8 files changed, 499 insertions, 59 deletions

diff --git a/science/afni/Makefile b/science/afni/Makefile
index d09ab6190453..7da45aa04035 100644
--- a/science/afni/Makefile
+++ b/science/afni/Makefile
@@ -11,7 +11,7 @@
 
 PORTNAME=	afni
 PORTVERSION=	2012.04.17.2129
-PORTREVISION=	7
+PORTREVISION=	8
 CATEGORIES=	science biology graphics
 MASTER_SITES=	http://personalpages.tds.net/~jwbacon/Ports/distfiles/AFNI/${PORTVERSION}/ \
 		http://www.acadix.biz/Ports/distfiles/AFNI/${PORTVERSION}/
@@ -23,26 +23,31 @@ EXTRACT_ONLY=	afni_src.tgz CA_EZ_v1.5-July3107.tgz
 MAINTAINER=	jwbacon@tds.net
 COMMENT=	Advanced Functional Neuro Imaging
 
-LIB_DEPENDS=	R:${PORTSDIR}/math/R \
-		gsl:${PORTSDIR}/math/gsl
+LICENSE=	GPLv2
+
+LIB_DEPENDS=	libXm.so:${PORTSDIR}/x11-toolkits/open-motif \
+		libR.so:${PORTSDIR}/math/R \
+		libgsl.so:${PORTSDIR}/math/gsl \
+		libnetcdf.so:${PORTSDIR}/science/netcdf-fortran
 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
 
-USES=		gettext iconv gmake motif
+CONFLICTS=	im-[0-9]* \
+		nifticlib-[0-9]* \
+		open-usp-tukubai-[0-9]*
 
-NO_STAGE=	yes
-BROKEN=	R_io.so fails to build with R-3.0.2
-DEPRECATED=	Broken for more than 6 months
-EXPIRATION_DATE=	2014-06-13
+USES=		gettext iconv gmake motif perl5
 
-.include <bsd.port.pre.mk>
+# Some prereqs use gcc anyway
+USE_GCC=	yes
 
-.if ${ARCH} == "sparc64"
-BROKEN=	Does not compile on sparc64: "undefined reference to '_mcount'"
-.endif
+.include <bsd.port.options.mk>
+
+BROKEN_sparc64=	Does not compile: "undefined reference to '_mcount'"
 
 USE_GL=		glw glu
 USE_XORG=	xi
@@ -55,12 +60,10 @@ ALL_TARGET=	vastness suma
 ###########################################################################
 # 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 \
@@ -85,52 +88,50 @@ post-extract:
 	@${REINPLACE_CMD} "s|%%PREFIX%%|${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
-.if !defined(NOPORTDOCS)
-	${MKDIR} ${DOCSDIR} ${PREFIX}/etc/mri
-	${INSTALL_DATA} ${STAGE}/doc/* ${DOCSDIR}
+	${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 ${PORT_OPTIONS:MDOCS}
+	${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:
-	@${CAT} ${WRKDIR}/pkg-message
-
-.include <bsd.port.post.mk>
+.include <bsd.port.mk>
diff --git a/science/afni/files/Makefile.FreeBSD_PORT b/science/afni/files/Makefile.FreeBSD_PORT
index aa079f5551bf..00521ba24363 100644
--- a/science/afni/files/Makefile.FreeBSD_PORT
+++ b/science/afni/files/Makefile.FreeBSD_PORT
@@ -53,7 +53,7 @@ ifeq (${ARCH}, ia64)
 CEXTRA += -DPIC -fPIC
 endif
 
-CFLAGS += ${CEXTRA}
+CFLAGS += -Wno-return-type -Wno-switch ${CEXTRA}
 CC     += ${CFLAGS}
 
 CCVOL  = ${CC}
@@ -67,6 +67,9 @@ IFLAGS = -I. -I${LOCALBASE}/include
 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 --git a/science/afni/files/patch-Makefile.INCLUDE b/science/afni/files/patch-Makefile.INCLUDE
index 589f7546e7ca..a27fa8ba3f2d 100644
--- a/science/afni/files/patch-Makefile.INCLUDE
+++ b/science/afni/files/patch-Makefile.INCLUDE
@@ -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 --git a/science/afni/files/patch-XmHTML-Makefile b/science/afni/files/patch-XmHTML-Makefile
new file mode 100644
index 000000000000..bd46f538596e
--- /dev/null
+++ b/science/afni/files/patch-XmHTML-Makefile
@@ -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 --git a/science/afni/files/patch-misc_math.c b/science/afni/files/patch-misc_math.c
index 08b62b57fe95..bf454306bb8d 100644
--- a/science/afni/files/patch-misc_math.c
+++ b/science/afni/files/patch-misc_math.c
@@ -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 --git a/science/afni/files/pkg-message.in b/science/afni/files/pkg-message.in
index 04b0f86e4681..d25dc21a0130 100644
--- a/science/afni/files/pkg-message.in
+++ b/science/afni/files/pkg-message.in
@@ -12,8 +12,15 @@ or DRI (graphics/dri).
 
 ---
 
-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 --git a/science/afni/pkg-descr b/science/afni/pkg-descr
index a4cd1efaa5c7..0ea153f1f534 100644
--- a/science/afni/pkg-descr
+++ b/science/afni/pkg-descr
@@ -2,4 +2,4 @@ This is a port of AFNI, Analysis of Functional Neuro Imaging.  AFNI is
 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 --git a/science/afni/pkg-plist b/science/afni/pkg-plist
index b104f83a875f..f2df2d3585b1 100644
--- a/science/afni/pkg-plist
+++ b/science/afni/pkg-plist
@@ -1,3 +1,4 @@
+@comment Generated by ports-mgmt/genplist
 bin/1dAstrip
 bin/1dBandpass
 bin/1dBport
@@ -339,7 +340,6 @@ bin/afni_abut
 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/ask_me.py
 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_tt
 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_vol2surf.so
 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