mirror of
https://git.FreeBSD.org/ports.git
synced 2024-12-22 04:17:44 +00:00
science/afni: bring back into shape.
- Stage support - Unexpire - Add license (GPLv2) - Use modern LIB_DEPENDS - Explicitly mention dependencies - Add CONFLICTS with im-*, nifticlib-* and open-usp-tukubai-* - Use perl5 and GCC - Tidy pkg-descr - Clean up pkg-plist - Bump PORTREVISION While here: - Use BROKEN_arch to avoid including bsd.port.pre.mk - Use PORT_OPTIONS:MDOCS instead of NOPORTDOCS - Remove obsolete post-install target PR: 186988 Submitted by: maintainer (jwbacon@tds.net)
This commit is contained in:
Rene Ladan
parent
d908e4fd4e
commit
39209af20c
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=358125
@ -11,7 +11,7 @@
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PORTNAME= afni
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PORTVERSION= 2012.04.17.2129
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PORTREVISION= 7
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PORTREVISION= 8
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CATEGORIES= science biology graphics
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MASTER_SITES= http://personalpages.tds.net/~jwbacon/Ports/distfiles/AFNI/${PORTVERSION}/ \
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http://www.acadix.biz/Ports/distfiles/AFNI/${PORTVERSION}/
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@ -23,26 +23,31 @@ EXTRACT_ONLY= afni_src.tgz CA_EZ_v1.5-July3107.tgz
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MAINTAINER= jwbacon@tds.net
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COMMENT= Advanced Functional Neuro Imaging
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LIB_DEPENDS= R:${PORTSDIR}/math/R \
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gsl:${PORTSDIR}/math/gsl
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LICENSE= GPLv2
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LIB_DEPENDS= libXm.so:${PORTSDIR}/x11-toolkits/open-motif \
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libR.so:${PORTSDIR}/math/R \
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libgsl.so:${PORTSDIR}/math/gsl \
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libnetcdf.so:${PORTSDIR}/science/netcdf-fortran
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RUN_DEPENDS= cjpeg:${PORTSDIR}/graphics/jpeg \
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mpeg_encode:${PORTSDIR}/multimedia/mpeg_encode \
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whirlgif:${PORTSDIR}/graphics/whirlgif \
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ppmtogif:${PORTSDIR}/graphics/netpbm \
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endian:${PORTSDIR}/sysutils/endian
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endian:${PORTSDIR}/sysutils/endian \
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qhull:${PORTSDIR}/math/qhull5
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USES= gettext iconv gmake motif
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CONFLICTS= im-[0-9]* \
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nifticlib-[0-9]* \
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open-usp-tukubai-[0-9]*
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NO_STAGE= yes
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BROKEN= R_io.so fails to build with R-3.0.2
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DEPRECATED= Broken for more than 6 months
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EXPIRATION_DATE= 2014-06-13
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USES= gettext iconv gmake motif perl5
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.include <bsd.port.pre.mk>
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# Some prereqs use gcc anyway
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USE_GCC= yes
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.if ${ARCH} == "sparc64"
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BROKEN= Does not compile on sparc64: "undefined reference to '_mcount'"
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.endif
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.include <bsd.port.options.mk>
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BROKEN_sparc64= Does not compile: "undefined reference to '_mcount'"
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USE_GL= glw glu
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USE_XORG= xi
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@ -55,12 +60,10 @@ ALL_TARGET= vastness suma
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###########################################################################
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# Install parameters
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MAN1= afni.1
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SUB_FILES= pkg-message afni.cshrc afni.profile
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INSTALL_WRKSRC= ${WRKSRC}/BSD
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STAGE= ${WRKSRC}/stage
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PRESTAGE= ${WRKSRC}/prestage
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X11R6_FILES= coxplot/Makefile \
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coxplot/Makefile.f2c \
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@ -85,52 +88,50 @@ post-extract:
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@${REINPLACE_CMD} "s|%%PREFIX%%|${PREFIX}|g" ${WRKDIR}/afni.1
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post-build:
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${MKDIR} ${STAGE}/bin \
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${STAGE}/scripts \
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${STAGE}/lib \
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${STAGE}/include \
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${STAGE}/trash \
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${STAGE}/doc \
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${STAGE}/share
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${MKDIR} ${PRESTAGE}/bin \
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${PRESTAGE}/scripts \
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${PRESTAGE}/lib \
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${PRESTAGE}/include \
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${PRESTAGE}/trash \
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${PRESTAGE}/doc \
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${PRESTAGE}/share
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${MV} ${INSTALL_WRKSRC}/libf2c.a \
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${STAGE}/trash
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${PRESTAGE}/trash
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${MV} ${INSTALL_WRKSRC}/*.a \
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${INSTALL_WRKSRC}/*.so \
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${STAGE}/lib
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${PRESTAGE}/lib
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${MV} ${INSTALL_WRKSRC}/funstuff \
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${INSTALL_WRKSRC}/AFNI.*rc \
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${INSTALL_WRKSRC}/afnigui* \
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${STAGE}/share
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${PRESTAGE}/share
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${MV} ${INSTALL_WRKSRC}/*.h \
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${STAGE}/include
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${PRESTAGE}/include
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${MV} ${INSTALL_WRKSRC}/README* \
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${STAGE}/doc
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${PRESTAGE}/doc
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${MV} ${INSTALL_WRKSRC}/abut ${INSTALL_WRKSRC}/afni_abut
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${MV} ${INSTALL_WRKSRC}/qhull ${INSTALL_WRKSRC}/afni_qhull
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for binary in `${FILE} ${INSTALL_WRKSRC}/* | fgrep 'ELF' | ${AWK} -F ':' ' { print $$1 }'` ; do \
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${MV} $${binary} ${STAGE}/bin ; \
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${MV} $${binary} ${PRESTAGE}/bin ; \
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done
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${MV} ${INSTALL_WRKSRC}/* \
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${STAGE}/scripts
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${PRESTAGE}/scripts
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do-install:
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${MKDIR} ${DATADIR} ${PREFIX}/lib/afni ${PREFIX}/include/afni
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${INSTALL_DATA} ${STAGE}/lib/* ${PREFIX}/lib/afni
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${INSTALL_DATA} ${STAGE}/include/* ${PREFIX}/include/afni
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${CP} -R ${STAGE}/share/* ${DATADIR}
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${INSTALL_PROGRAM} ${STAGE}/bin/* ${PREFIX}/bin
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${INSTALL_SCRIPT} ${STAGE}/scripts/* ${PREFIX}/bin
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${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/TTatlas* ${DATADIR}
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${INSTALL_DATA} ${WRKDIR}/CA_EZ_v1.5-July3107/* ${DATADIR}
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${INSTALL_MAN} ${WRKDIR}/afni.1 ${MAN1PREFIX}/man/man1
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.if !defined(NOPORTDOCS)
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${MKDIR} ${DOCSDIR} ${PREFIX}/etc/mri
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${INSTALL_DATA} ${STAGE}/doc/* ${DOCSDIR}
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${MKDIR} ${STAGEDIR}${DATADIR} \
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${STAGEDIR}${PREFIX}/lib/afni \
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${STAGEDIR}${PREFIX}/include/afni
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${INSTALL_DATA} ${PRESTAGE}/lib/* ${STAGEDIR}${PREFIX}/lib/afni
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${INSTALL_DATA} ${PRESTAGE}/include/* ${STAGEDIR}${PREFIX}/include/afni
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${CP} -R ${PRESTAGE}/share/* ${STAGEDIR}${DATADIR}
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${INSTALL_PROGRAM} ${PRESTAGE}/bin/* ${STAGEDIR}${PREFIX}/bin
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${INSTALL_SCRIPT} ${PRESTAGE}/scripts/* ${STAGEDIR}${PREFIX}/bin
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${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/TTatlas* ${STAGEDIR}${DATADIR}
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${INSTALL_DATA} ${WRKDIR}/CA_EZ_v1.5-July3107/* ${STAGEDIR}${DATADIR}
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${INSTALL_MAN} ${WRKDIR}/afni.1 ${STAGEDIR}${MAN1PREFIX}/man/man1
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.if ${PORT_OPTIONS:MDOCS}
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${MKDIR} ${STAGEDIR}${DOCSDIR} ${STAGEDIR}${PREFIX}/etc/mri
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${INSTALL_DATA} ${PRESTAGE}/doc/* ${STAGEDIR}${DOCSDIR}
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${INSTALL_SCRIPT} ${WRKDIR}/afni.cshrc ${WRKDIR}/afni.profile \
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${PREFIX}/etc/mri
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${STAGEDIR}${PREFIX}/etc/mri
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.endif
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post-install:
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@${CAT} ${WRKDIR}/pkg-message
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.include <bsd.port.post.mk>
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.include <bsd.port.mk>
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@ -53,7 +53,7 @@ ifeq (${ARCH}, ia64)
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CEXTRA += -DPIC -fPIC
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endif
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CFLAGS += ${CEXTRA}
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CFLAGS += -Wno-return-type -Wno-switch ${CEXTRA}
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CC += ${CFLAGS}
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CCVOL = ${CC}
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@ -67,6 +67,9 @@ IFLAGS = -I. -I${LOCALBASE}/include
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LFLAGS = -s -L. -L${LOCALBASE}/lib
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MAKE = gmake
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# Some build scripts pick up the wrong make, so Makefile.INCLUDE is edited
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# to use GMAKE
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GMAKE = gmake
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PLUGIN_SUFFIX = so
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PLUGIN_LFLAGS = -shared
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@ -1,5 +1,5 @@
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--- Makefile.INCLUDE.orig 2012-04-17 15:56:21.000000000 -0500
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+++ Makefile.INCLUDE 2012-04-18 13:39:29.000000000 -0500
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+++ Makefile.INCLUDE 2013-10-30 08:19:45.000000000 -0500
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@@ -48,7 +48,7 @@
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## AFNI package, but included because they are useful. Some of
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## them are Open Source programs, not from the AFNI group at all.
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@ -9,6 +9,51 @@
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# mpegtoppm in above list
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@@ -58,7 +58,7 @@
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PROGRAMS = afni to3d from3d abut 3dclust nsize 3dinfo 3dproject 3dmerge count \
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sfim tfim ftosh 3dttest 3ddup imrotate imreg imstat 3dnvals \
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fim2 imand FD2 sqwave immask imdump imaver 3dhistog 3dfim 3daxialize \
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- cdf 2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta \
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+ 2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta \
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waver 3dnewid 3dcalc ccalc imcalc 1dmatcalc 3drefit 3dbucket \
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3dNLfim 3dTSgen AlphaSim 3dFWHM plugout_tt 3dnoise plugout_ijk \
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3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna \
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@@ -70,7 +70,7 @@
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3dWavelets 3dfim+ imcutup imcat 3dWinsor 3dZeropad 3dTagalign \
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3dMean 3dAttribute cat_matvec 3dOverlap 3dClipLevel 3dZregrid \
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3dEntropy 3ddelay ent16 3dRowFillin 1dgrayplot 3dToutcount 1dsum \
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- 3dExtrema qhull strblast 3dConvolve 3dZcutup 3dZcat 3dTqual 3dGetrow \
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+ 3dExtrema strblast 3dConvolve 3dZcutup 3dZcat 3dTqual 3dGetrow \
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3dTcorrelate 3dAnatNudge 3dcopy Vecwarp 3dMINCtoAFNI 3dCM fdrval \
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3dAFNItoANALYZE siemens_vision ge_header mayo_analyze 3dAFNItoNIFTI \
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3dAutoTcorrelate 3dFDR rtfeedme 3dAutomask 3dAFNItoMINC 3dBrickStat \
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@@ -89,7 +89,7 @@
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3dBlurInMask 3dRank 3dFFT 1dgenARMA11 3dPeriodogram 1dAstrip \
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3dLocalPV 3dBandpass 3dSetupGroupInCorr 3dGroupInCorr 3dTcorr1D \
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3dClustSim 3dRetinoPhase 3dMaskToASCII 3dttest++ 3dDTtoDWI \
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- niccc rbox qdelaunay 3dkmeans 3dXYZcat 3dPolyfit 3dNwarpApply \
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+ niccc 3dkmeans 3dXYZcat 3dPolyfit 3dNwarpApply \
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1dCorrelate 3dCountSpikes 3dNwarpCalc dicom_hinfo apsearch 1dBport \
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3dNormalityTest \
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$(EXTRAS)
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@@ -97,7 +97,7 @@
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PROGRAMS_NOPLUG = afni to3d from3d abut 3dclust nsize 3dinfo 3dproject 3dmerge \
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sfim tfim ftosh 3dttest 3ddup imrotate imreg imstat 3dnoise count \
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fim2 imand FD2 sqwave immask imdump imaver 3dhistog 3dfim imupsam \
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- cdf 2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 3drefit \
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+ 2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 3drefit \
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waver 3dnewid 3dcalc ccalc imcalc 2dImReg 3dmaskave adwarp fdrval \
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3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna \
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imstack byteorder 3dDeconvolve 3dTcat 3drotate 3dvolreg 1dplot \
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@@ -133,7 +133,7 @@
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PROGRAMS_EXE = afni.exe to3d from3d abut 3dclust nsize 3dinfo 3dproject 3dmerge \
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sfim tfim ftosh 3dttest 3ddup imrotate imreg imstat 3dnvals count \
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||||
fim2 imand FD2 sqwave immask imdump imaver 3dhistog 3dfim 3dGetrow \
|
||||
- cdf 2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta \
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+ 2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta \
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waver 3dnewid 3dcalc ccalc imcalc 1dmatcalc 3drefit 3dbucket \
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3dAFNItoNIML AlphaSim 3dFWHM plugout_tt 3dnoise plugout_ijk \
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3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna \
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@@ -282,6 +282,9 @@
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3dbuc2fim:3dbuc2fim.o
|
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$(CC) -o 3dbuc2fim 3dbuc2fim.o $(LFLAGS) $(LLIBS)
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@ -19,3 +64,378 @@
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mritopgm:mritopgm.c
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$(CC) -o mritopgm mritopgm.c $(INFLAGS) $(LFLAGS) $(LLIBS)
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|
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@@ -2038,7 +2041,7 @@
|
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# remake netcdf objects with PIC
|
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shared_netcdf_attr:
|
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$(RM) netcdf_attr.o
|
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- $(MAKE) netcdf_attr.o CCMIN="${CCMIN} -fPIC"
|
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+ $(GMAKE) netcdf_attr.o CCMIN="${CCMIN} -fPIC"
|
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|
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# same as .a, but build as a shared object
|
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libmrix.a:$(IMOBJS) imseq.h display.h xim.h bbox.h xutil.h
|
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@@ -2228,13 +2231,13 @@
|
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|
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f2c:
|
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( cd f2cdir ; \
|
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- $(MAKE) f2c clean 'RM=$(RM)' 'CC=$(CC)' 'AR=$(AR)' 'CCMIN=$(CCMIN)' \
|
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+ $(GMAKE) f2c clean 'RM=$(RM)' 'CC=$(CC)' 'AR=$(AR)' 'CCMIN=$(CCMIN)' \
|
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'RANLIB=$(RANLIB)' 'LDFLAGS=$(LDFLAGS)' 'IFLAGS=$(ISFLAGS)' ; \
|
||||
$(MV) f2c .. ; )
|
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|
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libf2c.a:
|
||||
( cd f2cdir ; \
|
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- $(MAKE) libf2c.a clean 'RM=$(RM)' 'CC=$(CC)' 'AR=$(AR)' \
|
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+ $(GMAKE) libf2c.a clean 'RM=$(RM)' 'CC=$(CC)' 'AR=$(AR)' \
|
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'RANLIB=$(RANLIB)' 'LDFLAGS=$(LDFLAGS)' 'IFLAGS=$(ISFLAGS)' ; \
|
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$(MV) libf2c.a .. ; )
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|
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@@ -2249,7 +2252,7 @@
|
||||
|
||||
libdl.a:dlcompat/dlfcn.h dlcompat/dlopen.c
|
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( cd dlcompat ; \
|
||||
- $(MAKE) libdl.a ; \
|
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+ $(GMAKE) libdl.a ; \
|
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$(CP) libdl.a dlfcn.h .. ; \
|
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cd .. ; \
|
||||
$(RANLIB) libdl.a ; )
|
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@@ -2259,7 +2262,7 @@
|
||||
|
||||
libcoxplot.a:coxplot.h
|
||||
( cd coxplot ; \
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- $(MAKE) libcoxplot.a clean 'RM=$(RM)' 'CC=$(CC)' 'AR=$(AR)' \
|
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+ $(GMAKE) libcoxplot.a clean 'RM=$(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 ; \
|
||||
|
||||
11
science/afni/files/patch-XmHTML-Makefile
Normal file
11
science/afni/files/patch-XmHTML-Makefile
Normal file
@ -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
|
||||
|
||||
@ -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 */
|
||||
|
||||
@ -12,8 +12,15 @@ or DRI (graphics/dri).
|
||||
|
||||
---
|
||||
|
||||
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
|
||||
|
||||
---
|
||||
|
||||
|
||||
@ -1,3 +1,4 @@
|
||||
@comment Generated by ports-mgmt/genplist
|
||||
bin/1dAstrip
|
||||
bin/1dBandpass
|
||||
bin/1dBport
|
||||
@ -339,7 +340,6 @@ bin/afni_abut
|
||||
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/ask_me.py
|
||||
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_tt
|
||||
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_vol2surf.so
|
||||
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
|
||||
|
||||
Loading…
Reference in New Issue
Block a user