svn commit: r409693 - in head/science/afni: . files
Raphael Kubo da Costa
rakuco at FreeBSD.org
Sat Feb 27 22:03:32 UTC 2016
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 at 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 at 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 @@
- at 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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