'LGIFTI=$(LGIFTI)' ;					\
>+ 	$(MV) Dimon .. ; )
>+ 
>+ Imon: rickr/Imon.c rickr/Imon.h rickr/realtime.c rickr/realtime.h thd_iochan.o
>+ 	( cd rickr ; 							\
>+-	$(MAKE) Imon 'RM=$(RM)' 'CC=$(CC)' 'IFLAGS=$(ISFLAGS)'        	\
>++	$(GMAKE) Imon 'RM=$(RM)' 'CC=$(CC)' 'IFLAGS=$(ISFLAGS)'        	\
>+ 		  'LFLAGS=$(LFLAGS)' 'EXTRA_LIBS_2=$(EXTRA_LIBS_2)' ;	\
>+ 	$(MV) Imon .. ; )
>+ 
>+ serial_helper: rickr/serial_helper.c
>+ 	( cd rickr ;                                                    \
>+-	$(MAKE) serial_helper 'RM=$(RM)' 'CC=$(CC)' 'IFLAGS=$(ISFLAGS)'  \
>++	$(GMAKE) serial_helper 'RM=$(RM)' 'CC=$(CC)' 'IFLAGS=$(ISFLAGS)'  \
>+ 		  'LFLAGS=$(LFLAGS)' 'EXTRA_LIBS_2=$(EXTRA_LIBS_2)' ;	\
>+ 	$(MV) serial_helper .. ; )
>+ 
>+@@ -2334,7 +2337,7 @@
>+ 
>+ gtest:
>+ 	( cd gifti ; 							\
>+-	$(MAKE) gtest 'RM=$(RM)' 'CC=$(CC)' 'IFLAGS=$(ISFLAGS)'         \
>++	$(GMAKE) gtest 'RM=$(RM)' 'CC=$(CC)' 'IFLAGS=$(ISFLAGS)'         \
>+ 	                'LFLAGS=$(LFLAGS)' ;                            \
>+ 	$(MV) gtest .. ; )
>+ 
>+@@ -2343,7 +2346,7 @@
>+ 
>+ libvolpack.a:
>+ 	( cd volpack ;                                                       \
>+-	  $(MAKE) libvolpack.a clean 'RM=$(RM)' 'CC=$(CCVOL)' 'AR=$(AR)'     \
>++	  $(GMAKE) libvolpack.a clean 'RM=$(RM)' 'CC=$(CCVOL)' 'AR=$(AR)'     \
>+ 	        'RANLIB=$(RANLIB)' 'LDFLAGS=$(LDFLAGS)' 'IFLAGS=$(ISFLAGS)' ; \
>+ 	  $(MV) libvolpack.a .. ; )
>+ 
>+@@ -2358,7 +2361,7 @@
>+ 
>+ qhull:
>+ 	( cd qhulldir ;                                                  \
>+-	  $(MAKE) qhull rbox qdelaunay clean \
>++	  $(GMAKE) qhull rbox qdelaunay clean \
>+ 	        'RM=$(RM)' 'CC=$(CC)' 'LFLAGS=$(LFLAGS)' ; \
>+ 	  $(MV) qhull rbox qdelaunay .. ; )
>+ 
>+@@ -2366,26 +2369,26 @@
>+ 
>+ qhull.exe:
>+ 	( cd qhulldir ;                                                  \
>+-	  $(MAKE) qhull clean 'RM=$(RM)' 'CC=$(CC)' 'LFLAGS=$(LFLAGS)' ; \
>++	  $(GMAKE) qhull clean 'RM=$(RM)' 'CC=$(CC)' 'LFLAGS=$(LFLAGS)' ; \
>+ 	  $(MV) qhull.exe .. ; )
>+ 
>+ #######
>+ # 3DEdge library files - make them and move them up here
>+ 
>+ lib3DEdge.a:
>+-	( cd 3DEdge/src ; $(MAKE) clean lib3DEdge.a 'RM=$(RM)' 'AR=$(AR)' 'RANLIB=$(RANLIB)' 'CC=$(CCFAST)' 'IFLAGS=$(ISFLAGS)' 'LFLAGS=$(LFLAGS)' ; $(MV) *.a ../.. ; )
>++	( cd 3DEdge/src ; $(GMAKE) clean lib3DEdge.a 'RM=$(RM)' 'AR=$(AR)' 'RANLIB=$(RANLIB)' 'CC=$(CCFAST)' 'IFLAGS=$(ISFLAGS)' 'LFLAGS=$(LFLAGS)' ; $(MV) *.a ../.. ; )
>+ 
>+ #######
>+ # Eispack and CDF library files - make them and move them up here
>+ 
>+ eis_bakvec.o:
>+-	( cd eispack/ ; $(MAKE) all 'CC=$(CCFAST)' 'CCSVD=$(CCSVD)' ; $(MV) *.o .. ; )
>++	( cd eispack/ ; $(GMAKE) all 'CC=$(CCFAST)' 'CCSVD=$(CCSVD)' ; $(MV) *.o .. ; )
>+ 
>+ #######
>+ # Ditto for NIML objects
>+ 
>+ $(NIML_OBJS):niml.h
>+-	( cd niml/ ; $(MAKE) all 'CC=$(CC)' ; $(MV) *.o .. ; )
>++	( cd niml/ ; $(GMAKE) all 'CC=$(CC)' ; $(MV) *.o .. ; )
>+ 
>+ niml.h:niml/niml.h
>+ 	$(CP) niml/niml.h .
>+@@ -2399,7 +2402,7 @@
>+           CXX="" ; export CXX ; CC="${CCMIN}";export CC;  \
>+           $(RM) config.cache config.log config.status ;   \
>+           chmod ugo+x ./configure ;                       \
>+-          ./configure ; $(MAKE) libsrc/all ;              \
>++          ./configure ; $(GMAKE) libsrc/all ;              \
>+           $(CP) libsrc/netcdf.h  ../.. ;                  \
>+           $(MV) libsrc/attr.o    ../../netcdf_attr.o    ; \
>+           $(MV) libsrc/dim.o     ../../netcdf_dim.o     ; \
>+@@ -2414,14 +2417,14 @@
>+           $(MV) libsrc/v2i.o     ../../netcdf_v2i.o     ; \
>+           $(MV) libsrc/var.o     ../../netcdf_var.o     ; \
>+           $(RM) config.cache config.log config.status ;   \
>+-          $(MAKE) clean ; )
>++          $(GMAKE) clean ; )
>+ 
>+ #######
>+ # 27 Jul 2001 - for fun
>+ 
>+ gifsicle:
>+ 	( cd gifsicledir ;                                                  \
>+-	  $(MAKE) gifsicle clean 'RM=$(RM)' 'CC=$(CC)' 'LFLAGS=$(LFLAGS)' ; \
>++	  $(GMAKE) gifsicle clean 'RM=$(RM)' 'CC=$(CC)' 'LFLAGS=$(LFLAGS)' ; \
>+ 	  $(MV) gifsicle .. ; )
>+ 
>+ #######
>+@@ -2429,7 +2432,7 @@
>+ 
>+ mpeg_encode:
>+ 	( cd mpeg_encodedir ;                                                                   \
>+-	  $(MAKE) mpeg_encode clean 'RM=$(RM)' 'CC=$(CC)' 'LFLAGS=$(LFLAGS)' 'LLIBS=$(LLIBS)' ; \
>++	  $(GMAKE) mpeg_encode clean 'RM=$(RM)' 'CC=$(CC)' 'LFLAGS=$(LFLAGS)' 'LLIBS=$(LLIBS)' ; \
>+ 	  $(MV) mpeg_encode .. ; )
>+ 
>+ #######
>+@@ -2438,7 +2441,7 @@
>+ mpegtoppm:
>+ 	( cd mpegtoppm_dir ; chmod ugo+x ./configure ;                                         \
>+ 	  ./configure --disable-sdl --disable-mlib --without-x --disable-dependency-tracking --disable-accel-detect ; \
>+-	  $(MAKE) ; mv doc/sample2 ../mpegtoppm ; $(MAKE) clean ; )
>++	  $(GMAKE) ; mv doc/sample2 ../mpegtoppm ; $(GMAKE) clean ; )
>+ 
>+ #######
>+ # 11 Sep 2002 - for fun
>+@@ -2450,12 +2453,12 @@
>+ cjpeg:
>+ 	( cd jpeg-6b ; $(RM) Makefile jconfig.h ;                    \
>+           chmod ugo+x ./configure ; ./configure 'CC=$(CCMIN)' ; \
>+-          $(MAKE) ; $(MV) cjpeg djpeg libjpeg.a .. ;            \
>+-          $(MAKE) clean ; $(RM) Makefile )
>++          $(GMAKE) ; $(MV) cjpeg djpeg libjpeg.a .. ;            \
>++          $(GMAKE) clean ; $(RM) Makefile )
>+ 
>+ libXmHTML.a:
>+-	( cd XmHTML ; make lib 'CC=$(CC)' 'II=$(IFLAGS)' ; \
>+-		$(MV) lib/libXmHTML.a .. ; make clean   )
>++	( cd XmHTML ; gmake lib 'CC=$(CC)' 'II=$(IFLAGS)' ; \
>++		$(MV) lib/libXmHTML.a .. ; gmake clean   )
>+ 
>+ thd_xwebber.o:thd_xwebber.c
>+ 	$(CC) -c thd_xwebber.c -I./XmHTML/include $(INFLAGS)
>+@@ -2465,7 +2468,7 @@
>+ 
>+ libfftw.a:
>+ 	( cd fftw ;                                                    \
>+-	  $(MAKE) libfftw.a clean 'RM=$(RM)' 'CC=$(CCFAST)' 'AR=$(AR)' \
>++	  $(GMAKE) libfftw.a clean 'RM=$(RM)' 'CC=$(CCFAST)' 'AR=$(AR)' \
>+ 	        'RANLIB=$(RANLIB)' 'LDFLAGS=$(LDFLAGS)' 'IFLAGS=$(ISFLAGS)' ; \
>+ 	  $(MV) libfftw.a .. ; )
>+ 
>+@@ -2480,7 +2483,7 @@
>+ 
>+ libclam.a:
>+ 	( cd clamdir ;                                             \
>+-	  $(MAKE) libclam.a clean 'RM=$(RM)' 'CC=$(CC)' 'AR=$(AR)' \
>++	  $(GMAKE) libclam.a clean 'RM=$(RM)' 'CC=$(CC)' 'AR=$(AR)' \
>+ 	        'RANLIB=$(RANLIB)' 'IFLAGS=-I..' ;                 \
>+ 	  $(MV) libclam.a .. ; )
>+ 
>+@@ -2819,13 +2822,13 @@
>+ 3dkmeans: avovk/3dkmeans.c avovk/cluster_floatNOMASK.c avovk/thd_segtools_fNM.c
>+ 	( cd avovk ;	\
>+ 	./@MakeLocalMake	;\
>+-	$(MAKE) afni_all  ;	\
>++	$(GMAKE) afni_all  ;	\
>+ 	cd ../	;		)
>+ 
>+ libsegtools.a: avovk/cluster_floatNOMASK.c avovk/thd_segtools_fNM.c
>+ 	( cd avovk ;	\
>+ 	./@MakeLocalMake	;\
>+-	$(MAKE) libsegtools.a  ;	\
>++	$(GMAKE) libsegtools.a  ;	\
>+ 	$(CP) libsegtools.a ../;	\
>+ 	cd ../	;		)
>+ 
>+@@ -2836,13 +2839,13 @@
>+ ptaylor_all: 
>+ 	( cd ptaylor ;	\
>+ 	./@MakeLocalMake	;\
>+-	$(MAKE) all  ;	\
>++	$(GMAKE) all  ;	\
>+ 	cd ../	;		)
>+ 
>+ libtracktools.a: ptaylor/libtracktools.a
>+ 	( cd ptaylor ;	\
>+ 	./@MakeLocalMake	;\
>+-	$(MAKE) libtracktools.a  ;	\
>++	$(GMAKE) libtracktools.a  ;	\
>+ 	$(CP) libtracktools.a ../;	\
>+ 	cd ../	;		)
>+ 
>+@@ -2853,11 +2856,11 @@
>+ libSUMA.a: libmri.a libmrix.a libcoxplot.a libf2c.a
>+ 	( cd SUMA ;	\
>+ 	rm -f libSUMA.a	;\
>+-	$(MAKE) -f $(SUMA_MAKEFILE_NAME) clean MarchingCubes.o libSUMA.a 'INSTALLDIR=$(INSTALLDIR)' \
>++	$(GMAKE) -f $(SUMA_MAKEFILE_NAME) clean MarchingCubes.o libSUMA.a 'INSTALLDIR=$(INSTALLDIR)' \
>+ 	'SUMA_INCLUDE_PATH=$(SUMA_INCLUDE_PATH)' \
>+ 	'SUMA_BIN_ARCHIVE=$(SUMA_BIN_ARCHIVE)' \
>+ 	'RANLIB=$(RANLIB)' \
>+-        'MAKE=$(MAKE)'     \
>++        'MAKE=$(GMAKE)'     \
>+ 	'CC=$(CC)' 'RM=$(RM)' 'CEXTRA=$(CEXTRA)' 'MV=$(MV)' 'CP=$(CP)'	\
>+ 	'TAR=$(TAR)' 'MKDIR=$(MKDIR)';	\
>+ 	cd ../	;	\
>+@@ -2868,7 +2871,7 @@
>+ libgts.a:
>+ 	( cd SUMA ;	\
>+ 	rm -f libgts.a	;\
>+-	$(MAKE) -f $(SUMA_MAKEFILE_NAME) libgts.a ;	\
>++	$(GMAKE) -f $(SUMA_MAKEFILE_NAME) libgts.a ;	\
>+ 	cd ../	;	\
>+ 	if [ ! -d $(INSTALLDIR) ]; then $(MKDIR) -p $(INSTALLDIR); echo WARNING: directory $(INSTALLDIR) has been created. ; fi	;\
>+ 	$(CP) SUMA/libgts.a ${INSTALLDIR}; \
>+@@ -2877,11 +2880,11 @@
>+ libGLws.a:
>+ 	( cd SUMA ;	\
>+ 	rm -f libGLws.a	;\
>+-	$(MAKE) -f $(SUMA_MAKEFILE_NAME) libGLws.a 'INSTALLDIR=$(INSTALLDIR)' \
>++	$(GMAKE) -f $(SUMA_MAKEFILE_NAME) libGLws.a 'INSTALLDIR=$(INSTALLDIR)' \
>+ 	'SUMA_INCLUDE_PATH=$(SUMA_INCLUDE_PATH)' \
>+ 	'SUMA_BIN_ARCHIVE=$(SUMA_BIN_ARCHIVE)' \
>+ 	'RANLIB=$(RANLIB)' \
>+-        'MAKE=$(MAKE)'     \
>++        'MAKE=$(GMAKE)'     \
>+ 	'CC=$(CC)' 'RM=$(RM)' 'CEXTRA=$(CEXTRA)' 'MV=$(MV)' 'CP=$(CP)'	\
>+ 	'TAR=$(TAR)' 'MKDIR=$(MKDIR)';	\
>+ 	cd ../	;	\
>+@@ -2892,7 +2895,7 @@
>+ #link executables but check for libraries first and create them if needed	
>+ suma_exec:libGLws.a libSUMA.a libmri.a xutil.o LiteClue.o parser.o parser_int.o libmrix.a libcoxplot.a libf2c.a
>+ 	( cd SUMA ;	\
>+-	$(MAKE) -f $(SUMA_MAKEFILE_NAME) testGL suma ScaleToMap CompareSurfaces \
>++	$(GMAKE) -f $(SUMA_MAKEFILE_NAME) testGL suma ScaleToMap CompareSurfaces \
>+ 	MakeColorMap ROI2dataset 3dVol2Surf \
>+ 	3dSurf2Vol SurfMeasures SurfFWHM \
>+ 	ConvertSurface ConvertDset SurfClust IsoSurface \
>+@@ -2909,7 +2912,7 @@
>+ 	'SUMA_BIN_ARCHIVE=$(SUMA_BIN_ARCHIVE)' \
>+ 	'SUMA_GLIB_VER=$(SUMA_GLIB_VER)' \
>+ 	'RANLIB=$(RANLIB)' \
>+-        'MAKE=$(MAKE)'     \
>++        'MAKE=$(GMAKE)'     \
>+ 	'CC=$(CC)' 'RM=$(RM)' 'CEXTRA=$(CEXTRA)' 'MV=$(MV)' 'CP=$(CP)'		\
>+ 	'TAR=$(TAR)' 'MKDIR=$(MKDIR)';	\
>+ 	cd ../	;)
>+@@ -2918,14 +2921,14 @@
>+ #Do the GTS related stuff 	
>+ suma_gts_progs: libgts.a
>+ 	( cd SUMA ;	\
>+-	$(MAKE) -f $(SUMA_MAKEFILE_NAME) SurfMesh 'INSTALLDIR=$(INSTALLDIR)' \
>++	$(GMAKE) -f $(SUMA_MAKEFILE_NAME) SurfMesh 'INSTALLDIR=$(INSTALLDIR)' \
>+ 	'SUMA_INCLUDE_PATH=$(SUMA_INCLUDE_PATH)' \
>+ 	'SUMA_LINK_PATH=$(SUMA_LINK_PATH)' \
>+ 	'SUMA_LINK_LIB=$(SUMA_LINK_LIB)' \
>+ 	'SUMA_BIN_ARCHIVE=$(SUMA_BIN_ARCHIVE)' \
>+ 	'SUMA_GLIB_VER=$(SUMA_GLIB_VER)' \
>+ 	'RANLIB=$(RANLIB)' \
>+-        'MAKE=$(MAKE)'     \
>++        'MAKE=$(GMAKE)'     \
>+ 	'CC=$(CC)' 'RM=$(RM)' 'CEXTRA=$(CEXTRA)' 'MV=$(MV)' 'CP=$(CP)'		\
>+ 	'TAR=$(TAR)' 'MKDIR=$(MKDIR)';	\
>+ 	cd ../	;)
>+@@ -2934,14 +2937,14 @@
>+ #run make all in SUMA directory, USE FOR DEVELOPMENT ONLY	
>+ suma_all:libmri.a xutil.o LiteClue.o parser.o parser_int.o libmrix.a libcoxplot.a libf2c.a
>+ 	( cd SUMA ;	\
>+-	$(MAKE) -f $(SUMA_MAKEFILE_NAME) all 'INSTALLDIR=$(INSTALLDIR)' 'INSTALLDIR_SUMA=$(INSTALLDIR)' \
>++	$(GMAKE) -f $(SUMA_MAKEFILE_NAME) all 'INSTALLDIR=$(INSTALLDIR)' 'INSTALLDIR_SUMA=$(INSTALLDIR)' \
>+ 	'SUMA_INCLUDE_PATH=$(SUMA_INCLUDE_PATH)' \
>+ 	'SUMA_LINK_PATH=$(SUMA_LINK_PATH)' \
>+ 	'SUMA_LINK_LIB=$(SUMA_LINK_LIB)' \
>+ 	'SUMA_BIN_ARCHIVE=$(SUMA_BIN_ARCHIVE)' \
>+ 	'SUMA_GLIB_VER=$(SUMA_GLIB_VER)' \
>+ 	'RANLIB=$(RANLIB)' \
>+-        'MAKE=$(MAKE)'     \
>++        'MAKE=$(GMAKE)'     \
>+ 	'CC=$(CC)' 'RM=$(RM)' 'CEXTRA=$(CEXTRA)' 'MV=$(MV)' 'CP=$(CP)'		\
>+ 	'TAR=$(TAR)' 'MKDIR=$(MKDIR)';	\
>+ 	cd ../	;)
>+@@ -2950,14 +2953,14 @@
>+ #run make anew in SUMA directory, USE FOR DEVELOPMENT ONLY	
>+ suma_anew:libmri.a xutil.o LiteClue.o parser.o parser_int.o libmrix.a libcoxplot.a libf2c.a
>+ 	( cd SUMA ;	\
>+-	$(MAKE) -f $(SUMA_MAKEFILE_NAME) anew 'INSTALLDIR=$(INSTALLDIR)' 'INSTALLDIR_SUMA=$(INSTALLDIR)' \
>++	$(GMAKE) -f $(SUMA_MAKEFILE_NAME) anew 'INSTALLDIR=$(INSTALLDIR)' 'INSTALLDIR_SUMA=$(INSTALLDIR)' \
>+ 	'SUMA_INCLUDE_PATH=$(SUMA_INCLUDE_PATH)' \
>+ 	'SUMA_LINK_PATH=$(SUMA_LINK_PATH)' \
>+ 	'SUMA_LINK_LIB=$(SUMA_LINK_LIB)' \
>+ 	'SUMA_BIN_ARCHIVE=$(SUMA_BIN_ARCHIVE)' \
>+ 	'SUMA_GLIB_VER=$(SUMA_GLIB_VER)' \
>+ 	'RANLIB=$(RANLIB)' \
>+-        'MAKE=$(MAKE)'     \
>++        'MAKE=$(GMAKE)'     \
>+ 	'CC=$(CC)' 'RM=$(RM)' 'CEXTRA=$(CEXTRA)' 'MV=$(MV)' 'CP=$(CP)'		\
>+ 	'TAR=$(TAR)' 'MKDIR=$(MKDIR)';	\
>+ 	cd ../	;)
>+@@ -3080,7 +3083,7 @@
>+    SurfToSurf Surf2VolCoord ROIgrow SurfDsetInfo SurfInfo AnalyzeTrace \
>+    DriveSuma SurfDist SpharmReco SpharmDeco prompt_user SurfRetinoMap \
>+    ParseName 3dGenPriors 3dSeg SurfExtrema 3dinfill; \
>+-	$(MAKE) -f $(SUMA_MAKEFILE_NAME) testGL suma MakeColorMap ROI2dataset \
>++	$(GMAKE) -f $(SUMA_MAKEFILE_NAME) testGL suma MakeColorMap ROI2dataset \
>+    3dVol2Surf 3dSurf2Vol ScaleToMap SurfMeasures SurfFWHM \
>+ 	MapIcosahedron CreateIcosahedron CompareSurfaces ConvertSurface ConvertDset \
>+ 	SurfClust IsoSurface ConvexHull SurfaceMetrics SurfSmooth inspec \
>+@@ -3096,7 +3099,7 @@
>+ 	'SUMA_BIN_ARCHIVE=$(SUMA_BIN_ARCHIVE)' \
>+ 	'SUMA_GLIB_VER=$(SUMA_GLIB_VER)' \
>+ 	'RANLIB=$(RANLIB)' \
>+-        'MAKE=$(MAKE)'     \
>++        'MAKE=$(GMAKE)'     \
>+ 	'CC=$(CC)' 'RM=$(RM)' 'CEXTRA=$(CEXTRA)' 'MV=$(MV)' 'CP=$(CP)'\
>+ 	'TAR=$(TAR)' 'MKDIR=$(MKDIR)';	\
>+ 	cd ../	;)
>+@@ -3155,6 +3158,7 @@
>+ ####
>+ R_io.so:R_io.c libmri.a
>+ 	( if which R >/dev/null ; then \
>++	export MAKE=${GMAKE} ;\
>+ 	echo PKG_CPPFLAGS = $(INFLAGS)  > Makevars ;\
>+ 	echo PKG_LIBS =  $(LFLAGS) $(LLIBS) >> Makevars ;\
>+ 	R CMD SHLIB R_io.c ; \
>diff -ruN --exclude=CVS --exclude=.svn /usr/ports/science/afni/files/patch-XmHTML-Makefile /usr/wip/science/afni/files/patch-XmHTML-Makefile
>--- /usr/ports/science/afni/files/patch-XmHTML-Makefile	1969-12-31 18:00:00.000000000 -0600
>+++ /usr/wip/science/afni/files/patch-XmHTML-Makefile	2014-02-13 16:39:00.000000000 -0600
>@@ -0,0 +1,11 @@
>+--- XmHTML/Makefile.orig	2011-07-05 08:07:36.000000000 -0500
>++++ XmHTML/Makefile	2013-10-29 20:59:28.000000000 -0500
>+@@ -48,7 +48,7 @@
>+ RANLIB= ranlib
>+ 
>+ SHELL     = /bin/sh
>+-MAKE      = make 
>++MAKE      = gmake 
>+ # change this to makedepend if your system doesn't have gcc
>+ MAKEDEPEND= gccmakedep
>+ 
>diff -ruN --exclude=CVS --exclude=.svn /usr/ports/science/afni/files/patch-misc_math.c /usr/wip/science/afni/files/patch-misc_math.c
>--- /usr/ports/science/afni/files/patch-misc_math.c	2014-01-22 11:40:44.000000000 -0600
>+++ /usr/wip/science/afni/files/patch-misc_math.c	2014-02-13 16:39:00.000000000 -0600
>@@ -1,5 +1,5 @@
>---- misc_math.c.orig	2012-04-18 13:42:55.000000000 -0500
>-+++ misc_math.c	2012-04-18 13:43:41.000000000 -0500
>+--- misc_math.c.orig	2010-06-22 08:15:42.000000000 -0500
>++++ misc_math.c	2013-10-29 20:59:28.000000000 -0500
> @@ -1,6 +1,13 @@
>  
> +/* For older libm */
>diff -ruN --exclude=CVS --exclude=.svn /usr/ports/science/afni/files/pkg-message.in /usr/wip/science/afni/files/pkg-message.in
>--- /usr/ports/science/afni/files/pkg-message.in	2014-01-22 09:52:06.000000000 -0600
>+++ /usr/wip/science/afni/files/pkg-message.in	2014-02-23 12:30:22.000000000 -0600
>@@ -12,8 +12,15 @@
> 
> ---
> 
>-For large 3dDeconvolve analyses, you may need to increase the shared
>-memory limit on your system.
>+For large 3dDeconvolve analyses, you may need to increase one or
>+more of the following shared memory limits using sysctl (and
>+/etc/sysctl.conf to make the changes permanent):
>+
>+    kern.ipc.shmall
>+    kern.ipc.shmmax
>+    kern.ipc.shmmin
>+    kern.ipc.shmmni
>+    kern.ipc.shmseg
> 
> ---
> 
>diff -ruN --exclude=CVS --exclude=.svn /usr/ports/science/afni/pkg-descr /usr/wip/science/afni/pkg-descr
>--- /usr/ports/science/afni/pkg-descr	2014-01-22 09:44:51.000000000 -0600
>+++ /usr/wip/science/afni/pkg-descr	2014-02-13 16:39:00.000000000 -0600
>@@ -2,4 +2,4 @@
> a tool for analyzing 3 dimensional images, especially functional MRI
> images used in brain mapping research.
> 
>-WWW:	http://afni.nimh.nih.gov/afni/
>+WWW: http://afni.nimh.nih.gov/afni/
>diff -ruN --exclude=CVS --exclude=.svn /usr/ports/science/afni/pkg-plist /usr/wip/science/afni/pkg-plist
>--- /usr/ports/science/afni/pkg-plist	2014-01-22 09:16:56.000000000 -0600
>+++ /usr/wip/science/afni/pkg-plist	2014-02-23 12:32:10.000000000 -0600
>@@ -1,3 +1,4 @@
>+@comment Generated by ports-mgmt/genplist
> bin/1dAstrip
> bin/1dBandpass
> bin/1dBport
>@@ -339,7 +340,6 @@
> bin/afni_base.py
> bin/afni_history
> bin/afni_proc.py
>-bin/afni_qhull
> bin/afni_run_R
> bin/afni_util.py
> bin/afni_vcheck
>@@ -351,7 +351,6 @@
> bin/byteorder
> bin/cat_matvec
> bin/ccalc
>-bin/cdf
> bin/count
> bin/db_mod.py
> bin/demo.fixed.niml.do
>@@ -427,10 +426,8 @@
> bin/plugout_tta
> bin/prompt_user
> bin/python_module_test.py
>-bin/qdelaunay
> bin/quick.alpha.vals.py
> bin/quickspec
>-bin/rbox
> bin/realtime_receiver.py
> bin/rmz
> bin/rotcom
>@@ -579,6 +576,7 @@
> lib/afni/plug_volreg.so
> lib/afni/plug_wavelets.so
> lib/afni/plug_zeropad.so
>+man/man1/afni.1.gz
> %%DATADIR%%/AFNI.afnirc
> %%DATADIR%%/AFNI.sumarc
> %%DATADIR%%/Dist_Stamp

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Attachments on bug 186988: 140418 | 143565