Andrew,
I noticed that your afni packaging in the 10.7 tree depends on llvm-gcc. We
have
been trying to eliminate these whenever possible from the 10.7 tree since Apple
will be removing llvm-gcc from Xcode (with Xcode 4.6 being the last release with
llvm-gcc). We have two options. Clang can be used to compiled afni if the omp
support
isn't enabled (as MacPorts does). Alternatively, I have attached revised
packaging
that Depends on gcc47-shlibs and BuilDepends on gcc47-compiler so that the omp
support can be retained. The packaging passes 'fink -m' under Xcode 4.5.2 on
darwin12.
Jack
ps Note that I have appended the small patch...
--- AFNI_2010_10_19_1028/siemens_dicom_csa.c.orig 2012-12-27
14:01:22.000000000 -0500
+++ AFNI_2010_10_19_1028/siemens_dicom_csa.c 2012-12-27 14:07:04.000000000
-0500
@@ -452,7 +452,7 @@
if( ! mstr ) {
if( g_MDH_verb > 2 ) fprintf(stderr, "-- CFMST, no Mosaic string\n");
- return;
+ return 0;
}
off = mstr - instr; /* offset of Mosaic string into field */
@@ -470,7 +470,7 @@
if( s2 ) rem = rem2; /* after verbose, update remaining length */
- if( rem <= 0 ) return;
+ if( rem <= 0 ) return 0;
process_csa_data((unsigned char *)instr, el_len, g_MDH_verb,
g_MDH_verb>3, start_txt);
--- AFNI_2010_10_19_1028/thd_brainormalize.c.orig 2012-12-27
14:50:40.000000000 -0500
+++ AFNI_2010_10_19_1028/thd_brainormalize.c 2012-12-27 14:51:30.000000000
-0500
@@ -650,7 +650,7 @@
int *hsv , *csv ;
shortvox *tar ;
- if( n < 2 || ar == NULL ) return ;
+ if( n < 2 || ar == NULL ) return 0;
/* decreasing order desired? flip values */
@@ -669,7 +669,7 @@
else if( sval > stop ) stop = sval ;
}
nsv = stop-sbot+1 ; /* number of distinct values */
- if( nsv <= 1 ) return ;
+ if( nsv <= 1 ) return 0;
/* build hsv[i] = how many have value = sbot+i
csv[i] = how many have value < sbot+i, i=0..nsv-1 */
@@ -727,7 +727,7 @@
if( dec )
for( ii=0 ; ii < n ; ii++ ) ar[ii].val = -ar[ii].val ;
- return ;
+ return 0;
}
/*--------------------------------------------------------------------------*/
to the afni.patch in order to eliminate the compiler errors...
./siemens_dicom_csa.c:455:7: error: non-void function
'check_for_mosaic_slice_times' should return a value [-Wreturn-type]
return;
^
./siemens_dicom_csa.c:473:19: error: non-void function
'check_for_mosaic_slice_times' should return a value [-Wreturn-type]
if( rem <= 0 ) return;
^
thd_brainormalize.c:653:30: error: non-void function 'sort_shortvox' should
return a value [-Wreturn-type]
if( n < 2 || ar == NULL ) return ;
^
thd_brainormalize.c:672:19: error: non-void function 'sort_shortvox' should
return a value [-Wreturn-type]
if( nsv <= 1 ) return ;
^
thd_brainormalize.c:730:4: error: non-void function 'sort_shortvox' should
return a value [-Wreturn-type]
return ;
^
seen under clang.
Package: afni
Version: 2010.10.19.1028
Revision: 2
Maintainer: Andrew Davis <adda...@gmail.com>
Depends: glib2-shlibs, netpbm10-shlibs, openmotif4-shlibs, fontconfig2-shlibs,
gsl-shlibs, libiconv, libjpeg8-shlibs, libjpeg-bin, libpng15-shlibs,
xft2-shlibs, expat1-shlibs, gcc47-shlibs
BuildDepends: glib2-dev, netpbm10, openmotif4, fontconfig2-dev, gsl,
libiconv-dev, libiconv-bin, libjpeg8, libpng15, xft2-dev, gcc47-compiler, fink
(>= 0.24.12)
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: ae732d5b090d8c07cd5e676f8e975aa3
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
perl -pi -e 's|= cc|= gcc-fsf-4.7|g' Makefile.macosx_10.6_Intel_64
perl -pi -e 's|-no-cpp-precomp||g' Makefile.macosx_10.6_Intel_64
# 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
<<
--- 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
--- AFNI_2010_10_19_1028/siemens_dicom_csa.c.orig 2012-12-27
14:01:22.000000000 -0500
+++ AFNI_2010_10_19_1028/siemens_dicom_csa.c 2012-12-27 14:07:04.000000000
-0500
@@ -452,7 +452,7 @@
if( ! mstr ) {
if( g_MDH_verb > 2 ) fprintf(stderr, "-- CFMST, no Mosaic string\n");
- return;
+ return 0;
}
off = mstr - instr; /* offset of Mosaic string into field */
@@ -470,7 +470,7 @@
if( s2 ) rem = rem2; /* after verbose, update remaining length */
- if( rem <= 0 ) return;
+ if( rem <= 0 ) return 0;
process_csa_data((unsigned char *)instr, el_len, g_MDH_verb,
g_MDH_verb>3, start_txt);
--- AFNI_2010_10_19_1028/thd_brainormalize.c.orig 2012-12-27
14:50:40.000000000 -0500
+++ AFNI_2010_10_19_1028/thd_brainormalize.c 2012-12-27 14:51:30.000000000
-0500
@@ -650,7 +650,7 @@
int *hsv , *csv ;
shortvox *tar ;
- if( n < 2 || ar == NULL ) return ;
+ if( n < 2 || ar == NULL ) return 0;
/* decreasing order desired? flip values */
@@ -669,7 +669,7 @@
else if( sval > stop ) stop = sval ;
}
nsv = stop-sbot+1 ; /* number of distinct values */
- if( nsv <= 1 ) return ;
+ if( nsv <= 1 ) return 0;
/* build hsv[i] = how many have value = sbot+i
csv[i] = how many have value < sbot+i, i=0..nsv-1 */
@@ -727,7 +727,7 @@
if( dec )
for( ii=0 ; ii < n ; ii++ ) ar[ii].val = -ar[ii].val ;
- return ;
+ return 0;
}
/*--------------------------------------------------------------------------*/
------------------------------------------------------------------------------
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