Date: Sun, 23 Feb 2014 20:18:43 GMT From: Jason Bacon <jwbacon@tds.net> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/186988: maintainer update: science/afni Message-ID: <201402232018.s1NKIhXA041028@cgiserv.freebsd.org> Resent-Message-ID: <201402232020.s1NKK0Md018710@freefall.freebsd.org>
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>Number: 186988
>Category: ports
>Synopsis: maintainer update: science/afni
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: maintainer-update
>Submitter-Id: current-users
>Arrival-Date: Sun Feb 23 20:20:00 UTC 2014
>Closed-Date:
>Last-Modified:
>Originator: Jason Bacon
>Release: 10.0-RELEASE
>Organization:
Acadix Consulting, LLC
>Environment:
FreeBSD freebie.jbacon.dyndns.org 10.0-RELEASE FreeBSD 10.0-RELEASE #0 r260789: Thu Jan 16 22:34:59 UTC 2014 root@snap.freebsd.org:/usr/obj/usr/src/sys/GENERIC amd64
>Description:
Fixes BROKEN port for 10.0-RELEASE, eliminates NO_STAGE, and unbundles more dependencies.
>How-To-Repeat:
>Fix:
Patch attached with submission follows:
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 <bsd.port.pre.mk>
@@ -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
>Release-Note:
>Audit-Trail:
>Unformatted:
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