Index: head/science/afni/Makefile =================================================================== --- head/science/afni/Makefile (revision 513114) +++ head/science/afni/Makefile (revision 513115) @@ -1,171 +1,169 @@ # $FreeBSD$ PORTNAME= afni DISTVERSIONPREFIX= AFNI_ DISTVERSION= 19.1.20 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science biology graphics perl5 python MAINTAINER= jwb@FreeBSD.org COMMENT= Advanced Functional Neuro Imaging -DEPRECATED= Depends on deprecated libXp - LICENSE= GPLv2 BROKEN_sparc64= Does not compile: "undefined reference to '_mcount'" BUILD_DEPENDS= gm4:devel/m4 \ R:math/R LIB_DEPENDS= libexpat.so:textproc/expat2 \ libf2c.so:lang/f2c \ libgsl.so:math/gsl \ libnetcdff.so:science/netcdf-fortran \ libxml2.so:textproc/libxml2 \ libXm.so:x11-toolkits/open-motif \ libnetpbm.so:graphics/netpbm RUN_DEPENDS= endian:sysutils/endian \ mpeg_encode:multimedia/mpeg_encode \ qhull:math/qhull5 \ R:math/R USES= compiler:openmp gettext gl gmake gnome iconv jpeg:run motif \ perl5 python shebangfix tar:xz xorg USE_GNOME= glib20 USE_GITHUB= yes SHEBANG_FILES= scripts_install/* \ python_scripts/afni_python/*.py \ jzosky/*.py \ jzosky/lib_RetroTS/*.py \ discoraj/ClusterExplorer/*.py \ roopchansinghv/PsychoPy-NeuroFeedback-Demo/*.py \ roopchansinghv/PsychoPy-NeuroFeedback-Demo/*/*.py \ pkundu/*.py \ pkundu/meica.libs/*.py \ pkundu/meica.libs/*/*.py \ pkundu/meica.libs/*/*/*.py USE_GL= gl glu -USE_XORG= x11 xext xi xmu xp xt +USE_XORG= x11 xext xi xmu xt MAKE_ENV= CC="${CC}" R_SHARE_DIR=${LOCALBASE}/lib/R/share MAKE_JOBS_UNSAFE=yes WRKSRC_SUBDIR= src ALL_TARGET= vastness suma ########################################################################### # Install parameters SUB_FILES= pkg-message afni.cshrc afni.profile INSTALL_WRKSRC= ${WRKSRC}/BSD INSTALL_TMP= ${INSTALL_WRKSRC}-temp PRESTAGE= ${WRKSRC}/prestage OPTIONS_DEFINE= DOCS .include CONFLICTS= im-[0-9]* \ nifticlib-[0-9]* \ open-usp-tukubai-[0-9]* X11R6_FILES= coxplot/Makefile \ coxplot/Makefile.f2c \ 3DEdge/src/Makefile \ SUMA/SUMA_Makefile \ edt_blur.c \ suma_datasets.c \ SUMA/SUMA_Load_Surface_Object.c \ SUMA/SUMA_MiscFunc.c \ SUMA/SUMA_ParseCommands.c \ SUMA/GLUT/libglut/glut_event.c \ SUMA/SUMA_Surface_IO.c post-extract: .for f in ${X11R6_FILES} @${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} ${FILESDIR}/Makefile ${WRKSRC} @${RM} ${WRKSRC}/3DEdge/src/Makefile.orig # shebangfix misses /bin/python on 10.1 # @${REINPLACE_CMD} -e "s|/bin/python|${PYTHON_CMD}|g" \ # ${WRKSRC}/python_scripts/afni_python/lib_fat_Rfactor.py pre-configure: @${REINPLACE_CMD} -e "s|-lglib|-lglib-2.0|g" \ ${WRKSRC}/SUMA/SUMA_Makefile @${REINPLACE_CMD} \ -e 's|os\.path\.dirname(sys\.argv\[0\])|"${DATADIR}"|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 \ ${WRKSRC}/mri_dicom_stuff.h do-install: # AFNI install just dumps everything into one flat directory # Preserve original install dir and make a sacrificial temp copy # to be pruned and rearranged for easy staging @${RM} -r ${INSTALL_TMP} @${CP} -R ${INSTALL_WRKSRC} ${INSTALL_TMP} # Clean up and organize files into ${PRESTAGE}, destroying # temp copy in the process @${RM} -rf ${PRESTAGE} @${MKDIR} ${PRESTAGE}/bin \ ${PRESTAGE}/scripts \ ${PRESTAGE}/lib \ ${PRESTAGE}/include \ ${PRESTAGE}/trash \ ${PRESTAGE}/doc \ ${PRESTAGE}/share @${RM} ${INSTALL_TMP}/libf2c.a @${MV} ${INSTALL_TMP}/meica.libs \ ${INSTALL_TMP}/shiny \ ${INSTALL_TMP}/lib_RetroTS \ ${INSTALL_TMP}/afniInterfaceRT \ ${INSTALL_TMP}/funstuff \ ${INSTALL_TMP}/AFNI.*rc \ ${INSTALL_TMP}/afnigui* \ ${PRESTAGE}/share @${MV} ${INSTALL_TMP}/*.a \ ${INSTALL_TMP}/*.so \ ${PRESTAGE}/lib @${MV} ${INSTALL_TMP}/*.h ${PRESTAGE}/include @${CP} ${WRKDIR}/afni-AFNI_${PORTVERSION}/doc/README/* ${PRESTAGE}/doc @for binary in `${FILE} ${INSTALL_TMP}/* | fgrep 'ELF' | ${AWK} -F ':' ' { print $$1 }'` ; do \ ${MV} $${binary} ${PRESTAGE}/bin ; \ done @${MV} ${INSTALL_TMP}/* ${PRESTAGE}/scripts # Install to STAGEDIR using proper ports tools @${MKDIR} \ ${STAGEDIR}${DATADIR} \ ${STAGEDIR}${PREFIX}/lib/afni \ ${STAGEDIR}${PREFIX}/include/afni \ ${STAGEDIR}${DOCSDIR} \ ${STAGEDIR}${PREFIX}/etc/mri ${INSTALL_PROGRAM} ${PRESTAGE}/bin/* ${STAGEDIR}${PREFIX}/bin ${INSTALL_SCRIPT} ${PRESTAGE}/scripts/* ${STAGEDIR}${PREFIX}/bin ${INSTALL_DATA} ${PRESTAGE}/lib/* ${STAGEDIR}${PREFIX}/lib/afni ${INSTALL_DATA} ${PRESTAGE}/include/* ${STAGEDIR}${PREFIX}/include/afni (cd ${PRESTAGE}/share && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}) ${INSTALL_SCRIPT} ${WRKDIR}/afni.cshrc ${WRKDIR}/afni.profile \ ${STAGEDIR}${PREFIX}/etc/mri do-install-DOCS-on: ${INSTALL_DATA} ${PRESTAGE}/doc/* ${STAGEDIR}${DOCSDIR} .include Index: head/science/afni/files/Makefile =================================================================== --- head/science/afni/files/Makefile (revision 513114) +++ head/science/afni/files/Makefile (revision 513115) @@ -1,119 +1,119 @@ ################################################################## # # This Makefile is tested with FreeBSD 5.x # # Contributed by: # Jason W. Bacon # Medical College of Wisconsin # bacon@smithers.neuro.mcw.edu # # Before compiling afni, install the following packages: # # open-motif # # To compile SUMA you will also need the following packages: # # libiconv # gettext # gmake # # Note: SUMA has display problems on FreeBSD 4.8 and below that I # have not found time to resolve. I believe they are related # to the version of the GL libraries that ship with 4.x. # # SUMA works fine under FreeBSD 4.9 with GeForce drivers installed # and under FreeBSD 5.1. # # Note: The SUMA build process (as of Aug, 2003) requires GNU make, # which is ${LOCALBASE}/bin/gmake on BSD systems. # Be sure the MAKE macro below is set to gmake. # # Note: Compilation of netcdf-3.5.0 may fail due to m4's lack of # support for the -B option. Remove the -B10000 flag from # netcdf-3.5.0/src/configure BEFORE running make to avoid # this error. ( Or force configure to use gm4 by reversing # the order of "m4 gm4" to "gm4 m4" everywhere in the script } # This problem has been reported to the netcdf development team. # It seems to have been resolved as of the June, 2003 afni # source distribution. # USE_ZLIB = -DHAVE_ZLIB LZLIB = -lz USE_GIFTI = -DHAVE_GIFTI LGIFTI = -L${LOCALBASE}/lib -lexpat CC? = cc LD? = ${CC} CCDEBS = -DAFNI_DEBUG -DIMSEQ_DEBUG -DDISPLAY_DEBUG -DTHD_DEBUG CEXTRA = -DFreeBSD -DNO_GAMMA -DUSE_TRACING -DHAVE_XDBE -DSUMA_MOTIF_GLXAREA ifeq (${ARCH}, amd64) CEXTRA += -DPIC -fPIC endif ifeq (${ARCH}, ia64) CEXTRA += -DPIC -fPIC endif CFLAGS += -Wno-return-type -Wno-switch ${CEXTRA} CC += ${CFLAGS} CCVOL = ${CC} CCFAST = ${CC} -O3 CCMIN = ${CC} CCD = ${CC} ${CCDEBS} CCSVD = ${CC} -O0 CCOLD = ${CC} IFLAGS = -I. -I${LOCALBASE}/include LFLAGS = -s -L. -L${LOCALBASE}/lib MAKE = gmake # Some build scripts pick up the wrong make, so Makefile.INCLUDE is edited # to use MAKE_CMD MAKE_CMD = gmake PLUGIN_SUFFIX = so PLUGIN_LFLAGS = -shared PLUGIN_CC = ${CC} PLFLAGS = -s -rdynamic -L. -L${LOCALBASE}/lib AR = /usr/bin/ar RANLIB = /usr/bin/ranlib TAR = /usr/bin/tar MKDIR = /bin/mkdir TAPE = /dev/sa0 GZIP = /bin/gzip RM = /bin/rm -f MV = /bin/mv -f CP = /bin/cp -f LINT = /usr/bin/lint -a -b -u -v -x ${IFLAGS} ${CCDEFS} INSTALLDIR = ./BSD LIBDIR = ${INSTALLDIR} # for dynamic linking -LLIBS = -lmri -lf2c -lXm -lXp -lXpm -lXext -lXmu -lXt -lX11 -lm $(LZLIB) $(LGIFTI) +LLIBS = -lmri -lf2c -lXm -lXpm -lXext -lXmu -lXt -lX11 -lm $(LZLIB) $(LGIFTI) # vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv # For suma (NO STATIC LINKING OF GL libs) # Use -IGLw_local and -lGLws to avert the following suma runtime error due # to lack of extern modifier in GLwDrawA.h: # ** ERROR: glwMDrawingAreaWidgetClass is NULL # This may break if bundled GLw is not kept up-to-date, SUMA_INCLUDE_PATH = -IGLw_local -I${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 -lGLws -lGLU -lGL -lXmu -lXp -lXt -lXext -lX11 -lm $(LZLIB) -lxml2 -lexpat +SUMA_LINK_LIB = -lXm -lGLws -lGLU -lGL -lXmu -lXt -lXext -lX11 -lm $(LZLIB) -lxml2 -lexpat SUMA_MAKEFILE_NAME = SUMA_Makefile SUMA_BIN_ARCHIVE = SUMA_FreeBSD.tar SUMA_GLIB_VER = -2.0 # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ############################################################### include Makefile.INCLUDE