--- 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 quotize $(EXPROGS)
+EXTRAS   = 3dClustBust whirlgif myget Xphace rmz aiv mycat quotize $(EXPROGS)
 
 # mpegtoppm in above list
 
@@ -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   \
            waver 3dnewid 3dcalc ccalc imcalc 1dmatcalc 3drefit 3dbucket         \
            3dNLfim 3dTSgen AlphaSim 3dFWHM plugout_tt 3dnoise plugout_ijk       \
            3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna         \
@@ -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 \
            3dTcorrelate 3dAnatNudge 3dcopy Vecwarp 3dMINCtoAFNI 3dCM fdrval     \
            3dAFNItoANALYZE siemens_vision ge_header mayo_analyze 3dAFNItoNIFTI  \
            3dAutoTcorrelate 3dFDR rtfeedme 3dAutomask 3dAFNItoMINC 3dBrickStat  \
@@ -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        \
            1dCorrelate 3dCountSpikes 3dNwarpCalc dicom_hinfo apsearch 1dBport   \
            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    \
                   waver 3dnewid 3dcalc ccalc imcalc 2dImReg 3dmaskave adwarp fdrval \
                   3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna      \
                   imstack byteorder 3dDeconvolve 3dTcat 3drotate 3dvolreg 1dplot    \
@@ -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 \
                waver 3dnewid 3dcalc ccalc imcalc 1dmatcalc 3drefit 3dbucket       \
                3dAFNItoNIML    AlphaSim 3dFWHM plugout_tt 3dnoise plugout_ijk     \
                3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna       \
@@ -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)
 
+3dClustBust:3dClustBust.c
+	$(CC) -o 3dClustBust 3dClustBust.c $(INFLAGS) $(LFLAGS) $(LLIBS)
+
 mritopgm:mritopgm.c
 	$(CC) -o mritopgm mritopgm.c $(INFLAGS) $(LFLAGS) $(LLIBS)
 
@@ -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 ; $(MAKE) lib 'CC=$(CC)' 'II=$(IFLAGS)' ; \
+		$(MV) lib/libXmHTML.a .. ; $(MAKE) clean   )
 
 thd_xwebber.o:thd_xwebber.c
 	$(CC) -c thd_xwebber.c -I./XmHTML/include $(INFLAGS)
@@ -3518,8 +3521,9 @@ toyR: toyR.c AFNI_embeddedRCall.o
 ####
 R_io.so:R_io.c libmri.a
 	( if which R >/dev/null ; then \
-	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 ; )