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