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[cvs] dists/10.7/stable/main/finkinfo/sci afni.info, NONE, 1.1 afni.patch, NONE, 1.1
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From: Alexander H. <ale...@us...> - 2012-11-30 18:19:45
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Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv14107/10.7/stable/main/finkinfo/sci Added Files: afni.info afni.patch Log Message: Bring back to Fink: https://sourceforge.net/tracker/?func=detail&atid=414256&aid=3115124&group_id=17203 --- NEW FILE: afni.patch --- --- AFNI_2010_10_19_1028.orig/Makefile 2010-11-18 17:35:31.000000000 -0500 +++ AFNI_2010_10_19_1028/Makefile 2010-11-18 15:45:59.000000000 -0500 @@ -1,7 +1,7 @@ # This Makefile is for Mac OSX 10.6 (Snow Leopard) for 64 bit AFNI -SW_ROOT = /sw +SW_ROOT = @PREFIX@ USE_ZLIB = -DHAVE_ZLIB LZLIB = -lz @@ -6,7 +6,7 @@ USE_ZLIB = -DHAVE_ZLIB LZLIB = -lz USE_GIFTI = -DHAVE_GIFTI -LGIFTI = $(SW_ROOT)/lib/libexpat.a +LGIFTI = -lexpat # ---------------------------------------------------------------------- # X configuration @@ -12,13 +12,13 @@ # X configuration # # uncomment to build using local /usr/local/afniX 'X' tree -USE_LOCAL_X_TREE = 1 +#USE_LOCAL_X_TREE = 1 ifdef USE_LOCAL_X_TREE XROOT = $(SW_ROOT) XROOT_I = -I$(XROOT)/include XROOT_L = -L$(XROOT)/lib else - XROOT = /sw + XROOT = @PREFIX@ XROOT_L = -L$(XROOT)/lib endif @@ -30,7 +30,7 @@ XLIBS = $(XROOT)/lib64/libXm.a $(XROOT)/lib64/libXt.a else # default is static motif - XLIBS = $(XROOT)/lib/libXm.a -lXt + XLIBS = -lXm -lXt endif # in case user wants to override with system dynamic libs @@ -49,8 +49,8 @@ OMPFLAG = -fopenmp -DUSE_OMP -IFLAGS = -I. $(XROOT_I) -I/usr/local/include -I/usr/X11R6/include -I/sw/include -LFLAGS = -L. $(XROOT_L) -L/usr/lib -L/usr/local/lib -L/usr/X11R6/lib -L/sw/lib -Wl,-x -Wl,-multiply_defined -Wl,warning -Wl,-bind_at_load +IFLAGS = -I. $(XROOT_I) -I@PREFIX@/include -I/usr/X11R6/include +LFLAGS = -L. $(XROOT_L) -L@PREFIX@/lib -L/usr/X11R6/lib -Wl,-x -Wl,-multiply_defined -Wl,warning -Wl,-bind_at_load CCSVD = cc -m64 -O0 -no-cpp-precomp @@ -75,8 +75,10 @@ LINT = /usr/bin/lint -a -b -u -v -x $(IFLAGS) $(CCDEFS) -INSTALLDIR = macosx_10.6_Intel_64 -LIBDIR = $(INSTALLDIR) +INSTALLDIR = @INSTALLPREFIX@/bin +LIBDIR = @INSTALLPREFIX@/lib/@PACKAGENAME@ +DOCDIR = @INSTALLPREFIX@/share/doc/@PACKAGENAME@ +INCLUDEDIR = @INSTALLPREFIX@/include/@PACKAGENAME@ SHOWOFF = -DSHOWOFF=macosx_10.6_Intel_64 INSTALL_PREREQ = suma @@ -87,7 +89,7 @@ # for dynamic linking -LLIBS = -lmri -lf2c $(XLIBS) -lXft -lfontconfig -lpng -liconv -lXmu -lXp -lXpm -lXext -lX11 $(LZLIB) $(LGIFTI) -lm -lc +LLIBS = -lmri -lf2c $(XLIBS) -lXft -lfontconfig -lpng -liconv -lXmu -lXp -lXpm -lXext -lX11 $(LZLIB) $(LGIFTI) -lm -lc -ljpeg # vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv # For suma diff -urN AFNI_2010_10_19_1028.orig/Makefile.INCLUDE AFNI_2010_10_19_1028/Makefile.INCLUDE --- AFNI_2010_10_19_1028/SUMA/SUMA_Makefile.orig 2011-09-15 02:13:26.000000000 -0400 +++ AFNI_2010_10_19_1028/SUMA/SUMA_Makefile 2011-09-15 02:29:44.000000000 -0400 @@ -35,15 +35,15 @@ CCMIN = cc CCD = $(CC) $(CCDEBS) # IFLAGS = -I. -I/usr/include -I/usr/include/sys -I/usr/X11R6/include -IFLAGS = -I. -I/usr/X11R6/include -I/sw/include -LFLAGS = -L. -L/usr/X11R6/lib -L/sw/lib -Wl,-multiply_defined -Wl,suppress +IFLAGS = -I. -I/usr/X11R6/include -I@PREFIX@/include +LFLAGS = -L. -L@PREFIX@/lib -L/usr/X11R6/lib -Wl,-multiply_defined -Wl,suppress CCSVD = cc -O0 -fPIC -no-cpp-precomp PLUGIN_SUFFIX = so PLUGIN_LFLAGS = -flat_namespace -bundle -undefined suppress PLUGIN_CC = $(CC) -dynamic -fno-common -PLFLAGS = -dynamic -L. -L/usr/X11R6/lib -L/sw/lib -Wl,-multiply_defined -Wl,suppress +PLFLAGS = -dynamic -L. -L@PREFIX@/lib -L/usr/X11R6/lib -Wl,-multiply_defined -Wl,suppress SPECIAL = -faltivec -framework Accelerate -DUSE_ALTIVEC endif @@ -59,10 +59,10 @@ ifndef SUMA_INCLUDE_PATH #Don't prepend -Igts/src -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include/ here since only one program needs them -SUMA_INCLUDE_PATH = -I/usr/X11R6/include -I./ -I../ -Igts/src -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I/sw/include +SUMA_INCLUDE_PATH = -I./ -I../ -I@PREFIX@/include/glib-2.0 -I@PREFIX@/lib/glib-2.0/include -I@PREFIX@/include -I/usr/X11R6/include -Igts/src endif ifndef SUMA_LINK_PATH -SUMA_LINK_PATH = -L/usr/lib -L/usr/X11R6/lib -L../ -L/usr/local/lib -L/sw/lib +SUMA_LINK_PATH = -L../ -L@PREFIX@/lib -L/usr/X11R6/lib endif ifndef SUMA_LINK_LIB #No need for those unless you are using SUMA_MOTIF_GLXAREA @@ -84,7 +84,7 @@ endif ifndef TAR -TAR = /sw/bin/tar +TAR = @PREFIX@/bin/tar endif ifndef RM --- AFNI_2010_10_19_1028.orig/Makefile.INCLUDE 2011-05-25 15:15:23.000000000 -0400 +++ AFNI_2010_10_19_1028/Makefile.INCLUDE 2011-09-15 03:17:49.000000000 -0400 @@ -46,7 +46,7 @@ ## 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 $(EXPROGS) +EXTRAS = whirlgif mpeg_encode myget Xphace rmz aiv $(EXPROGS) # mpegtoppm in above list @@ -213,6 +213,12 @@ $(INSTALLDIR): if [ ! -d $(INSTALLDIR) ]; then $(MKDIR) -p $(INSTALLDIR); echo Made directory $(INSTALLDIR); fi +$(DOCDIR): + if [ ! -d $(DOCDIR) ]; then $(MKDIR) -p $(DOCDIR); echo Made directory $(DOCDIR); fi +$(LIBDIR): + if [ ! -d $(LIBDIR) ]; then $(MKDIR) -p $(LIBDIR); echo Made directory $(LIBDIR); fi +$(INCLUDEDIR): + if [ ! -d $(INCLUDEDIR) ]; then $(MKDIR) -p $(INCLUDEDIR); echo Made directory $(INCLUDEDIR); fi ### for those on crippled systems @@ -1568,21 +1574,23 @@ ### Put things in their places -install: $(INSTALLDIR) $(INSTALL_PREREQ) +install: $(DOCDIR) $(INSTALLDIR) $(INSTALL_PREREQ) $(MV) $(PROGRAMS) $(INSTALLDIR) $(CP) $(SCRIPTS) $(INSTALLDIR) $(CP) $(PY_DIR)/*.py $(R_DIR)/*.R $(INSTALLDIR) - if [ -f README.environment ]; then $(CP) README.* $(INSTALLDIR); fi; - if [ -f AFNI.afnirc ]; then $(CP) AFNI.afnirc $(INSTALLDIR); fi; - if [ -f AFNI.sumarc ]; then $(CP) AFNI.sumarc $(INSTALLDIR); fi; + if [ -f README.environment ]; then $(CP) README.* $(DOCDIR); fi; + if [ -f AFNI.afnirc ]; then $(CP) AFNI.afnirc $(DOCDIR); fi; + if [ -f AFNI.sumarc ]; then $(CP) AFNI.sumarc $(DOCDIR); fi; + if [ -f TTatlas+tlrc.HEAD ]; then $(CP) TTatlas* $(DOCDIR); fi; install_noplug: $(INSTALLDIR) $(MV) $(PROGRAMS_NOPLUG) $(INSTALLDIR) $(CP) $(SCRIPTS) $(INSTALLDIR) $(CP) $(PY_DIR)/*.py $(R_DIR)/*.R $(INSTALLDIR) -install_lib: $(LIBDIR) - $(CP) libmri.a libmrix.a libf2c.a libcoxplot.a libvolpack.a $(LIBHEADERS) $(LIBDIR) +install_lib: $(LIBDIR) $(INCLUDEDIR) + $(CP) libmri.a libmrix.a libf2c.a libcoxplot.a libvolpack.a $(LIBDIR) + $(CP) $(LIBHEADERS) $(INCLUDEDIR) # CYGWIN: must put the .exe suffix on the "mv" command for some reason @@ -1968,8 +1976,8 @@ $(AR) q libmrix.a $(IMOBJS) $(RANLIB) libmrix.a -shared_objs: $(INSTALLDIR) libmri.so libmrix.so - $(MV) libmri.so libmrix.so $(INSTALLDIR) +shared_objs: $(LIBDIR) libmri.so libmrix.so + $(MV) libmri.so libmrix.so $(LIBDIR) ################################################################### # Plugin stuff @@ -2032,10 +2040,10 @@ laconte_plugins: plug_3dsvm.$(SO) -install_plugins: $(INSTALLDIR) - $(MV) *.$(PLUGIN_SUFFIX) $(INSTALLDIR) - $(CP) faces/face_*.jpg faces/splash_*.jpg poems/poem_*.txt $(INSTALLDIR) - echo Plugins put in directory $(INSTALLDIR): +install_plugins: $(LIBDIR) + $(MV) *.$(PLUGIN_SUFFIX) $(LIBDIR) + $(CP) faces/face_*.jpg faces/splash_*.jpg poems/poem_*.txt $(LIBDIR) + echo Plugins put in directory $(LIBDIR): echo Do not forget to setenv AFNI_PLUGINPATH appropriately .c.$(SO):afni_plugin.h afni.h 3ddata.h @@ -2736,6 +2744,7 @@ ( cd SUMA ; \ rm -f libSUMA.a ;\ $(MAKE) -f $(SUMA_MAKEFILE_NAME) clean MarchingCubes.o libSUMA.a 'INSTALLDIR=$(INSTALLDIR)' \ + 'LIBDIR=$(LIBDIR)' \ 'SUMA_INCLUDE_PATH=$(SUMA_INCLUDE_PATH)' \ 'SUMA_BIN_ARCHIVE=$(SUMA_BIN_ARCHIVE)' \ 'RANLIB=$(RANLIB)' \ @@ -2743,8 +2752,8 @@ 'CC=$(CC)' 'RM=$(RM)' 'CEXTRA=$(CEXTRA)' 'MV=$(MV)' 'CP=$(CP)' \ 'TAR=$(TAR)' 'MKDIR=$(MKDIR)'; \ cd ../ ; \ - if [ ! -d $(INSTALLDIR) ]; then $(MKDIR) -p $(INSTALLDIR); echo WARNING: directory $(INSTALLDIR) has been created. ; fi ;\ - $(CP) SUMA/libSUMA.a ${INSTALLDIR}; \ + if [ ! -d $(LIBDIR) ]; then $(MKDIR) -p $(LIBDIR); echo WARNING: directory $(LIBDIR) has been created. ; fi ;\ + $(CP) SUMA/libSUMA.a ${LIBDIR}; \ $(CP) SUMA/libSUMA.a ./; ) libgts.a: @@ -2752,14 +2761,15 @@ rm -f libgts.a ;\ $(MAKE) -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}; \ + if [ ! -d $(LIBDIR) ]; then $(MKDIR) -p $(LIBDIR); echo WARNING: directory $(LIBDIR) has been created. ; fi ;\ + $(CP) SUMA/libgts.a ${LIBDIR}; \ $(CP) SUMA/libgts.a ./; ) libGLws.a: ( cd SUMA ; \ rm -f libGLws.a ;\ $(MAKE) -f $(SUMA_MAKEFILE_NAME) libGLws.a 'INSTALLDIR=$(INSTALLDIR)' \ + 'LIBDIR=$(LIBDIR)' \ 'SUMA_INCLUDE_PATH=$(SUMA_INCLUDE_PATH)' \ 'SUMA_BIN_ARCHIVE=$(SUMA_BIN_ARCHIVE)' \ 'RANLIB=$(RANLIB)' \ @@ -2767,8 +2777,8 @@ 'CC=$(CC)' 'RM=$(RM)' 'CEXTRA=$(CEXTRA)' 'MV=$(MV)' 'CP=$(CP)' \ 'TAR=$(TAR)' 'MKDIR=$(MKDIR)'; \ cd ../ ; \ - if [ ! -d $(INSTALLDIR) ]; then $(MKDIR) -p $(INSTALLDIR); echo WARNING: directory $(INSTALLDIR) has been created. ; fi ;\ - $(CP) SUMA/libGLws.a ${INSTALLDIR}; \ + if [ ! -d $(LIBDIR) ]; then $(MKDIR) -p $(LIBDIR); echo WARNING: directory $(LIBDIR) has been created. ; fi ;\ + $(CP) SUMA/libGLws.a ${LIBDIR}; \ $(CP) SUMA/libGLws.a ./; ) ### #link executables but check for libraries first and create them if needed --- NEW FILE: afni.info --- Package: afni Version: 2010.10.19.1028 Revision: 1 Maintainer: Andrew Davis <ad...@gm...> Depends: glib2-shlibs, netpbm10-shlibs, openmotif4-shlibs, fontconfig2-shlibs, gsl-shlibs, libiconv, libjpeg8-shlibs, libjpeg-bin, libpng15-shlibs, xft2-shlibs, expat1-shlibs BuildDepends: glib2-dev, netpbm10, openmotif4, fontconfig2-dev, gsl, libiconv-dev, libiconv-bin, libjpeg8, libpng15, xft2-dev, fink (>= 0.24.12), llvm-gcc Architecture: x86_64 CustomMirror: << Primary: http://mrires.stjosham.on.ca/~addavis/ << Source: mirror:custom:filedrop/AFNI_2010_10_19_1028.tgz Source-MD5: 32f4b16a5ba30c380e87d8bf37971528 Source2: mirror:custom:filedrop/TTatlas+tlrc.BRIK.gz Source2-MD5: f5a107b049bc426af5342565f4e5beee Source3: mirror:custom:filedrop/TTatlas+tlrc.HEAD Source3-MD5: b41f1b82547ddce386b97c0ba620974f PatchFile: %n.patch PatchFile-MD5: 784ef79646aee20bdbc17b41d477f46e SourceRename: %n-%v.tar.gz SourceDirectory: AFNI_2010_10_19_1028 HomePage: http://afni.nimh.nih.gov/afni/about/ License: GPL Description: Analyze functional MRI data DescDetail: << AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity. It runs on Unix+X11+Motif systems, including SGI, Solaris, Linux, and Mac OS X. It is available free (in C source code format, and some precompiled binaries) for research purposes. << DescUsage: << README and rc files located in: %p/share/doc/afni/ Copy %p/share/doc/afni/AFNI.afnirc to ~/.afnirc and edit it appropriately AFNI_PLUGINPATH has been set to %p/lib/afni:%p/include/afni See README.setup and README.environment for documentation << PatchScript: << #!/usr/bin/env bash -e # use llvm-gcc on 10.7/10.8 if [ `uname -r | cut -d. -f1` -ge 11 ]; then perl -pi -e 's|= cc|= llvm-gcc-4.2 -D_FORTIFY_SOURCE=0|g' Makefile.macosx_10.6_Intel_64 fi # kill -lglib with fire perl -pi -e 's/(lglib)/\1-2.0/' Makefile.macosx_10.6_Intel_64 SUMA/SUMA_Makefile SUMA/SUMA_Makefile_NoDev # Use the right makefile if [ %m = x86_64 ]; then makeFile="Makefile.macosx_10.6_Intel_64" echo "Using Makefile for %m: ${makeFile}" else exit 10 fi cp ${makeFile} Makefile # Grab the TTatlas files mv ../TTatlas+tlrc.BRIK.gz ../TTatlas+tlrc.HEAD ./ # Update patchfile with percent expansions sed 's|@PREFIX@|%p|g' < %{PatchFile} | sed 's|@INSTALLPREFIX@|%i|g' | sed 's|@PACKAGENAME@|%n|g' | patch -p1 << UseMaxBuildJobs: false CompileScript: << #!/usr/bin/env bash -e make all plugins << InstallScript: << #!/usr/bin/env bash -e echo "Installing with: make install install_plugins install_lib" make install install_plugins install_lib echo "" echo "README and rc files located in: %p/share/doc/afni/" echo "Copy %p/share/doc/afni/AFNI.afnirc to ~/.afnirc and edit it appropriately" echo "AFNI_PLUGINPATH has been set to %p/lib/afni:%p/include/afni:%p/share/doc/afni:%p/bin" echo "See README.setup and README.environment for documentation" echo "" << RuntimeVars: << AFNI_PLUGINPATH: %p/lib/afni:%p/include/afni:%p/share/doc/afni:%p/bin << |