--- 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 @@ ## 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) # 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) +3dClustBust:3dClustBust.c + $(CC) -o 3dClustBust 3dClustBust.c $(INFLAGS) $(LFLAGS) $(LLIBS) + 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 ; $(RM) Makefile ) libXmHTML.a: - ( cd XmHTML ; make lib 'CC=$(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)' \ + $(MAKE_CMD) libfftw.a clean 'RM=$(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=$(MKDIR)'; \ cd ../ ;) @@ -3155,6 +3158,7 @@ #### R_io.so:R_io.c libmri.a ( if which R >/dev/null ; then \ + export MAKE=${MAKE_CMD} ;\ echo PKG_CPPFLAGS = $(INFLAGS) > Makevars ;\ echo PKG_LIBS = $(LFLAGS) $(LLIBS) >> Makevars ;\ R CMD SHLIB R_io.c ; \