Date: Sat, 27 Feb 2016 22:03:30 +0000 (UTC) From: Raphael Kubo da Costa <rakuco@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r409693 - in head/science/afni: . files Message-ID: <201602272203.u1RM3UoC056952@repo.freebsd.org>
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Author: rakuco Date: Sat Feb 27 22:03:29 2016 New Revision: 409693 URL: https://svnweb.freebsd.org/changeset/ports/409693 Log: 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) Added: head/science/afni/files/Makefile - copied, changed from r409692, head/science/afni/files/Makefile.FreeBSD_PORT head/science/afni/files/patch-netcdf-3.5.0_src_configure (contents, props changed) head/science/afni/files/patch-nifti_cifti_afni__xml.h (contents, props changed) Deleted: head/science/afni/files/Makefile.FreeBSD_PORT Modified: head/science/afni/Makefile head/science/afni/distinfo head/science/afni/files/patch-Makefile.INCLUDE head/science/afni/files/patch-XmHTML-Makefile head/science/afni/files/patch-misc_math.c head/science/afni/files/pkg-message.in head/science/afni/pkg-plist Modified: head/science/afni/Makefile ============================================================================== --- head/science/afni/Makefile Sat Feb 27 21:35:18 2016 (r409692) +++ head/science/afni/Makefile Sat Feb 27 22:03:29 2016 (r409693) @@ -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> Modified: head/science/afni/distinfo ============================================================================== --- head/science/afni/distinfo Sat Feb 27 21:35:18 2016 (r409692) +++ head/science/afni/distinfo Sat Feb 27 22:03:29 2016 (r409693) @@ -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 Copied and modified: head/science/afni/files/Makefile (from r409692, head/science/afni/files/Makefile.FreeBSD_PORT) ============================================================================== --- head/science/afni/files/Makefile.FreeBSD_PORT Sat Feb 27 21:35:18 2016 (r409692, copy source) +++ head/science/afni/files/Makefile Sat Feb 27 22:03:29 2016 (r409693) @@ -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 # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ############################################################### Modified: head/science/afni/files/patch-Makefile.INCLUDE ============================================================================== --- head/science/afni/files/patch-Makefile.INCLUDE Sat Feb 27 21:35:18 2016 (r409692) +++ head/science/afni/files/patch-Makefile.INCLUDE Sat Feb 27 22:03:29 2016 (r409693) @@ -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 ; ) Modified: head/science/afni/files/patch-XmHTML-Makefile ============================================================================== --- head/science/afni/files/patch-XmHTML-Makefile Sat Feb 27 21:35:18 2016 (r409692) +++ head/science/afni/files/patch-XmHTML-Makefile Sat Feb 27 22:03:29 2016 (r409693) @@ -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 Modified: head/science/afni/files/patch-misc_math.c ============================================================================== --- head/science/afni/files/patch-misc_math.c Sat Feb 27 21:35:18 2016 (r409692) +++ head/science/afni/files/patch-misc_math.c Sat Feb 27 22:03:29 2016 (r409693) @@ -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 */ Added: head/science/afni/files/patch-netcdf-3.5.0_src_configure ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/afni/files/patch-netcdf-3.5.0_src_configure Sat Feb 27 22:03:29 2016 (r409693) @@ -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 Added: head/science/afni/files/patch-nifti_cifti_afni__xml.h ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/afni/files/patch-nifti_cifti_afni__xml.h Sat Feb 27 22:03:29 2016 (r409693) @@ -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. Modified: head/science/afni/files/pkg-message.in ============================================================================== --- head/science/afni/files/pkg-message.in Sat Feb 27 21:35:18 2016 (r409692) +++ head/science/afni/files/pkg-message.in Sat Feb 27 22:03:29 2016 (r409693) @@ -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 limi --- -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. ============================================================================= Modified: head/science/afni/pkg-plist ============================================================================== --- head/science/afni/pkg-plist Sat Feb 27 21:35:18 2016 (r409692) +++ head/science/afni/pkg-plist Sat Feb 27 22:03:29 2016 (r409693) @@ -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 *** DIFF OUTPUT TRUNCATED AT 1000 LINES ***
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