Update to 2015.11.13.

Upgrade to a more recent snapshot, and stop requiring GCC. PR: 206930 Submitted by: Jason Bacon <bacon4000@gmail.com> (maintainer)
author: Raphael Kubo da Costa <rakuco@FreeBSD.org> 2016-02-27 22:03:29 +0000
committer: Raphael Kubo da Costa <rakuco@FreeBSD.org> 2016-02-27 22:03:29 +0000
commit: 3ae338d181e661aa00c8f42ddd7081ffd600900c (patch)
tree: 3dfad55162ffbd0d9772a34aef2dca44ed5e370a /science/afni
parent: e13f5b87d6e381c543bb3066d1bf09e5e655432a (diff)
download: ports-3ae338d181e661aa00c8f42ddd7081ffd600900c.tar.gz
ports-3ae338d181e661aa00c8f42ddd7081ffd600900c.zip
10 files changed, 794 insertions, 445 deletions
diff --git a/science/afni/Makefile b/science/afni/Makefile
index 1e7e5003da7b..14254ed12663 100644
--- a/science/afni/Makefile
+++ b/science/afni/Makefile
@@ -10,26 +10,23 @@
 # you can download the latest sources and build manually.
 
 PORTNAME=	afni
-PORTVERSION=	2012.04.17.2129
-PORTREVISION=	12
+PORTVERSION=	2015.11.13
 CATEGORIES=	science biology graphics
-MASTER_SITES=	http://www.acadix.biz/Ports/distfiles/AFNI/${PORTVERSION}/
-DISTFILES=	afni_src.tgz afni.1 3dClustBust.c \
-		TTatlas+tlrc.BRIK.gz TTatlas+tlrc.HEAD CA_EZ_v1.5-July3107.tgz
-DIST_SUBDIR=	AFNI-${PORTVERSION}
-EXTRACT_ONLY=	afni_src.tgz CA_EZ_v1.5-July3107.tgz
+MASTER_SITES=	http://www.acadix.biz/Ports/distfiles/
 
 MAINTAINER=	bacon4000@gmail.com
 COMMENT=	Advanced Functional Neuro Imaging
 
 LICENSE=	GPLv2
 
+BUILD_DEPENDS=	gm4:${PORTSDIR}/devel/m4
 LIB_DEPENDS=	libXm.so:${PORTSDIR}/x11-toolkits/open-motif \
 		libR.so:${PORTSDIR}/math/R \
 		libgsl.so:${PORTSDIR}/math/gsl \
-		libnetcdff.so:${PORTSDIR}/science/netcdf-fortran
+		libnetcdff.so:${PORTSDIR}/science/netcdf-fortran \
+		libxml2.so:${PORTSDIR}/textproc/libxml2 \
+		libf2c.so:${PORTSDIR}/lang/f2c
 RUN_DEPENDS=	mpeg_encode:${PORTSDIR}/multimedia/mpeg_encode \
-		whirlgif:${PORTSDIR}/graphics/whirlgif \
 		ppmtogif:${PORTSDIR}/graphics/netpbm \
 		endian:${PORTSDIR}/sysutils/endian \
 		qhull:${PORTSDIR}/math/qhull5
@@ -38,22 +35,23 @@ CONFLICTS=	im-[0-9]* \
 		nifticlib-[0-9]* \
 		open-usp-tukubai-[0-9]*
 
-USES=		gettext gmake iconv jpeg:run motif perl5 shebangfix
-SHEBANG_FILES=	suma_change_spec 3dPAR2AFNI.pl
+USES=		gettext gmake iconv jpeg:run motif perl5 python shebangfix tar:xz
+SHEBANG_FILES=	suma_change_spec \
+		3dPAR2AFNI.pl \
+		python_scripts/afni_restproc.py \
+		python_scripts/lib_fat_Rfactor.py \
+		pkundu/meica.libs/siemens_me2nii.py
+USE_GNOME=	glib20
 
-# Some prereqs use gcc anyway
-USE_GCC=	yes
-
-OPTIONS_DEFINE=	DOCS
+.include <bsd.port.options.mk>
 
 BROKEN_sparc64=	Does not compile: "undefined reference to '_mcount'"
 
 USE_GL=		glw glu
 USE_XORG=	xi
-MAKE_ENV=	CC="${CC}"
+MAKE_ENV=	CC="${CC}" R_SHARE_DIR=${LOCALBASE}/lib/R/share
 MAKE_JOBS_UNSAFE=yes
 
-WRKSRC=		${WRKDIR}/afni_src
 ALL_TARGET=	vastness suma
 
 ###########################################################################
@@ -77,14 +75,36 @@ X11R6_FILES=	coxplot/Makefile \
 		SUMA/SUMA_Surface_IO.c
 
 post-extract:
-	@${CP} -f ${FILESDIR}/Makefile.FreeBSD_PORT ${WRKSRC}/Makefile
 .for f in ${X11R6_FILES}
-	@${REINPLACE_CMD} -e 's|/usr/X11R6|$${LOCALBASE}|g' ${WRKSRC}/${f}
+	@${REINPLACE_CMD} \
+		-e 's|/usr/X11R6|$${LOCALBASE}|g' ${WRKSRC}/${f}
 .endfor
-	@${REINPLACE_CMD} -E 's|AFNI_[0-9_]+|${PORTVERSION}|g' ${WRKSRC}/AFNI_label.h
-	@${CP} ${DISTDIR}/${DIST_SUBDIR}/afni.1 ${WRKDIR}
-	@${CP} ${DISTDIR}/${DIST_SUBDIR}/3dClustBust.c ${WRKSRC}
-	@${REINPLACE_CMD} "s|%%PREFIX%%|${PREFIX}|g" ${WRKDIR}/afni.1
+	@${REINPLACE_CMD} \
+		-E 's|AFNI_[0-9_]+|${PORTVERSION}|g' ${WRKSRC}/AFNI_label.h
+	@${REINPLACE_CMD} \
+		-e "s|%%PREFIX%%|${PREFIX}|g" ${WRKSRC}/afni.1
+	@${CP} ${FILESDIR}/Makefile ${WRKSRC}
+	@${RM} ${WRKSRC}/3DEdge/src/Makefile.orig
+
+# shebangfix misses /bin/python on 10.1
+post-patch:
+	${REINPLACE_CMD} -e "s|-lglib|-lglib-2.0|g" \
+		${WRKSRC}/SUMA/SUMA_Makefile
+	${REINPLACE_CMD} -e "s|/bin/python|${PYTHON_CMD}|g" \
+		${WRKSRC}/python_scripts/lib_fat_Rfactor.py
+	${REINPLACE_CMD} \
+		-e 's|os\.path\.dirname(sys\.argv\[0\])|"${PREFIX}/libexec"|g' \
+		${WRKSRC}/pkundu/meica.py
+	${REINPLACE_CMD} \
+		-e 's|g_info|afni_g_info|g' \
+		${WRKSRC}/rickr/Dimon.c \
+		${WRKSRC}/rickr/Dimon1.c \
+		${WRKSRC}/afni_history_rickr.c \
+		${WRKSRC}/mri_dicom_stuff.c \
+		${WRKSRC}/mri_process_siemens.c \
+		${WRKSRC}/mri_read_dicom.c \
+		${WRKSRC}/to3d.c \
+		${WRKSRC}/mri_dicom_stuff.h
 
 post-build:
 	${MKDIR} ${PRESTAGE}/bin \
@@ -107,31 +127,32 @@ post-build:
 		${PRESTAGE}/include
 	${MV}	${INSTALL_WRKSRC}/README* \
 		${PRESTAGE}/doc
-	${MV}	${INSTALL_WRKSRC}/abut ${INSTALL_WRKSRC}/afni_abut
 	for binary in `${FILE} ${INSTALL_WRKSRC}/* | fgrep 'ELF' | ${AWK} -F ':' ' { print $$1 }'` ; do \
 		${MV} $${binary} ${PRESTAGE}/bin ; \
 	done
 	${MV}	${INSTALL_WRKSRC}/* \
 		${PRESTAGE}/scripts
+	${MV}	${PRESTAGE}/scripts/meica.libs ${PRESTAGE}
 
 do-install:
 	${MKDIR} ${STAGEDIR}${DATADIR} \
 		${STAGEDIR}${PREFIX}/lib/afni \
 		${STAGEDIR}${PREFIX}/include/afni
+	for f in ${PRESTAGE}/lib/*; do \
+		${STRIP_CMD} $${f}; \
+	done
 	${INSTALL_DATA} ${PRESTAGE}/lib/* ${STAGEDIR}${PREFIX}/lib/afni
 	${INSTALL_DATA} ${PRESTAGE}/include/* ${STAGEDIR}${PREFIX}/include/afni
-	${CP} -R ${PRESTAGE}/share/* ${STAGEDIR}${DATADIR}
+	cd ${PRESTAGE}/share && ${COPYTREE_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
-	${MKDIR} ${STAGEDIR}${PREFIX}/etc/mri
+	cd ${PRESTAGE} && ${COPYTREE_BIN} meica.libs \
+		${STAGEDIR}${PREFIX}/libexec
+	${INSTALL_DATA} ${WRKSRC}/Atlases/* ${STAGEDIR}${DATADIR}
+	${INSTALL_MAN} ${WRKSRC}/afni.1 ${STAGEDIR}${MAN1PREFIX}/man/man1
+	${MKDIR} ${STAGEDIR}${DOCSDIR} ${STAGEDIR}${PREFIX}/etc/mri
+	${INSTALL_DATA} ${PRESTAGE}/doc/* ${STAGEDIR}${DOCSDIR}
 	${INSTALL_SCRIPT} ${WRKDIR}/afni.cshrc ${WRKDIR}/afni.profile \
 		${STAGEDIR}${PREFIX}/etc/mri
 
-do-install-DOCS-on:
-	${MKDIR} ${STAGEDIR}${DOCSDIR}
-	${INSTALL_DATA} ${PRESTAGE}/doc/* ${STAGEDIR}${DOCSDIR}
-
 .include <bsd.port.mk>
diff --git a/science/afni/distinfo b/science/afni/distinfo
index 43783afdeb8c..95dcb05123df 100644
--- a/science/afni/distinfo
+++ b/science/afni/distinfo
@@ -1,12 +1,2 @@
-SHA256 (AFNI-2012.04.17.2129/afni_src.tgz) = 815ff58ef10f2174211e507ac4d527a0025f31e0a54976f5915f8ff3a0a95209
-SIZE (AFNI-2012.04.17.2129/afni_src.tgz) = 18635542
-SHA256 (AFNI-2012.04.17.2129/afni.1) = f134d1f869b1dfd618c61e58fd24b9c4dcfea9c25bc5b1c26dbbb141719cd6f8
-SIZE (AFNI-2012.04.17.2129/afni.1) = 1667
-SHA256 (AFNI-2012.04.17.2129/3dClustBust.c) = 2ca07ff08acc41d7c8895d06ae9effa2c6058aada45fc5381b63a726600dded2
-SIZE (AFNI-2012.04.17.2129/3dClustBust.c) = 106517
-SHA256 (AFNI-2012.04.17.2129/TTatlas+tlrc.BRIK.gz) = 0b5b087006e07e05c5f0c8306acaade955924f744457cec0c00844cc2e9e67cd
-SIZE (AFNI-2012.04.17.2129/TTatlas+tlrc.BRIK.gz) = 159912
-SHA256 (AFNI-2012.04.17.2129/TTatlas+tlrc.HEAD) = 57262785bcc87ef5aa0f0cddc82d67c15e799ac9e2e12127e8eeb4d348ccf55e
-SIZE (AFNI-2012.04.17.2129/TTatlas+tlrc.HEAD) = 1830
-SHA256 (AFNI-2012.04.17.2129/CA_EZ_v1.5-July3107.tgz) = 4300ec3e94b7dfd43f70b3f321f8aa290bd9f6e6420a414f251dbd790df8af02
-SIZE (AFNI-2012.04.17.2129/CA_EZ_v1.5-July3107.tgz) = 2654150
+SHA256 (afni-2015.11.13.tar.xz) = b8647ed2f522a520d90cbfd3da70d34849cec421678ff3baf0ecbb6e9e72414b
+SIZE (afni-2015.11.13.tar.xz) = 48722840
diff --git a/science/afni/files/Makefile.FreeBSD_PORT b/science/afni/files/Makefile
index 75dadc8694eb..124f70fc9155 100644
--- a/science/afni/files/Makefile.FreeBSD_PORT
+++ b/science/afni/files/Makefile
@@ -40,6 +40,8 @@
 
 USE_ZLIB = -DHAVE_ZLIB
 LZLIB    = -lz
+USE_GIFTI = -DHAVE_GIFTI
+LGIFTI    = -L${LOCALBASE}/lib -lexpat
 
 CC?     = cc
 LD?     = ${CC}
@@ -94,17 +96,18 @@ LIBDIR = ${INSTALLDIR}
 
 # for dynamic linking
 
-LLIBS  = -lmri -lf2c -lXm -lXp -lXpm -lXext -lXmu -lXt -lX11 -lm $(LZLIB)
+LLIBS  = -lmri -lf2c -lXm -lXp -lXpm -lXext -lXmu -lXt -lX11 -lm $(LZLIB) $(LGIFTI)
 
 # vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv
 # For suma (NO STATIC LINKING OF GL libs)
-SUMA_INCLUDE_PATH = -I${LOCALBASE}/include -I./ -I../ -I../niml/ -Igts/src 
+SUMA_INCLUDE_PATH = -I${LOCALBASE}/include/glib-2.0 -I${LOCALBASE}/lib/glib-2.0/include -I${LOCALBASE}/include -I./ -I../ -I../niml/ -Igts/src 
 SUMA_LINK_PATH = -L/usr/lib -L${LOCALBASE}/lib -L../
 #use -lGLw if you have libGLw.a or libGLw.so* or 
 #  -lMesaGLw if you have Mesa's version (libMesaGLw*) of libGLw
-SUMA_LINK_LIB = -lXm -lGLw -lGLU -lGL -lXmu -lXp -lXt -lXext -lX11 -lm $(LZLIB)
+SUMA_LINK_LIB = -lXm -lGLw -lGLU -lGL -lXmu -lXp -lXt -lXext -lX11 -lm $(LZLIB) -lxml2 -lexpat
 SUMA_MAKEFILE_NAME = SUMA_Makefile
 SUMA_BIN_ARCHIVE = SUMA_FreeBSD.tar
+SUMA_GLIB_VER = -2.0
 # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 ###############################################################
diff --git a/science/afni/files/patch-Makefile.INCLUDE b/science/afni/files/patch-Makefile.INCLUDE
index 19058fc5be2c..11cff7353590 100644
--- a/science/afni/files/patch-Makefile.INCLUDE
+++ b/science/afni/files/patch-Makefile.INCLUDE
@@ -1,60 +1,69 @@
---- Makefile.INCLUDE.orig	2012-04-17 15:56:21.000000000 -0500
-+++ Makefile.INCLUDE	2013-10-30 08:19:45.000000000 -0500
-@@ -48,7 +48,7 @@
+--- Makefile.INCLUDE.orig	2015-11-06 21:25:04 UTC
++++ Makefile.INCLUDE
+@@ -50,7 +50,7 @@ MISC    = AFNI_atlas_spaces.niml AFNI.Xd
  ## AFNI package, but included because they are useful.  Some of
  ## them are Open Source programs, not from the AFNI group at all.
  
--EXTRAS   = cjpeg djpeg whirlgif mpeg_encode myget Xphace rmz aiv mycat $(EXPROGS)
-+EXTRAS   = myget Xphace rmz aiv 3dClustBust $(EXPROGS)
+-EXTRAS   = cjpeg djpeg whirlgif mpeg_encode myget Xphace rmz aiv mycat quotize $(EXPROGS)
++EXTRAS   = 3dClustBust whirlgif myget Xphace rmz aiv mycat quotize $(EXPROGS)
  
  # mpegtoppm in above list
  
-@@ -58,7 +58,7 @@
+@@ -60,7 +60,7 @@ EXTRAS   = cjpeg djpeg whirlgif mpeg_enc
  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       \
++               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 @@
+@@ -72,7 +72,7 @@ PROGRAMS = afni to3d from3d abut 3dclust
             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       \
++           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 @@
+@@ -92,7 +92,7 @@ PROGRAMS = afni to3d from3d abut 3dclust
             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                       \
++           niccc 3dkmeans 3dXYZcat 3dPolyfit 3dNwarpApply        \
             1dCorrelate 3dCountSpikes 3dNwarpCalc dicom_hinfo apsearch 1dBport   \
-            3dNormalityTest                                                      \
-            $(EXTRAS)
-@@ -97,7 +97,7 @@
+            3dNormalityTest 3dmask_tool FIRdesign help_format 2perm 3dClustCount \
+            column_cat 3dUnifize 3dNwarpCat 3dQwarp 3dLocalHistog 3dNwarpAdjust  \
+@@ -104,7 +104,7 @@ PROGRAMS = afni to3d from3d abut 3dclust
  PROGRAMS_NOPLUG = afni to3d from3d abut 3dclust nsize 3dinfo 3dproject 3dmerge      \
                    sfim tfim ftosh 3dttest 3ddup imrotate imreg imstat 3dnoise count \
                    fim2 imand FD2 sqwave immask imdump imaver 3dhistog 3dfim imupsam \
 -                      cdf 2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 3drefit    \
-+                      2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 3drefit        \
++                      2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 3drefit    \
                    waver 3dnewid 3dcalc ccalc imcalc 2dImReg 3dmaskave adwarp fdrval \
                    3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna      \
                    imstack byteorder 3dDeconvolve 3dTcat 3drotate 3dvolreg 1dplot    \
-@@ -133,7 +133,7 @@
+@@ -144,7 +144,7 @@ PROGRAMS_NOPLUG = afni to3d from3d abut 
  PROGRAMS_EXE = afni.exe to3d from3d abut 3dclust nsize 3dinfo 3dproject 3dmerge   \
                 sfim tfim ftosh 3dttest 3ddup imrotate imreg imstat 3dnvals count  \
                 fim2 imand FD2 sqwave immask imdump imaver 3dhistog 3dfim 3dGetrow \
 -                   cdf 2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta \
-+                   2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta     \
++                   2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta \
                 waver 3dnewid 3dcalc ccalc imcalc 1dmatcalc 3drefit 3dbucket       \
                 3dAFNItoNIML    AlphaSim 3dFWHM plugout_tt 3dnoise plugout_ijk     \
                 3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna       \
-@@ -282,6 +282,9 @@
+@@ -276,7 +276,7 @@ prog_list:
+ 	echo "$(PROGRAMS) $(SCRIPTS) $(SUMA_PROGS) $(SUMA_GTS_PROGS)    \
+                 $(PY_SCRIPTS)" | tr ' ' '\n' | LC_COLLATE=C sort | uniq \
+ 		> ___prog_list.txt
+-	make -s -f ptaylor/Makefile.ptaylor.INCLUDE echo_progs | \
++	$(MAKE) -s -f ptaylor/Makefile.ptaylor.INCLUDE echo_progs | \
+ 		tr ' ' '\n' | LC_COLLATE=C sort | uniq >> ___prog_list.txt
+ 	cat ___prog_list.txt | LC_COLLATE=C sort | uniq >> prog_list.txt
+ 	\rm -f ___prog_list.txt
+@@ -364,6 +364,9 @@ byteorder:byteorder.o
  3dbuc2fim:3dbuc2fim.o
  	$(CC) -o 3dbuc2fim 3dbuc2fim.o $(LFLAGS) $(LLIBS)
  
@@ -64,378 +73,27 @@
  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"
-+	$(MAKE_CMD) netcdf_attr.o CCMIN="${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)' \
-+	  $(MAKE_CMD) f2c clean 'RM=$(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)'            \
-+	  $(MAKE_CMD) libf2c.a clean 'RM=$(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 ;          \
-+	  $(MAKE_CMD) 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)'        \
-+	  $(MAKE_CMD) libcoxplot.a clean 'RM=$(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)'      \
-+	$(MAKE_CMD) file_tool 'RM=$(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)'        	\
-+	$(MAKE_CMD) Dimon 'RM=$(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)'        	\
-+	$(MAKE_CMD) Imon 'RM=$(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)'  \
-+	$(MAKE_CMD) serial_helper 'RM=$(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)'         \
-+	$(MAKE_CMD) gtest 'RM=$(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)'     \
-+	  $(MAKE_CMD) libvolpack.a clean 'RM=$(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 \
-+	  $(MAKE_CMD) qhull rbox qdelaunay clean \
- 	        'RM=$(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)' ; \
-+	  $(MAKE_CMD) qhull clean 'RM=$(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 ; $(MAKE_CMD) clean lib3DEdge.a 'RM=$(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/ ; $(MAKE_CMD) all 'CC=$(CCFAST)' 'CCSVD=$(CCSVD)' ; $(MV) *.o .. ; )
- 
- #######
- # Ditto for NIML objects
- 
- $(NIML_OBJS):niml.h
--	( cd niml/ ; $(MAKE) all 'CC=$(CC)' ; $(MV) *.o .. ; )
-+	( cd niml/ ; $(MAKE_CMD) all 'CC=$(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 ; $(MAKE_CMD) 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 ; )
-+          $(MAKE_CMD) clean ; )
- 
- #######
- # 27 Jul 2001 - for fun
- 
- gifsicle:
- 	( cd gifsicledir ;                                                  \
--	  $(MAKE) gifsicle clean 'RM=$(RM)' 'CC=$(CC)' 'LFLAGS=$(LFLAGS)' ; \
-+	  $(MAKE_CMD) gifsicle clean 'RM=$(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)' ; \
-+	  $(MAKE_CMD) mpeg_encode clean 'RM=$(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 ; )
-+	  $(MAKE_CMD) ; mv doc/sample2 ../mpegtoppm ; $(MAKE_CMD) 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 )
-+          $(MAKE_CMD) ; $(MV) cjpeg djpeg libjpeg.a .. ;            \
-+          $(MAKE_CMD) clean ; $(RM) Makefile )
+@@ -2728,8 +2731,8 @@ cjpeg:
+           $(MAKE) 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   )
++	( cd XmHTML ; $(MAKE) lib 'CC=$(CC)' 'II=$(IFLAGS)' ; \
++		$(MV) lib/libXmHTML.a .. ; $(MAKE) 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)' \
-+	  $(MAKE_CMD) libfftw.a clean 'RM=$(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)' \
-+	  $(MAKE_CMD) libclam.a clean 'RM=$(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  ;	\
-+	$(MAKE_CMD) afni_all  ;	\
- 	cd ../	;		)
- 
- libsegtools.a: avovk/cluster_floatNOMASK.c avovk/thd_segtools_fNM.c
- 	( cd avovk ;	\
- 	./@MakeLocalMake	;\
--	$(MAKE) libsegtools.a  ;	\
-+	$(MAKE_CMD) libsegtools.a  ;	\
- 	$(CP) libsegtools.a ../;	\
- 	cd ../	;		)
- 
-@@ -2836,13 +2839,13 @@
- ptaylor_all: 
- 	( cd ptaylor ;	\
- 	./@MakeLocalMake	;\
--	$(MAKE) all  ;	\
-+	$(MAKE_CMD) all  ;	\
- 	cd ../	;		)
- 
- libtracktools.a: ptaylor/libtracktools.a
- 	( cd ptaylor ;	\
- 	./@MakeLocalMake	;\
--	$(MAKE) libtracktools.a  ;	\
-+	$(MAKE_CMD) 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)' \
-+	$(MAKE_CMD) -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=$(MAKE_CMD)'     \
- 	'CC=$(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 ;	\
-+	$(MAKE_CMD) -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)' \
-+	$(MAKE_CMD) -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=$(MAKE_CMD)'     \
- 	'CC=$(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 \
-+	$(MAKE_CMD) -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=$(MAKE)'     \
-+        'MAKE=$(MAKE_CMD)'     \
- 	'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)' \
-+	$(MAKE_CMD) -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=$(MAKE)'     \
-+        'MAKE=$(MAKE_CMD)'     \
- 	'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)' \
-+	$(MAKE_CMD) -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=$(MAKE_CMD)'     \
- 	'CC=$(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)' \
-+	$(MAKE_CMD) -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=$(MAKE_CMD)'     \
- 	'CC=$(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 \
-+	$(MAKE_CMD) -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=$(MAKE)'     \
-+        'MAKE=$(MAKE_CMD)'     \
- 	'CC=$(CC)' 'RM=$(RM)' 'CEXTRA=$(CEXTRA)' 'MV=$(MV)' 'CP=$(CP)'\
- 	'TAR=$(TAR)' 'MKDIR=$(MKDIR)';	\
- 	cd ../	;)
-@@ -3155,6 +3158,7 @@
+@@ -3518,8 +3521,9 @@ toyR: toyR.c AFNI_embeddedRCall.o
  ####
  R_io.so:R_io.c libmri.a
  	( if which R >/dev/null ; then \
-+	export MAKE=${MAKE_CMD} ;\
- 	echo PKG_CPPFLAGS = $(INFLAGS)  > Makevars ;\
- 	echo PKG_LIBS =  $(LFLAGS) $(LLIBS) >> Makevars ;\
- 	R CMD SHLIB R_io.c ; \
+-	echo PKG_CPPFLAGS = $(INFLAGS)  > Makevars ;\
+-	echo PKG_LIBS =  $(LFLAGS) $(LLIBS) >> Makevars ;\
+-	R CMD SHLIB R_io.c ; \
++	echo PKG_CPPFLAGS = $(INFLAGS) -I${LOCALBASE}/lib/R/include > Makevars ;\
++	echo PKG_LIBS =  $(LFLAGS) $(LLIBS) -L${LOCALBASE}/lib/R/lib >> Makevars ;\
++	# Fails because R uses 'make' instead of gmake R CMD SHLIB -n R_io.c; \
++	$(MAKE) -f 'Makevars' -f '/usr/local/lib/R/etc/Makeconf' -f '/usr/local/lib/R/share/make/shlib.mk' SHLIB='R_io.so' OBJECTS='R_io.o';\
+ 	else echo WARNING: Cannot build R_io.so because R is not installed;\
+ 	fi ; )
diff --git a/science/afni/files/patch-XmHTML-Makefile b/science/afni/files/patch-XmHTML-Makefile
index bd46f538596e..cafc4095d50b 100644
--- a/science/afni/files/patch-XmHTML-Makefile
+++ b/science/afni/files/patch-XmHTML-Makefile
@@ -1,6 +1,6 @@
---- 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 @@
+--- XmHTML/Makefile.orig	2015-11-06 21:25:06 UTC
++++ XmHTML/Makefile
+@@ -48,7 +48,7 @@ AR    = ar cq 
  RANLIB= ranlib
  
  SHELL     = /bin/sh
diff --git a/science/afni/files/patch-misc_math.c b/science/afni/files/patch-misc_math.c
index bf454306bb8d..50623944f078 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	2010-06-22 08:15:42.000000000 -0500
-+++ misc_math.c	2013-10-29 20:59:28.000000000 -0500
+--- misc_math.c.orig	2015-11-06 21:25:08 UTC
++++ misc_math.c
 @@ -1,6 +1,13 @@
  
 +/* For older libm */
diff --git a/science/afni/files/patch-netcdf-3.5.0_src_configure b/science/afni/files/patch-netcdf-3.5.0_src_configure
new file mode 100644
index 000000000000..e7a491b4a1ac
--- /dev/null
+++ b/science/afni/files/patch-netcdf-3.5.0_src_configure
@@ -0,0 +1,43 @@
+--- netcdf-3.5.0/src/configure.orig	2015-11-06 21:25:09 UTC
++++ netcdf-3.5.0/src/configure
+@@ -933,10 +933,10 @@ echo "configure:928: checking for top-le
+ 
+ 
+ 
+-    echo "checking for m4 preprocessor" 1>&6
+-echo "configure:938: checking for m4 preprocessor" >&5
++    echo "checking for gm4 preprocessor" 1>&6
++echo "configure:938: checking for gm4 preprocessor" >&5
+     case "${M4-unset}" in
+-	unset) for ac_prog in m4 gm4
++	unset) for ac_prog in gm4
+ do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+ set dummy $ac_prog; ac_word=$2
+@@ -969,9 +969,9 @@ fi
+ 
+ test -n "$M4" && break
+ done
+-test -n "$M4" || M4="m4"
++test -n "$M4" || M4="gm4"
+  ;;
+-	*) for ac_prog in $M4 m4 gm4
++	*) for ac_prog in $M4 gm4
+ do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+ set dummy $ac_prog; ac_word=$2
+@@ -1004,11 +1004,11 @@ fi
+ 
+ test -n "$M4" && break
+ done
+-test -n "$M4" || M4="m4"
++test -n "$M4" || M4="gm4"
+  ;;
+     esac
+-    echo $ac_n "checking m4 flags""... $ac_c" 1>&6
+-echo "configure:1012: checking m4 flags" >&5
++    echo $ac_n "checking gm4 flags""... $ac_c" 1>&6
++echo "configure:1012: checking gm4 flags" >&5
+     case "${M4FLAGS-unset}" in
+ 	unset) M4FLAGS=-B10000 ;;
+     esac
diff --git a/science/afni/files/patch-nifti_cifti_afni__xml.h b/science/afni/files/patch-nifti_cifti_afni__xml.h
new file mode 100644
index 000000000000..a71c92562531
--- /dev/null
+++ b/science/afni/files/patch-nifti_cifti_afni__xml.h
@@ -0,0 +1,10 @@
+--- nifti/cifti/afni_xml.h.orig	2015-11-06 21:25:14 UTC
++++ nifti/cifti/afni_xml.h
+@@ -5,6 +5,7 @@
+ #define AXML_MAX_ELEN  128   /* maximum element length */
+ 
+ #include <stdio.h>
++#include <inttypes.h>
+ 
+ /* ----------------------------------------------------------------------
+    This code is for generic reading of xml into structures.
diff --git a/science/afni/files/pkg-message.in b/science/afni/files/pkg-message.in
index d25dc21a0130..e0bde55e31aa 100644
--- a/science/afni/files/pkg-message.in
+++ b/science/afni/files/pkg-message.in
@@ -12,6 +12,12 @@ or DRI (graphics/dri).
 
 ---
 
+FreeBSD ports for other AFNI versions are available at
+
+    https://github.com/outpaddling/freebsd-ports-wip
+
+---
+
 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):
@@ -24,12 +30,9 @@ more of the following shared memory limits using sysctl (and
 
 ---
 
-The program "abut" has been renamed "afni_abut" to resolve a collision
-with the unixstat port.
-
----
-
 AFNI_PLUGIN_PATH should be set to %%PREFIX%%/lib/afni:%%DATADIR%%
 AFNI_GLOBAL_SESSION should be set to %%DATADIR%%.
+You can do this by sourcing %%PREFIX%%/etc/mri/afni.profiles for 
+Bourne-style shells or or %%PREFIX%%/etc/mri/afni.cshrc for C-style shells.
 
 =============================================================================
diff --git a/science/afni/pkg-plist b/science/afni/pkg-plist
index eb92e2b0807a..b44514a4eec0 100644
--- a/science/afni/pkg-plist
+++ b/science/afni/pkg-plist
@@ -1,8 +1,8 @@
-@comment Generated by ports-mgmt/genplist
 bin/1dAstrip
 bin/1dBandpass
 bin/1dBport
 bin/1dCorrelate
+bin/1dDW_Grad_o_Mat
 bin/1dFlagMotion
 bin/1dGC.R
 bin/1dMarry
@@ -28,6 +28,7 @@ bin/1dsvd
 bin/1dtranspose
 bin/24swap
 bin/2dImReg
+bin/2perm
 bin/2swap
 bin/3dABoverlap
 bin/3dAFNIto3D
@@ -40,6 +41,7 @@ bin/3dANALYZEtoAFNI
 bin/3dANOVA
 bin/3dANOVA2
 bin/3dANOVA3
+bin/3dAOV.R
 bin/3dAcost
 bin/3dAllineate
 bin/3dAnatNudge
@@ -57,17 +59,22 @@ bin/3dCM
 bin/3dCRUISEtoAFNI
 bin/3dClipLevel
 bin/3dClustBust
+bin/3dClustCount
 bin/3dClustSim
+bin/3dConformist
 bin/3dConvolve
 bin/3dCountSpikes
 bin/3dDFT
 bin/3dDTeig
 bin/3dDTtoDWI
+bin/3dDTtoNoisyDWI
 bin/3dDWItoDT
+bin/3dDWUncert
 bin/3dDeconvolve
 bin/3dDeconvolve_f
 bin/3dDespike
 bin/3dDetrend
+bin/3dEigsToDT
 bin/3dEmpty
 bin/3dEntropy
 bin/3dErrtsCormat
@@ -79,9 +86,11 @@ bin/3dFWHMx
 bin/3dFourier
 bin/3dFriedman
 bin/3dGC.R
+bin/3dGenFeatureDist
 bin/3dGenPriors
 bin/3dGetrow
 bin/3dGroupInCorr
+bin/3dHist
 bin/3dICA.R
 bin/3dICC.R
 bin/3dICC_REML.R
@@ -89,36 +98,57 @@ bin/3dIntracranial
 bin/3dInvFMRI
 bin/3dKS.R
 bin/3dKruskalWallis
+bin/3dLME
 bin/3dLME.R
 bin/3dLRflip
 bin/3dLSS
 bin/3dLocalBistat
+bin/3dLocalHistog
 bin/3dLocalPV
 bin/3dLocalSVD
 bin/3dLocalstat
 bin/3dMEMA
 bin/3dMEMA.R
 bin/3dMINCtoAFNI
+bin/3dMVM
+bin/3dMVM.R
 bin/3dMannWhitney
 bin/3dMaskToASCII
+bin/3dMatch
 bin/3dMax
 bin/3dMean
 bin/3dMedianFilter
 bin/3dNLfim
+bin/3dNetCorr
 bin/3dNormalityTest
 bin/3dNotes
+bin/3dNwarpAdjust
 bin/3dNwarpApply
 bin/3dNwarpCalc
+bin/3dNwarpCat
+bin/3dNwarpFuncs
+bin/3dNwarpXYZ
 bin/3dOverlap
 bin/3dPAR2AFNI.pl
+bin/3dPFM
+bin/3dPFM.R
 bin/3dPeriodogram
 bin/3dPolyfit
+bin/3dProbTrackID
+bin/3dPval
+bin/3dQwarp
 bin/3dREMLfit
+bin/3dROIMaker
 bin/3dROIstats
+bin/3dRSFC
 bin/3dRank
+bin/3dRankizer
+bin/3dReHo
 bin/3dRegAna
 bin/3dRetinoPhase
 bin/3dRowFillin
+bin/3dRprogDemo
+bin/3dRprogDemo.R
 bin/3dSeg
 bin/3dSetupGroupInCorr
 bin/3dSignatures
@@ -129,6 +159,8 @@ bin/3dStatClust
 bin/3dSurf2Vol
 bin/3dSurfMask
 bin/3dSynthesize
+bin/3dTORTOISEtoHere
+bin/3dTRfix
 bin/3dTSgen
 bin/3dTagalign
 bin/3dTcat
@@ -139,13 +171,17 @@ bin/3dTfitter
 bin/3dThreetoRGB
 bin/3dTnorm
 bin/3dToutcount
+bin/3dToyProg
+bin/3dTproject
 bin/3dTqual
+bin/3dTrackID
 bin/3dTshift
 bin/3dTsmooth
 bin/3dTsort
 bin/3dTstat
 bin/3dTwotoComplex
 bin/3dUndump
+bin/3dUnifize
 bin/3dUniformize
 bin/3dUpsample
 bin/3dVol2Surf
@@ -178,6 +214,7 @@ bin/3dinfill
 bin/3dinfo
 bin/3dkmeans
 bin/3dmaskSVD
+bin/3dmask_tool
 bin/3dmaskave
 bin/3dmaskdump
 bin/3dmatcalc
@@ -221,6 +258,7 @@ bin/@DoPerRoi.py
 bin/@DriveAfni
 bin/@DriveSuma
 bin/@ElectroGrid
+bin/@ExamineGenFeatDists
 bin/@FS_roi_label
 bin/@FSlabel2dset
 bin/@FindAfniDsetPath
@@ -233,7 +271,16 @@ bin/@GetAfniOrient
 bin/@GetAfniPrefix
 bin/@GetAfniRes
 bin/@GetAfniView
+bin/@Install_3dPFM_Demo
+bin/@Install_AfniRetinoDemo
+bin/@Install_ClustScat_Demo
+bin/@Install_DBSproc
+bin/@Install_FATCAT_DEMO
+bin/@Install_FATMVM_DEMO
 bin/@Install_InstaCorr_Demo
+bin/@Install_MEICA_Demo
+bin/@Install_RSFMRI_Motion_Group_Demo
+bin/@Install_TSrestMovieDemo
 bin/@IsoMasks
 bin/@MakeLabelTable
 bin/@NoExt
@@ -257,17 +304,22 @@ bin/@Shift_Volume
 bin/@ShowDynamicRange
 bin/@Spharm.examples
 bin/@SurfSmooth.HEAT_07.examples
+bin/@T1scale
 bin/@TimeDiff
 bin/@ToRAI
 bin/@UpdateAfni
 bin/@VolCenter
+bin/@afni.run.me
 bin/@align_partial_oblique
 bin/@auto_align
 bin/@auto_tlrc
 bin/@build_afni_Xlib
 bin/@clean_help_dir
 bin/@clip_volume
+bin/@compute_gcor
 bin/@demo_prompt
+bin/@diff.files
+bin/@diff.tree
 bin/@escape-
 bin/@fast_roi
 bin/@fix_FSsphere
@@ -277,11 +329,15 @@ bin/@help.AFNI
 bin/@isOblique
 bin/@make_plug_diff
 bin/@make_stim_file
+bin/@move.to.series.dirs
 bin/@np
 bin/@parse_afni_name
 bin/@parse_name
 bin/@radial_correlate
+bin/@simulate_motion
 bin/@statauxcode
+bin/@toMNI_Awarp
+bin/@toMNI_Qwarpar
 bin/@update.afni.binaries
 bin/AFNI_Batch_R
 bin/AFNI_atlas_spaces.niml
@@ -289,6 +345,7 @@ bin/AFNIio.R
 bin/AFNIplot.R
 bin/AlphaSim
 bin/AnalyzeTrace
+bin/BrainSkin
 bin/CompareSurfaces
 bin/ConvertDset
 bin/ConvertSurface
@@ -296,12 +353,17 @@ bin/ConvexHull
 bin/CreateIcosahedron
 bin/DTIStudioFibertoSegments
 bin/Dimon
+bin/Dimon1
 bin/DriveSuma
 bin/ExamineXmat
 bin/ExamineXmat.R
 bin/FD2
+bin/FIRdesign
 bin/FSread_annot
+bin/GLTsymtest
+bin/HalloSuma
 bin/Ifile
+bin/InstaTract
 bin/IsoSurface
 bin/Level2.R
 bin/MakeColorMap
@@ -334,13 +396,17 @@ bin/SurfToSurf
 bin/SurfaceMetrics
 bin/Vecwarp
 bin/Xphace
+bin/abut
 bin/adwarp
 bin/afni
-bin/afni_abut
 bin/afni_base.py
 bin/afni_history
+bin/afni_open
 bin/afni_proc.py
+bin/afni_restproc.py
 bin/afni_run_R
+bin/afni_skeleton.py
+bin/afni_system_check.py
 bin/afni_util.py
 bin/afni_vcheck
 bin/afni_xmat.py
@@ -348,9 +414,12 @@ bin/aiv
 bin/align_epi_anat.py
 bin/apsearch
 bin/ask_me.py
+bin/auto_warp.py
 bin/byteorder
 bin/cat_matvec
 bin/ccalc
+bin/cifti_tool
+bin/column_cat
 bin/count
 bin/db_mod.py
 bin/demo.fixed.niml.do
@@ -360,6 +429,13 @@ bin/dicom_hinfo
 bin/dicom_to_raw
 bin/eg_main_chrono.py
 bin/ent16
+bin/fat_lat_csv.py
+bin/fat_mat_sel.py
+bin/fat_mvm_gridconv.py
+bin/fat_mvm_prep.py
+bin/fat_mvm_review.py
+bin/fat_mvm_scripter.py
+bin/fat_roi_row.py
 bin/fdrval
 bin/fftest
 bin/file_tool
@@ -371,12 +447,16 @@ bin/ge_header
 bin/gen_epi_review.py
 bin/gen_group_command.py
 bin/gen_ss_review_scripts.py
+bin/gen_ss_review_table.py
+bin/gifti_tool
 bin/gui_uber_align_test.py
 bin/gui_uber_skel.py
 bin/gui_uber_subj.py
 bin/gui_uber_ttest.py
 bin/gui_xmat.py
+bin/help_format
 bin/im2niml
+bin/images_equal
 bin/imand
 bin/imaver
 bin/imcalc
@@ -392,32 +472,42 @@ bin/imupsam
 bin/inspec
 bin/lib_RR_plot.py
 bin/lib_afni1D.py
+bin/lib_fat_Rfactor.py
+bin/lib_fat_funcs.py
+bin/lib_fat_plot_sel.py
 bin/lib_matplot.py
 bin/lib_qt_gui.py
 bin/lib_realtime.py
 bin/lib_subjects.py
 bin/lib_surf_clustsim.py
+bin/lib_system_check.py
 bin/lib_textdata.py
 bin/lib_timing.py
 bin/lib_uber_align.py
 bin/lib_uber_skel.py
 bin/lib_uber_subject.py
 bin/lib_uber_ttest.py
+bin/lib_vars_object.py
 bin/lib_wx.py
 bin/lpc_align.py
 bin/make_pq_script.py
 bin/make_random_timing.py
 bin/make_stim_times.py
+bin/map_TrackID
 bin/mayo_analyze
+bin/meica.py
 bin/module_test_lib.py
 bin/mritopgm
+bin/mycat
 bin/myget
 bin/neuro_deconvolve.py
 bin/nicat
 bin/niccc
 bin/nifti1_test
+bin/nifti1_tool
 bin/nifti_tool
 bin/niml_feedme
+bin/niprobe
 bin/nsize
 bin/option_list.py
 bin/plugout_drive
@@ -428,6 +518,10 @@ bin/prompt_user
 bin/python_module_test.py
 bin/quick.alpha.vals.py
 bin/quickspec
+bin/quotize
+bin/rPkgsInstall
+bin/rPkgsInstall.R
+bin/read_matlab_files.py
 bin/realtime_receiver.py
 bin/rmz
 bin/rotcom
@@ -450,19 +544,23 @@ bin/uber_skel.py
 bin/uber_subject.py
 bin/uber_ttest.py
 bin/ui_xmat.py
+bin/uniq_images
 bin/waver
 bin/whereami
+bin/whirlgif
 bin/xmat_tool.py
 etc/mri/afni.cshrc
 etc/mri/afni.profile
 include/afni/3ddata.h
 include/afni/AFNI_label.h
 include/afni/Amalloc.h
+include/afni/Aomp.h
 include/afni/afni_environ.h
 include/afni/afni_suma.h
 include/afni/afni_warp.h
 include/afni/coxplot.h
 include/afni/cs.h
+include/afni/cs_qsort_small.h
 include/afni/cs_sort_template.h
 include/afni/debugtrace.h
 include/afni/editvol.h
@@ -473,6 +571,7 @@ include/afni/list_struct.h
 include/afni/machdep.h
 include/afni/mcw_glob.h
 include/afni/mcw_malloc.h
+include/afni/misc_math.h
 include/afni/mri_dicom_stuff.h
 include/afni/mri_warpfield.h
 include/afni/mrilib.h
@@ -484,10 +583,14 @@ include/afni/niml.h
 include/afni/r_idisp.h
 include/afni/r_misc.h
 include/afni/r_new_resam_dset.h
+include/afni/rcmat.h
 include/afni/tagset.h
+include/afni/thd_atlas.h
 include/afni/thd_compress.h
 include/afni/thd_iochan.h
 include/afni/thd_maker.h
+include/afni/thd_ttatlas_CA_EZ.h
+include/afni/thd_ttatlas_query.h
 include/afni/vecmat.h
 include/afni/vol2surf.h
 include/afni/volpack.h
@@ -501,6 +604,9 @@ lib/afni/libmrix.a
 lib/afni/libvolpack.a
 lib/afni/model_beta.so
 lib/afni/model_constant.so
+lib/afni/model_conv_PRF.so
+lib/afni/model_conv_PRF_6.so
+lib/afni/model_conv_cosine4.so
 lib/afni/model_conv_diffgamma.so
 lib/afni/model_convgamma.so
 lib/afni/model_convgamma2a.so
@@ -576,11 +682,296 @@ lib/afni/plug_vol2surf.so
 lib/afni/plug_volreg.so
 lib/afni/plug_wavelets.so
 lib/afni/plug_zeropad.so
+libexec/meica.libs/alignp_mepi_anat.py
+libexec/meica.libs/mdp/__init__.py
+libexec/meica.libs/mdp/caching/__init__.py
+libexec/meica.libs/mdp/caching/caching_extension.py
+libexec/meica.libs/mdp/classifier_node.py
+libexec/meica.libs/mdp/configuration.py
+libexec/meica.libs/mdp/extension.py
+libexec/meica.libs/mdp/graph/__init__.py
+libexec/meica.libs/mdp/graph/graph.py
+libexec/meica.libs/mdp/helper_funcs.py
+libexec/meica.libs/mdp/hinet/__init__.py
+libexec/meica.libs/mdp/hinet/flownode.py
+libexec/meica.libs/mdp/hinet/hinet.css
+libexec/meica.libs/mdp/hinet/htmlvisitor.py
+libexec/meica.libs/mdp/hinet/layer.py
+libexec/meica.libs/mdp/hinet/switchboard.py
+libexec/meica.libs/mdp/hinet/switchboard_factory.py
+libexec/meica.libs/mdp/linear_flows.py
+libexec/meica.libs/mdp/nodes/__init__.py
+libexec/meica.libs/mdp/nodes/classifier_nodes.py
+libexec/meica.libs/mdp/nodes/convolution_nodes.py
+libexec/meica.libs/mdp/nodes/em_nodes.py
+libexec/meica.libs/mdp/nodes/expansion_nodes.py
+libexec/meica.libs/mdp/nodes/fda_nodes.py
+libexec/meica.libs/mdp/nodes/ica_nodes.py
+libexec/meica.libs/mdp/nodes/ica_nodes.py~
+libexec/meica.libs/mdp/nodes/ica_nodes_old.py
+libexec/meica.libs/mdp/nodes/isfa_nodes.py
+libexec/meica.libs/mdp/nodes/jade.py
+libexec/meica.libs/mdp/nodes/libsvm_classifier.py
+libexec/meica.libs/mdp/nodes/lle_nodes.py
+libexec/meica.libs/mdp/nodes/misc_nodes.py
+libexec/meica.libs/mdp/nodes/neural_gas_nodes.py
+libexec/meica.libs/mdp/nodes/nipals.py
+libexec/meica.libs/mdp/nodes/pca_nodes.py
+libexec/meica.libs/mdp/nodes/rbm_nodes.py
+libexec/meica.libs/mdp/nodes/regression_nodes.py
+libexec/meica.libs/mdp/nodes/scikits_nodes.py
+libexec/meica.libs/mdp/nodes/sfa_nodes.py
+libexec/meica.libs/mdp/nodes/shogun_svm_classifier.py
+libexec/meica.libs/mdp/nodes/svm_classifiers.py
+libexec/meica.libs/mdp/nodes/xsfa_nodes.py
+libexec/meica.libs/mdp/parallel/__init__.py
+libexec/meica.libs/mdp/parallel/parallelclassifiers.py
+libexec/meica.libs/mdp/parallel/parallelflows.py
+libexec/meica.libs/mdp/parallel/parallelhinet.py
+libexec/meica.libs/mdp/parallel/parallelnodes.py
+libexec/meica.libs/mdp/parallel/pp_slave_script.py
+libexec/meica.libs/mdp/parallel/pp_slave_wrapper.py
+libexec/meica.libs/mdp/parallel/pp_support.py
+libexec/meica.libs/mdp/parallel/process_schedule.py
+libexec/meica.libs/mdp/parallel/scheduling.py
+libexec/meica.libs/mdp/parallel/thread_schedule.py
+libexec/meica.libs/mdp/repo_revision.py
+libexec/meica.libs/mdp/signal_node.py
+libexec/meica.libs/mdp/test/__init__.py
+libexec/meica.libs/mdp/test/_tools.py
+libexec/meica.libs/mdp/test/benchmark_mdp.py
+libexec/meica.libs/mdp/test/conftest.py
+libexec/meica.libs/mdp/test/ide_run.py
+libexec/meica.libs/mdp/test/run_tests.py
+libexec/meica.libs/mdp/test/test_AdaptiveCutoffNode.py
+libexec/meica.libs/mdp/test/test_Convolution2DNode.py
+libexec/meica.libs/mdp/test/test_CutoffNode.py
+libexec/meica.libs/mdp/test/test_EtaComputerNode.py
+libexec/meica.libs/mdp/test/test_FANode.py
+libexec/meica.libs/mdp/test/test_FDANode.py
+libexec/meica.libs/mdp/test/test_GaussianClassifier.py
+libexec/meica.libs/mdp/test/test_GeneralExpansionNode.py
+libexec/meica.libs/mdp/test/test_GrowingNeuralGasNode.py
+libexec/meica.libs/mdp/test/test_HistogramNode.py
+libexec/meica.libs/mdp/test/test_HitParadeNode.py
+libexec/meica.libs/mdp/test/test_ICANode.py
+libexec/meica.libs/mdp/test/test_ISFANode.py
+libexec/meica.libs/mdp/test/test_KNNClassifier.py
+libexec/meica.libs/mdp/test/test_LinearRegressionNode.py
+libexec/meica.libs/mdp/test/test_NearestMeanClassifier.py
+libexec/meica.libs/mdp/test/test_NeuralGasNode.py
+libexec/meica.libs/mdp/test/test_NoiseNode.py
+libexec/meica.libs/mdp/test/test_PCANode.py
+libexec/meica.libs/mdp/test/test_PolynomialExpansionNode.py
+libexec/meica.libs/mdp/test/test_PreseverDimNode.py
+libexec/meica.libs/mdp/test/test_RBFExpansionNode.py
+libexec/meica.libs/mdp/test/test_RBM.py
+libexec/meica.libs/mdp/test/test_SFA2Node.py
+libexec/meica.libs/mdp/test/test_SFANode.py
+libexec/meica.libs/mdp/test/test_TimeDelayNodes.py
+libexec/meica.libs/mdp/test/test_TimeFrameNode.py
+libexec/meica.libs/mdp/test/test_VariadicCumulator.py
+libexec/meica.libs/mdp/test/test_WhiteningNode.py
+libexec/meica.libs/mdp/test/test_caching.py
+libexec/meica.libs/mdp/test/test_classifier.py
+libexec/meica.libs/mdp/test/test_config.py
+libexec/meica.libs/mdp/test/test_contrib.py
+libexec/meica.libs/mdp/test/test_copying.py
+libexec/meica.libs/mdp/test/test_extension.py
+libexec/meica.libs/mdp/test/test_fastica.py
+libexec/meica.libs/mdp/test/test_flows.py
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+libexec/meica.libs/mdp/test/test_metaclass_and_extensions.py
+libexec/meica.libs/mdp/test/test_namespace_fixups.py
+libexec/meica.libs/mdp/test/test_node_covariance.py
+libexec/meica.libs/mdp/test/test_node_metaclass.py
+libexec/meica.libs/mdp/test/test_node_operations.py
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+libexec/meica.libs/mdp/utils/slideshow.css
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+libexec/meica.libs/mdp/utils/templet.py
+libexec/meica.libs/mdp/utils/temporarydir.py
+libexec/meica.libs/nibabel/COMMIT_INFO.txt
+libexec/meica.libs/nibabel/__init__.py
+libexec/meica.libs/nibabel/affines.py
+libexec/meica.libs/nibabel/analyze.py
+libexec/meica.libs/nibabel/arrayproxy.py
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+libexec/meica.libs/nibabel/environment.py
+libexec/meica.libs/nibabel/eulerangles.py
+libexec/meica.libs/nibabel/externals/__init__.py
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+libexec/meica.libs/nibabel/externals/tests/__init__.py
+libexec/meica.libs/nibabel/externals/tests/test_netcdf.py
+libexec/meica.libs/nibabel/fileholders.py
+libexec/meica.libs/nibabel/filename_parser.py
+libexec/meica.libs/nibabel/freesurfer/__init__.py
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+libexec/meica.libs/nibabel/funcs.py
+libexec/meica.libs/nibabel/gifti/__init__.py
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 %%PORTDOCS%%%%DOCSDIR%%/README.3dsvm.realtime
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author	Raphael Kubo da Costa <rakuco@FreeBSD.org>	2016-02-27 22:03:29 +0000
committer	Raphael Kubo da Costa <rakuco@FreeBSD.org>	2016-02-27 22:03:29 +0000
commit	3ae338d181e661aa00c8f42ddd7081ffd600900c (patch)
tree	3dfad55162ffbd0d9772a34aef2dca44ed5e370a /science/afni
parent	e13f5b87d6e381c543bb3066d1bf09e5e655432a (diff)
download	ports-3ae338d181e661aa00c8f42ddd7081ffd600900c.tar.gz ports-3ae338d181e661aa00c8f42ddd7081ffd600900c.zip