I made another attempt at a full build over the weekend, using MacPorts' 4.9 version of GCC.

The tarball of AFNI from Jan 26 built fine, even without having to fix the inlined function definitions, or the void return in Dimon. Installing MacPorts' openmpi-gcc49 port seemed to let everything compile properly, with OpenMP. 3dAllineate's help message even had the correct number of hyper-threaded cores on my Yosemite machine.

Here's the Makefile I used. "All" I had to do was to replace the call to OS X's compiler, linker, and archiver to the ones from MacPorts. I also moved the definition of CCOMP from Makefile.INCLUDE to this file, just b/c I was redefining the compilers here. But with these changes, I did not need to make the changes mentioned in the other messages in this thread.


# This Makefile is for Mac OSX 10.10 (Yosemite) for 64 bit AFNI, using GCC 4.9 from MacPorts

SW_ROOT = /opt/local

USE_ZLIB = -DHAVE_ZLIB
LZLIB = -lz
USE_GIFTI = -DHAVE_GIFTI
LGIFTI = -lexpat

# ----------------------------------------------------------------------
# X configuration
#

XROOT = /opt/local
XROOT_L = -L$(XROOT)/lib

XLIBS = -lXm -ljpeg -lXt

# ----------------------------------------------------------------------


CCDEBS = -DAFNI_DEBUG -DIMSEQ_DEBUG -DDISPLAY_DEBUG -DTHD_DEBUG
CEXTRA = -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -DDONT_USE_MCW_MALLOC $(LESSTIF_DEFS)
# CC = /usr/bin/gcc -O2 -DDARWIN $(CEXTRA)
# CCVOL = /usr/bin/gcc -O2 -DDARWIN $(CEXTRA)
# CCFAST = /usr/bin/gcc -O2 -DDARWIN $(CEXTRA)
# CCMIN = /usr/bin/gcc -m64
CC = /opt/local/bin/gcc-mp-4.9 -O2 -DDARWIN $(CEXTRA)
CCVOL = /opt/local/bin/gcc-mp-4.9 -O2 -DDARWIN $(CEXTRA)
CCFAST = /opt/local/bin/gcc-mp-4.9 -O2 -DDARWIN $(CEXTRA)
CCMIN = /opt/local/bin/gcc-mp-4.9 -m64
CCD = $(CC) $(CCDEBS)
CCOLD = $(CC)

OMPFLAG = -fopenmp -DUSE_OMP
CCOMP = /opt/local/bin/gcc-mp-4.9 $(OMPFLAG)

INSTALLDIR = /opt/local/bin/AFNI

EXTRA_INSTALL_FILES =

EXTRA_INSTALL_COMMANDS = ( cd $(INSTALLDIR) ; \
ln -sf libglib.dylib libglib-1.2.0.dylib ; \
ln -sf libfontconfig.1.dylib libfontconfig.dylib ; \
if [ -d $(HOME)/EXTRAPROGS ]; then $(CP) $(HOME)/EXTRAPROGS/* . ; fi ; )

IFLAGS = -I. $(XROOT_I) -I/usr/include -I/usr/X11R6/include -I$(SW_ROOT)/include
LFLAGS = -L. $(XROOT_L) -L/usr/lib -L/usr/X11R6/lib -L$(SW_ROOT)/lib -Wl,-x -Wl,-multiply_defined -Wl,warning -Wl,-bind_at_load

# CCSVD = /usr/bin/gcc -m64 -O0
CCSVD = /opt/local/bin/gcc-mp-4.9 -m64 -O0

PLUGIN_SUFFIX = so
PLUGIN_LFLAGS = -m64 -bundle -flat_namespace -undefined suppress -Wl,-x
PLUGIN_CC = $(CC) -dynamic -fno-common
PLFLAGS = -m64 -dynamic $(LFLAGS)

# include the line below if you want to include vector arith in 3dDeconvolve_f
# SPECIAL = -framework Accelerate -DUSE_ACCELERATE

# AR = /usr/bin/ar
# RANLIB = /usr/bin/ranlib
AR = /opt/local/bin/ar
RANLIB = /opt/local/bin/ranlib
TAR = /usr/bin/tar
MKDIR = /bin/mkdir
GZIP = /usr/bin/gzip
# LD = /usr/bin/gcc
LD = /opt/local/bin/gcc-mp-4.9

RM = /bin/rm -f
MV = /bin/mv -f
CP = /bin/cp -f

LINT = /usr/bin/lint -a -b -u -v -x $(IFLAGS) $(CCDEFS)

LIBDIR = $(INSTALLDIR)
SHOWOFF = -DSHOWOFF=macosx_10.10_Intel_64

INSTALL_PREREQ = suma
#INSTALL_PREREQ = suma
# uncomment if the Gnu Scientific Library is installed (libgsl, libgslcblas)
# GSLPROGS = balloon
EXPROGS = gifti_tool $(GSLPROGS)

# for dynamic linking

LLIBS = -lmri -lf2c $(XLIBS) -lXft -lfontconfig -lpng -liconv -lXmu -lXp -lXpm -lXext -lX11 $(LZLIB) $(LGIFTI) -lm -lc

# vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv
# For suma
# ZSS Aug. 08. LibGLw.a now made locally and called libGLws.a

# -------------------------------------------------------------------
# # OSX 10.5 has issues with libGL, where the multiple copies cause a cycle
# (somehow). Get around this by using -dylib_file (in a strange way).

SUMA_GLLIB = /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib
SUMA_GL_DYLIB_CMD = -dylib_file $(SUMA_GLLIB): $(SUMA_GLLIB)
# -------------------------------------------------------------------

GLw_IPATH =
GLw_LIB = -lGLw
#uncomment next two lines if you want to use libGLws.a, SUMA's copy of GLw
GLw_IPATH = -IGLw_local
GLw_LIB = libGLws.a


SUMA_INCLUDE_PATH = $(GLw_IPATH) -I.. -I../niml $(IFLAGS) -Igts/src -I${SW_ROOT}/lib/glib-2.0/include
SUMA_LINK_PATH = $(XROOT_L) $(LFLAGS) -L..

SUMA_LINK_LIB = $(XLIBS) $(GLw_LIB) $(LLIBS) -lGLU -lGL -lmri -lf2c -lmx -L${SW_ROOT}/lib/ -lglib $(SUMA_GL_DYLIB_CMD)
SUMA_MAKEFILE_NAME = SUMA_Makefile
SUMA_BIN_ARCHIVE = SUMA_MacOSX.tar

# ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^


###############################################################

MAKE = make
include Makefile.INCLUDE