On Oct 5, 2017, at 1:42 PM, Sol Jerome <solj@utdallas.edu> wrote:
The header file does not exist.
Here is the output from `make`:
# make
make: *** No rule to make target `lta_convert.help.xml.h', needed by `all'. Stop.
Here is the content of the Makefile:
# Makefile.in generated by automake 1.13.4 from Makefile.am.
# lta_convert/Makefile. Generated from Makefile.in by configure.
# Copyright (C) 1994-2013 Free Software Foundation, Inc.
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
# PARTICULAR PURPOSE.
am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
am__make_running_with_option = \
case $${target_option-} in \
?) ;; \
*) echo "am__make_running_with_option: internal error: invalid" \
"target option '$${target_option-}' specified" >&2; \
exit 1;; \
esac; \
has_opt=no; \
sane_makeflags=$$MAKEFLAGS; \
if $(am__is_gnu_make); then \
sane_makeflags=$$MFLAGS; \
else \
case $$MAKEFLAGS in \
*\\[\ \ ]*) \
bs=\\; \
sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \
| sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
esac; \
fi; \
skip_next=no; \
strip_trailopt () \
{ \
flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \
}; \
for flg in $$sane_makeflags; do \
test $$skip_next = yes && { skip_next=no; continue; }; \
case $$flg in \
*=*|--*) continue;; \
-*I) strip_trailopt 'I'; skip_next=yes;; \
-*I?*) strip_trailopt 'I';; \
-*O) strip_trailopt 'O'; skip_next=yes;; \
-*O?*) strip_trailopt 'O';; \
-*l) strip_trailopt 'l'; skip_next=yes;; \
-*l?*) strip_trailopt 'l';; \
-[dEDm]) skip_next=yes;; \
-[JT]) skip_next=yes;; \
esac; \
case $$flg in \
*$$target_option*) has_opt=yes; break;; \
esac; \
done; \
test $$has_opt = yes
am__make_dryrun = (target_option=n; $(am__make_running_with_option))
am__make_keepgoing = (target_option=k; $(am__make_running_with_option))
pkgdatadir = $(datadir)/freesurfer
pkgincludedir = $(includedir)/freesurfer
pkglibdir = $(libdir)/freesurfer
pkglibexecdir = $(libexecdir)/freesurfer
am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
install_sh_DATA = $(install_sh) -c -m 644
install_sh_PROGRAM = $(install_sh) -c
install_sh_SCRIPT = $(install_sh) -c
INSTALL_HEADER = $(INSTALL_DATA)
transform = $(program_transform_name)
NORMAL_INSTALL = :
PRE_INSTALL = :
POST_INSTALL = :
NORMAL_UNINSTALL = :
PRE_UNINSTALL = :
POST_UNINSTALL = :
build_triplet = x86_64-redhat-linux-gnu
host_triplet = Linux-centos4_x86_64
target_triplet = x86_64-redhat-linux-gnu
bin_PROGRAMS = lta_convert$(EXEEXT)
DIST_COMMON = $(top_srcdir)/Makefile.extra $(srcdir)/Makefile.in \
$(srcdir)/Makefile.am $(top_srcdir)/config/mkinstalldirs \
$(top_srcdir)/config/depcomp
subdir = lta_convert
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/acinclude.m4 \
$(top_srcdir)/m4/autotroll.m4 $(top_srcdir)/configure.in
am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
$(ACLOCAL_M4)
mkinstalldirs = $(SHELL) $(top_srcdir)/config/mkinstalldirs
CONFIG_HEADER = $(top_builddir)/config.h
CONFIG_CLEAN_FILES =
CONFIG_CLEAN_VPATH_FILES =
am__installdirs = "$(DESTDIR)$(bindir)" "$(DESTDIR)$(foodir)" \
"$(DESTDIR)$(foo2dir)"
PROGRAMS = $(bin_PROGRAMS)
am_lta_convert_OBJECTS = lta_convert.$(OBJEXT)
lta_convert_OBJECTS = $(am_lta_convert_OBJECTS)
lta_convert_DEPENDENCIES = $(addprefix $(top_builddir)/, $(LIBS_MGH))
AM_V_lt = $(am__v_lt_$(V))
am__v_lt_ = $(am__v_lt_$(AM_DEFAULT_VERBOSITY))
am__v_lt_0 = --silent
am__v_lt_1 =
lta_convert_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CXX $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CXXLD) $(AM_CXXFLAGS) \
$(CXXFLAGS) $(lta_convert_LDFLAGS) $(LDFLAGS) -o $@
AM_V_P = $(am__v_P_$(V))
am__v_P_ = $(am__v_P_$(AM_DEFAULT_VERBOSITY))
am__v_P_0 = false
am__v_P_1 = :
AM_V_GEN = $(am__v_GEN_$(V))
am__v_GEN_ = $(am__v_GEN_$(AM_DEFAULT_VERBOSITY))
am__v_GEN_0 = @echo " GEN " $@;
am__v_GEN_1 =
AM_V_at = $(am__v_at_$(V))
am__v_at_ = $(am__v_at_$(AM_DEFAULT_VERBOSITY))
am__v_at_0 = @
am__v_at_1 =
DEFAULT_INCLUDES = -I. -I$(top_builddir)
depcomp = $(SHELL) $(top_srcdir)/config/depcomp
am__depfiles_maybe = depfiles
am__mv = mv -f
CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
LTCXXCOMPILE = $(LIBTOOL) $(AM_V_lt) --tag=CXX $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=compile $(CXX) $(DEFS) \
$(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \
$(AM_CXXFLAGS) $(CXXFLAGS)
AM_V_CXX = $(am__v_CXX_$(V))
am__v_CXX_ = $(am__v_CXX_$(AM_DEFAULT_VERBOSITY))
am__v_CXX_0 = @echo " CXX " $@;
am__v_CXX_1 =
CXXLD = $(CXX)
CXXLINK = $(LIBTOOL) $(AM_V_lt) --tag=CXX $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CXXLD) $(AM_CXXFLAGS) \
$(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
AM_V_CXXLD = $(am__v_CXXLD_$(V))
am__v_CXXLD_ = $(am__v_CXXLD_$(AM_DEFAULT_VERBOSITY))
am__v_CXXLD_0 = @echo " CXXLD " $@;
am__v_CXXLD_1 =
SOURCES = $(lta_convert_SOURCES)
DIST_SOURCES = $(lta_convert_SOURCES)
am__can_run_installinfo = \
case $$AM_UPDATE_INFO_DIR in \
n|no|NO) false;; \
*) (install-info --version) >/dev/null 2>&1;; \
esac
am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
am__vpath_adj = case $$p in \
$(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
*) f=$$p;; \
esac;
am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
am__install_max = 40
am__nobase_strip_setup = \
srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
am__nobase_strip = \
for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
am__nobase_list = $(am__nobase_strip_setup); \
for p in $$list; do echo "$$p $$p"; done | \
sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
$(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
if (++n[$$2] == $(am__install_max)) \
{ print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
END { for (dir in files) print dir, files[dir] }'
am__base_list = \
sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
am__uninstall_files_from_dir = { \
test -z "$$files" \
|| { test ! -d "$$dir" && test ! -f "$$dir" && test ! -r "$$dir"; } \
|| { echo " ( cd '$$dir' && rm -f" $$files ")"; \
$(am__cd) "$$dir" && rm -f $$files; }; \
}
DATA = $(foo_DATA) $(foo2_DATA)
am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
# Read a list of newline-separated strings from the standard input,
# and print each of them once, without duplicates. Input order is
# *not* preserved.
am__uniquify_input = $(AWK) '\
BEGIN { nonempty = 0; } \
{ items[$$0] = 1; nonempty = 1; } \
END { if (nonempty) { for (i in items) print i; }; } \
'
# Make sure the list of sources is unique. This is necessary because,
# e.g., the same source file might be shared among _SOURCES variables
# for different programs/libraries.
am__define_uniq_tagged_files = \
list='$(am__tagged_files)'; \
unique=`for i in $$list; do \
if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
done | $(am__uniquify_input)`
ETAGS = etags
CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = ${SHELL} /builddir/build/BUILD/freesurfer-6.0.0/config/missing aclocal-1.13
AMTAR = $${TAR-tar}
AM_DEFAULT_VERBOSITY = 1
ANN_CFLAGS = -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/ann/current/include
ANN_DIR = NO
ANN_LIB = /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/ann/current/lib
ANN_LIBS = -L/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/ann/current/lib
AR = ar
AUTOCONF = ${SHELL} /builddir/build/BUILD/freesurfer-6.0.0/config/missing autoconf
AUTOHEADER = ${SHELL} /builddir/build/BUILD/freesurfer-6.0.0/config/missing autoheader
AUTOMAKE = ${SHELL} /builddir/build/BUILD/freesurfer-6.0.0/config/missing automake-1.13
AWK = gawk
BLT_CFLAGS =
BLT_LIBS =
BOOST_CFLAGS =
BOOST_DIR =
BOOST_LIB =
BOOST_LIBS =
BOOST_PO_LIB =
BYTEORDER = 1234
CC = gcc
CCDEPMODE = depmode=none
CCLD = g++
CFLAGS = -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic
CPP = gcc -E
CPPFLAGS = -g -O3 -msse2 -mfpmath=sse -Wall -DUSE_SSE_MATHFUN -fopenmp -DHAVE_OPENMP -m64 -DLinux -DANSI -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/mni/1.5/include
CPPUNIT_CFLAGS = -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/cppunit/current/include
CPPUNIT_DIR = /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/cppunit/current
CPPUNIT_LIB = /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/cppunit/current/lib
CPPUNIT_LIBS = -L/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/cppunit/current/lib
CPUCAPS = model name : Intel(R) Xeon(R) CPU E5-2440 0 @ 2.40GHz
CPUTYPE = intel_haswell
CUDA_CFLAGS = -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/CUDA/current/include
CUDA_DIR = /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/CUDA/current
CUDA_LIBS = -L/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/CUDA/current/lib64 -lcudart
CXX = g++
CXXCPP = g++ -E
CXXDEPMODE = depmode=none
CXXFLAGS = -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic
CYGPATH_W = echo
DEFS = -DHAVE_CONFIG_H
DEPDIR = .deps
DYNAMIC_LIB_EXT = .so
ECHO = echo
ECHO_C =
ECHO_N = -n
ECHO_T =
EGREP = /usr/bin/grep -E
EXEEXT =
EXPAT_CFLAGS =
EXPAT_LIBS =
F77 = gfortran
FCLIBS =
FFLAGS = -g -O3 -msse2 -mfpmath=sse
FLTK_CXXFLAGS =
FLTK_DIR =
FLTK_LDFLAGS =
FLTK_LIB =
FLTK_LIBS =
GDCM_CFLAGS =
GDCM_DIR =
GDCM_LIB =
GDCM_LIBS =
GLU_CFLAGS =
GLU_LIBS = -lGLU -lGL -L/lib64 -lX11 -lm
GL_CFLAGS =
GL_LIBS = -lGL -L/lib64 -lX11 -lm
GREP = /usr/bin/grep
GTS_CFLAGS =
GTS_DIR =
GTS_LIBS =
HAS_GZIP = 1
HAS_ZCAT = 1
HAVE_OPENGL = -DHAVE_OPENGL
INSTALL = /usr/bin/install -c
INSTALL_DATA = ${INSTALL} -m 644
INSTALL_PROGRAM = ${INSTALL}
INSTALL_SCRIPT = ${INSTALL}
INSTALL_STRIP_PROGRAM = $(install_sh) -c -s
ITK_CFLAGS = -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/include/InsightToolkit -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/include/InsightToolkit/Algorithms -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/include/InsightToolkit/BasicFilters -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/include/InsightToolkit/Common -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/include/InsightToolkit/IO -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/include/InsightToolkit/Numerics -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/include/InsightToolkit/Numerics/Statistics -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/include/InsightToolkit/Review -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/include/InsightToolkit/Review/Statistics -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/include/InsightToolkit/SpatialObject -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/include/InsightToolkit/Utilities
ITK_DIR = /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current
ITK_LIB = /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit
ITK_LIBS = -L/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit
JPEG_CFLAGS =
JPEG_LIBS =
KWWIDGETS_CFLAGS = -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/KWWidgets/current/include/KWWidgets
KWWIDGETS_CXXFLAGS = -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/KWWidgets/current/include/KWWidgets
KWWIDGETS_DIR = /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/KWWidgets/current
KWWIDGETS_LIBS = -L/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/KWWidgets/current/lib/KWWidgets
LATEX =
LDFLAGS = -L/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/current/lib -L/usr/lib64 -L/usr/X11R6/lib64 -Wl,-z,relro -fopenmp -L/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/mni/1.5/lib -L/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/vxl/current/lib -L/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit
LDFLAGS_TCL = -L/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/tcltktixblt/current/lib
LIBDIRS_MGH = utils rgb unix dicom hipsstubs
LIBOBJS =
LIBS = /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKIO.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKAlgorithms.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKCommon.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKNumerics.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKMetaIO.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKniftiio.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKNrrdIO.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkpng.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitksys.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitktiff.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkv3p_netlib.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkzlib.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkgdcm.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkopenjpeg.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkjpeg8.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkjpeg12.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkjpeg16.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKDICOMParser.a /usr/lib64/libuuid.so -lz -lm -lcrypt -ldl -lpthread /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/mni/current/lib/libvolume_io.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/mni/current/lib/libminc.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/mni/current/lib/libnetcdf.a -lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib
LIBS_CUDA_MGH = utils/libutils_cuda.a fsgdf/libfsgdf.a rgb/librgb.a unix/libunix.a dicom/libdicom.a hipsstubs/libhipsstubs.a log/liblog.a xml2/libxml2.a jpeg/libjpeg.a tiff/libtiff.a expat/libexpat.a
LIBS_GDCM =
LIBS_ICC =
LIBS_ITK = /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKIO.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKAlgorithms.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKCommon.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKNumerics.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKMetaIO.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKniftiio.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKNrrdIO.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkpng.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitksys.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitktiff.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkv3p_netlib.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkzlib.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkgdcm.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkopenjpeg.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkjpeg8.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkjpeg12.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkjpeg16.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKDICOMParser.a /usr/lib64/libuuid.so
LIBS_MGH = utils/libutils.a fsgdf/libfsgdf.a rgb/librgb.a unix/libunix.a dicom/libdicom.a hipsstubs/libhipsstubs.a log/liblog.a xml2/libxml2.a jpeg/libjpeg.a tiff/libtiff.a expat/libexpat.a
LIBS_MNI = /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/mni/current/lib/libvolume_io.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/mni/current/lib/libminc.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/mni/current/lib/libnetcdf.a
LIBS_NIFTI =
LIBS_OPEN64 =
LIBS_OPENGL = -lGLU -lGL -L/lib64 -lX11 -lm
LIBS_TCL = -lBLT -ltix8.1.8.4 -ltk8.4 -ltcl8.4
LIBS_TCL_OPENGL = -lBLT -ltix8.1.8.4 -ltk8.4 -ltcl8.4 -lGLU -lGL -L/lib64 -lX11 -lm
LIBS_VXL = -lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib
LIBS_XAWPLUS = -lXt -lXpm -lXawPlus
LIBTOOL = $(SHELL) $(top_builddir)/libtool
LIB_BLAS = /usr/lib64/libblas.a
LIB_BLT = -lBLT
LIB_BLT_JPEG = /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/tiffjpegglut/current/lib/libjpeg.a
LIB_CRYPT = -lcrypt
LIB_CUDA =
LIB_EXPAT =
LIB_G2C_A =
LIB_GFORTRAN = -lgfortran
LIB_JPEG =
LIB_LAPACK = /usr/lib64/liblapack.a
LIB_NETCDF = /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/mni/current/lib/libnetcdf.a
LIB_TCL = -ltcl8.4
LIB_TIFF =
LIB_TIX = -ltix8.1.8.4
LIB_TK = -ltk8.4
LIB_UUID = /usr/lib64/libuuid.so
LN_S = ln -s
LTLIBOBJS =
MAKEINFO = ${SHELL} /builddir/build/BUILD/freesurfer-6.0.0/config/missing makeinfo
MKDIR_P = /usr/bin/mkdir -p
MNI_CFLAGS = -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/mni/1.5/include
MNI_DIR = /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/mni/1.5
MNI_LIBS = -L/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/mni/1.5/lib
MOC = /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/current/bin/moc
MPI_CFLAGS =
MPI_DIR =
MPI_LIB =
MPI_LIBS =
NIFTI_CFLAGS =
NIFTI_DIR =
NIFTI_LIB =
NIFTI_LIBS =
NVCC = /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/CUDA/current/bin/nvcc
NVCCFLAGS = -arch sm_11 --ptxas-options=-v -g
OBJEXT = o
OPENCL_CFLAGS =
OPENCL_LIBS =
OPENCV_CXXFLAGS =
OPENCV_DIR = no
OPENCV_LIBS =
OPENMP_FLAG = -fopenmp
OS = Linux
OS_CPPFLAGS =
OS_LDFLAGS =
PACKAGE = freesurfer
PACKAGE_BUGREPORT = freesurfer@nmr.mgh.harvard.edu
PACKAGE_NAME = Freesurfer
PACKAGE_STRING = Freesurfer stable6
PACKAGE_TARNAME = freesurfer
PACKAGE_URL =
PACKAGE_VERSION = stable6
PATH_SEPARATOR = :
PETSC_CFLAGS = -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/petsc/current/include
PETSC_DIR = /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/petsc/current
PETSC_LIB = /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/petsc/current/lib
PETSC_LIBS = -L/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/petsc/current/lib
POW_LIB =
PTHREAD_CC = gcc
PTHREAD_CFLAGS =
PTHREAD_LIBS =
QMAKE = /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/current/bin/qmake
QT_CFLAGS = -pipe -O2 -Wall -W -D_REENTRANT -fPIC $(QT_DEFINES)
QT_CPPFLAGS = -DQT_NO_DEBUG -DQT_OPENGL_LIB -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_SCRIPT_LIB -DQT_SCRIPTTOOLS_LIB -DQT_CORE_LIB -I. -I. -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/5.6.2/5.6/gcc_64/include -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/5.6.2/5.6/gcc_64/include/QtOpenGL -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/5.6.2/5.6/gcc_64/include/QtWidgets -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/5.6.2/5.6/gcc_64/include/QtGui -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/5.6.2/5.6/gcc_64/include/QtScript -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/5.6.2/5.6/gcc_64/include/QtScriptTools -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/5.6.2/5.6/gcc_64/include/QtCore -I. -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/5.6.2/5.6/gcc_64/mkspecs/linux-g++
QT_CXXFLAGS = -pipe -O2 -std=gnu++0x -Wall -W -D_REENTRANT -fPIC $(QT_DEFINES)
QT_DEFINES = -DQT_NO_DEBUG -DQT_OPENGL_LIB -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_SCRIPT_LIB -DQT_SCRIPTTOOLS_LIB -DQT_CORE_LIB
QT_DIR = /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/current/bin/..
QT_INCPATH = -I. -I. -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/5.6.2/5.6/gcc_64/include -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/5.6.2/5.6/gcc_64/include/QtOpenGL -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/5.6.2/5.6/gcc_64/include/QtWidgets-I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/5.6.2/5.6/gcc_64/include/QtGui -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/5.6.2/5.6/gcc_64/include/QtScript -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/5.6.2/5.6/gcc_64/include/QtScriptTools -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/5.6.2/5.6/gcc_64/include/QtCore -I. -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/5.6.2/5.6/gcc_64/mkspecs/linux-g++
QT_LDFLAGS = -Wl,-O1 -Wl,-rpath,/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/current/lib -Wl,-rpath-link,/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/current/lib
QT_LFLAGS = -Wl,-O1 -Wl,-rpath,/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/current/lib -Wl,-rpath-link,/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/current/lib
QT_LIBS = -L/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/current/lib -lQt5OpenGL -L/usr/lib64 -lQt5Widgets -lQt5Gui -lQt5Script -L/usr/pubsw/packages/qt/5.6.2/5.6/gcc_64/lib -lQt5ScriptTools -lQt5Core -lGL -lpthread
QT_PATH = /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/current/bin
QT_VERSION_MAJOR = 4
RANLIB = ranlib
RCC = /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/current/bin/rcc
SET_MAKE =
SHARED_CFLAGS = -fPIC
SHARED_LDFLAGS = -shared
SHELL = /bin/sh
STRIP = strip
TCL_CFLAGS = -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/tcltktixblt/current/include
TCL_DIR = /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/tcltktixblt/current
TCL_LIB = /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/tcltktixblt/current/lib
TCL_LIBS = -L/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/tcltktixblt/current/lib
TEEM_32BIT = 0
TEEM_DIO = 0
TEEM_ENDIAN = 1234
TEEM_QNANHIBIT = 1
TESTS_ENVIRONMENT = SURFER_FRONTDOOR=1 LD_LIBRARY_PATH=/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/tcltktixblt/current/lib:/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/vtk/current/lib/vtk-5.6:/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/cppunit/current/lib
TIFF_CFLAGS =
TIFF_LIBS =
TIXWISH =
UIC = /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/current/bin/uic
VERSION = stable6
VTK_CFLAGS = -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/vtk/current/include/vtk-5.6
VTK_COCOA_CFLAGS =
VTK_COCOA_CXXFLAGS =
VTK_COCOA_DIR =
VTK_COCOA_LIB = NO
VTK_COCOA_LIBS = -LNO
VTK_COCOA_LIB_VTK =
VTK_CXXFLAGS = -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/vtk/current/include/vtk-5.6
VTK_DIR = /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/vtk/current
VTK_EXPAT_LIB = ../expat/libexpat.a
VTK_FREETYPE_LIB = -lfreetype
VTK_HDF5_LIB =
VTK_JPEG_LIB = ../jpeg/libjpeg.a
VTK_LIB = /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/vtk/current/lib/vtk-5.6
VTK_LIBS = -L/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/vtk/current/lib/vtk-5.6
VTK_LIB_VTK = /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/vtk/current/lib/vtk-5.6
VTK_LSDYNA_LIB =
VTK_METAIO_LIB = -lvtkmetaio
VTK_MPEG2ENCODE_LIB =
VTK_NETCDFCXX_LIB =
VTK_PNG_LIB = -lvtkpng
VTK_SQLITE_LIB = -lvtksqlite
VTK_TIFF_LIB = ../tiff/libtiff.a
VTK_VERDICT_LIB = -lvtkverdict
VTK_Z_LIB = -lvtkzlib
VXL_CFLAGS = -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/vxl/current/include/vxl/core -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/vxl/current/include/vxl/vcl -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/vxl/current/include/vxl/v3p/netlib -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/vxl/current/include/vxl/v3p/netlib/opt
VXL_DIR = /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/vxl/current
VXL_LIB = /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/vxl/current/lib
VXL_LIBS = -L/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/vxl/current/lib
WXWIDGETS_CFLAGS = -I/usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/lib/wx/include/gtk2-ansi-release-static-2.8 -I/usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/include/wx-2.8 -D_FILE_OFFSET_BITS=64 -D_LARGE_FILES -D_LARGEFILE_SOURCE=1 -D__WXGTK__ -pthread
WXWIDGETS_CXXFLAGS = -I/usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/lib/wx/include/gtk2-ansi-release-static-2.8 -I/usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/include/wx-2.8 -D_FILE_OFFSET_BITS=64 -D_LARGE_FILES -D_LARGEFILE_SOURCE=1 -D__WXGTK__ -pthread
WXWIDGETS_DIR = /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/wxWidgets/current
WXWIDGETS_GL_LIBS = -L/usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/lib -pthread -L/usr/X11R6/lib64 -L/usr/lib64 /usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/lib/libwx_gtk2_gl-2.8.a /usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/lib/libwx_base-2.8.a -lGL -lGLU -lz -ldl -lm
WXWIDGETS_LIBS = -L/usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/lib -pthread -L/usr/X11R6/lib64 /usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/lib/libwx_gtk2_richtext-2.8.a /usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/lib/libwx_gtk2_aui-2.8.a /usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/lib/libwx_gtk2_xrc-2.8.a /usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/lib/libwx_gtk2_qa-2.8.a /usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/lib/libwx_gtk2_html-2.8.a /usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/lib/libwx_gtk2_adv-2.8.a /usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/lib/libwx_gtk2_core-2.8.a /usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/lib/libwx_base_xml-2.8.a /usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/lib/libwx_base_net-2.8.a /usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/lib/libwx_base-2.8.a -Wl,--export-dynamic -pthread -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgdk_pixbuf-2.0 -lpangoxft-1.0 -lpangox-1.0 -lpango-1.0 -lgobject-2.0 -lgmodule-2.0 -lgthread-2.0 -lglib-2.0 -lXinerama -lXxf86vm -lSM -lpng ../jpeg/libjpeg.a ../tiff/libtiff.a ../expat/libexpat.a -lz -ldl -lm -lwx_gtk2_gl-2.8
WXWIDGETS_OPTIONAL_LIBS =
XAWPLUS_CFLAGS = -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/xawplus/current/include
XAWPLUS_CXXFLAGS = -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/xawplus/current/include
XAWPLUS_DIR = /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/xawplus/current
XAWPLUS_LIBS = -L/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/xawplus/current/lib
XMKMF =
XMLLINT = xmllint
XXD =
X_LIBS = -L/lib64 -lX11 -L/lib64 -lXmu
abs_builddir = /builddir/build/BUILD/freesurfer-6.0.0/lta_convert
abs_srcdir = /builddir/build/BUILD/freesurfer-6.0.0/lta_convert
abs_top_builddir = /builddir/build/BUILD/freesurfer-6.0.0
abs_top_srcdir = /builddir/build/BUILD/freesurfer-6.0.0
ac_ct_CC = gcc
ac_ct_CXX = g++
ac_ct_F77 = gfortran
acx_pthread_config =
am__include = include
am__leading_dot = .
am__quote =
am__tar = tar --format=ustar -chf - "$$tardir"
am__untar = tar -xf -
bindir = /usr/bin
build = x86_64-redhat-linux-gnu
build_alias = x86_64-redhat-linux-gnu
build_cpu = x86_64
build_os = linux-gnu
build_vendor = centos4
builddir = .
datadir = /usr/share
datarootdir = ${prefix}/share
docdir = ${datarootdir}/doc/${PACKAGE_TARNAME}
dvidir = ${docdir}
exec_prefix = /usr
gl_cflags =
gl_libs =
host = Linux-centos4_x86_64
host_alias = x86_64-redhat-linux-gnu
host_cpu = x86_64
host_os = linux-gnu
host_vendor = centos4
htmldir = ${docdir}
includedir = /usr/include
infodir = /usr/share/info
install_sh = ${SHELL} /builddir/build/BUILD/freesurfer-6.0.0/config/install-sh
libdir = /usr/lib64
libexecdir = /usr/libexec
localedir = ${datarootdir}/locale
localstatedir = /var
mandir = /usr/share/man
mkdir_p = $(MKDIR_P)
oldincludedir = /usr/include
pdfdir = ${docdir}
prefix = /opt/freesurfer/6.0.0
program_transform_name = s&^&&
psdir = ${docdir}
sbindir = /usr/sbin
sharedstatedir = /var/lib
srcdir = .
sysconfdir = /etc
target = x86_64-redhat-linux-gnu
target_alias =
target_cpu = x86_64
target_os = linux-gnu
target_vendor = redhat
top_build_prefix = ../
top_builddir = ..
top_srcdir = ..
AM_CFLAGS = -I$(top_srcdir)/include
AM_CXXFLAGS = -I$(top_srcdir)/include
BUILT_SOURCES = lta_convert.help.xml.h lta_convert.help.xml.html
foodir = $(prefix)/docs/xml
foo_DATA = lta_convert.help.xml
foo2dir = $(prefix)/docs/html
foo2_DATA = lta_convert.help.xml.html
lta_convert_SOURCES = lta_convert.cpp
lta_convert_LDADD = $(addprefix $(top_builddir)/, $(LIBS_MGH))
lta_convert_LDFLAGS = $(OS_LDFLAGS)
# Our release target. Include files to be excluded here. They will be
# found and removed after 'make install' is run during the 'make
# release' target.
EXCLUDE_FILES =
all: $(BUILT_SOURCES)
$(MAKE) $(AM_MAKEFLAGS) all-am
.SUFFIXES:
.SUFFIXES: .cpp .lo .o .obj
$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(top_srcdir)/Makefile.extra $(am__configure_deps)
@for dep in $?; do \
case '$(am__configure_deps)' in \
*$$dep*) \
( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
&& { if test -f $@; then exit 0; else break; fi; }; \
exit 1;; \
esac; \
done; \
echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu lta_convert/Makefile'; \
$(am__cd) $(top_srcdir) && \
$(AUTOMAKE) --gnu lta_convert/Makefile
.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
*config.status*) \
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
*) \
echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
esac;
$(top_srcdir)/Makefile.extra:
$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
$(top_srcdir)/configure: $(am__configure_deps)
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
$(ACLOCAL_M4): $(am__aclocal_m4_deps)
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
$(am__aclocal_m4_deps):
install-binPROGRAMS: $(bin_PROGRAMS)
@$(NORMAL_INSTALL)
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
if test -n "$$list"; then \
echo " $(MKDIR_P) '$(DESTDIR)$(bindir)'"; \
$(MKDIR_P) "$(DESTDIR)$(bindir)" || exit 1; \
fi; \
for p in $$list; do echo "$$p $$p"; done | \
sed 's/$(EXEEXT)$$//' | \
while read p p1; do if test -f $$p \
|| test -f $$p1 \
; then echo "$$p"; echo "$$p"; else :; fi; \
done | \
sed -e 'p;s,.*/,,;n;h' \
-e 's|.*|.|' \
-e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
sed 'N;N;N;s,\n, ,g' | \
$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
{ d=$$3; if (dirs[d] != 1) { print "d", d; dirs[d] = 1 } \
if ($$2 == $$4) files[d] = files[d] " " $$1; \
else { print "f", $$3 "/" $$4, $$1; } } \
END { for (d in files) print "f", d, files[d] }' | \
while read type dir files; do \
if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \
test -z "$$files" || { \
echo " $(INSTALL_PROGRAM_ENV) $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(bindir)$$dir'"; \
$(INSTALL_PROGRAM_ENV) $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL_PROGRAM) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \
} \
; done
uninstall-binPROGRAMS:
@$(NORMAL_UNINSTALL)
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
files=`for p in $$list; do echo "$$p"; done | \
sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
-e 's/$$/$(EXEEXT)/' \
`; \
test -n "$$list" || exit 0; \
echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
cd "$(DESTDIR)$(bindir)" && rm -f $$files
clean-binPROGRAMS:
@list='$(bin_PROGRAMS)'; test -n "$$list" || exit 0; \
echo " rm -f" $$list; \
rm -f $$list || exit $$?; \
test -n "$(EXEEXT)" || exit 0; \
list=`for p in $$list; do echo "$$p"; done | sed 's/$(EXEEXT)$$//'`; \
echo " rm -f" $$list; \
rm -f $$list
lta_convert$(EXEEXT): $(lta_convert_OBJECTS) $(lta_convert_DEPENDENCIES) $(EXTRA_lta_convert_DEPENDENCIES)
@rm -f lta_convert$(EXEEXT)
$(AM_V_CXXLD)$(lta_convert_LINK) $(lta_convert_OBJECTS) $(lta_convert_LDADD) $(LIBS)
mostlyclean-compile:
-rm -f *.$(OBJEXT)
distclean-compile:
-rm -f *.tab.c
#include ./$(DEPDIR)/lta_convert.Po
.cpp.o:
# $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
# $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
# $(AM_V_CXX)source='$<' object='$@' libtool=no
# DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp)
$(AM_V_CXX)$(CXXCOMPILE) -c -o $@ $<
.cpp.obj:
# $(AM_V_CXX)$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
# $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
# $(AM_V_CXX)source='$<' object='$@' libtool=no
# DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp)
$(AM_V_CXX)$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
.cpp.lo:
# $(AM_V_CXX)$(LTCXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
# $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Plo
# $(AM_V_CXX)source='$<' object='$@' libtool=yes
# DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp)
$(AM_V_CXX)$(LTCXXCOMPILE) -c -o $@ $<
mostlyclean-libtool:
-rm -f *.lo
clean-libtool:
-rm -rf .libs _libs
install-fooDATA: $(foo_DATA)
@$(NORMAL_INSTALL)
@list='$(foo_DATA)'; test -n "$(foodir)" || list=; \
if test -n "$$list"; then \
echo " $(MKDIR_P) '$(DESTDIR)$(foodir)'"; \
$(MKDIR_P) "$(DESTDIR)$(foodir)" || exit 1; \
fi; \
for p in $$list; do \
if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
echo "$$d$$p"; \
done | $(am__base_list) | \
while read files; do \
echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(foodir)'"; \
$(INSTALL_DATA) $$files "$(DESTDIR)$(foodir)" || exit $$?; \
done
uninstall-fooDATA:
@$(NORMAL_UNINSTALL)
@list='$(foo_DATA)'; test -n "$(foodir)" || list=; \
files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
dir='$(DESTDIR)$(foodir)'; $(am__uninstall_files_from_dir)
install-foo2DATA: $(foo2_DATA)
@$(NORMAL_INSTALL)
@list='$(foo2_DATA)'; test -n "$(foo2dir)" || list=; \
if test -n "$$list"; then \
echo " $(MKDIR_P) '$(DESTDIR)$(foo2dir)'"; \
$(MKDIR_P) "$(DESTDIR)$(foo2dir)" || exit 1; \
fi; \
for p in $$list; do \
if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
echo "$$d$$p"; \
done | $(am__base_list) | \
while read files; do \
echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(foo2dir)'"; \
$(INSTALL_DATA) $$files "$(DESTDIR)$(foo2dir)" || exit $$?; \
done
uninstall-foo2DATA:
@$(NORMAL_UNINSTALL)
@list='$(foo2_DATA)'; test -n "$(foo2dir)" || list=; \
files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
dir='$(DESTDIR)$(foo2dir)'; $(am__uninstall_files_from_dir)
ID: $(am__tagged_files)
$(am__define_uniq_tagged_files); mkid -fID $$unique
tags: tags-am
TAGS: tags
tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
set x; \
here=`pwd`; \
$(am__define_uniq_tagged_files); \
shift; \
if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
test -n "$$unique" || unique=$$empty_fix; \
if test $$# -gt 0; then \
$(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
"$$@" $$unique; \
else \
$(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
$$unique; \
fi; \
fi
ctags: ctags-am
CTAGS: ctags
ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
$(am__define_uniq_tagged_files); \
test -z "$(CTAGS_ARGS)$$unique" \
|| $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
$$unique
GTAGS:
here=`$(am__cd) $(top_builddir) && pwd` \
&& $(am__cd) $(top_srcdir) \
&& gtags -i $(GTAGS_ARGS) "$$here"
cscopelist: cscopelist-am
cscopelist-am: $(am__tagged_files)
list='$(am__tagged_files)'; \
case "$(srcdir)" in \
[\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
*) sdir=$(subdir)/$(srcdir) ;; \
esac; \
for i in $$list; do \
if test -f "$$i"; then \
echo "$(subdir)/$$i"; \
else \
echo "$$sdir/$$i"; \
fi; \
done >> $(top_builddir)/cscope.files
distclean-tags:
-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
distdir: $(DISTFILES)
@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
list='$(DISTFILES)'; \
dist_files=`for file in $$list; do echo $$file; done | \
sed -e "s|^$$srcdirstrip/||;t" \
-e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
case $$dist_files in \
*/*) $(MKDIR_P) `echo "$$dist_files" | \
sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
sort -u` ;; \
esac; \
for file in $$dist_files; do \
if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
if test -d $$d/$$file; then \
dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
if test -d "$(distdir)/$$file"; then \
find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
fi; \
if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
fi; \
cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
else \
test -f "$(distdir)/$$file" \
|| cp -p $$d/$$file "$(distdir)/$$file" \
|| exit 1; \
fi; \
done
$(MAKE) $(AM_MAKEFLAGS) \
top_distdir="$(top_distdir)" distdir="$(distdir)" \
dist-hook
check-am: all-am
check: $(BUILT_SOURCES)
$(MAKE) $(AM_MAKEFLAGS) check-am
all-am: Makefile $(PROGRAMS) $(DATA)
installdirs:
for dir in "$(DESTDIR)$(bindir)" "$(DESTDIR)$(foodir)" "$(DESTDIR)$(foo2dir)"; do \
test -z "$$dir" || $(MKDIR_P) "$$dir"; \
done
install: $(BUILT_SOURCES)
$(MAKE) $(AM_MAKEFLAGS) install-am
install-exec: install-exec-am
install-data: install-data-am
uninstall: uninstall-am
install-am: all-am
@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
installcheck: installcheck-am
install-strip:
if test -z '$(STRIP)'; then \
$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
install; \
else \
$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
"INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'" install; \
fi
mostlyclean-generic:
clean-generic:
distclean-generic:
-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
maintainer-clean-generic:
@echo "This command is intended for maintainers to use"
@echo "it deletes files that may require special tools to rebuild."
-test -z "$(BUILT_SOURCES)" || rm -f $(BUILT_SOURCES)
clean: clean-am
clean-am: clean-binPROGRAMS clean-generic clean-libtool clean-local \
mostlyclean-am
distclean: distclean-am
-rm -rf ./$(DEPDIR)
-rm -f Makefile
distclean-am: clean-am distclean-compile distclean-generic \
distclean-tags
dvi: dvi-am
dvi-am:
html: html-am
html-am:
info: info-am
info-am:
install-data-am: install-foo2DATA install-fooDATA
install-dvi: install-dvi-am
install-dvi-am:
install-exec-am: install-binPROGRAMS
install-html: install-html-am
install-html-am:
install-info: install-info-am
install-info-am:
install-man:
install-pdf: install-pdf-am
install-pdf-am:
install-ps: install-ps-am
install-ps-am:
installcheck-am:
maintainer-clean: maintainer-clean-am
-rm -rf ./$(DEPDIR)
-rm -f Makefile
maintainer-clean-am: distclean-am maintainer-clean-generic
mostlyclean: mostlyclean-am
mostlyclean-am: mostlyclean-compile mostlyclean-generic \
mostlyclean-libtool
pdf: pdf-am
pdf-am:
ps: ps-am
ps-am:
uninstall-am: uninstall-binPROGRAMS uninstall-foo2DATA \
uninstall-fooDATA
.MAKE: all check install install-am install-strip
.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \
clean-binPROGRAMS clean-generic clean-libtool clean-local \
cscopelist-am ctags ctags-am dist-hook distclean \
distclean-compile distclean-generic distclean-libtool \
distclean-tags distdir dvi dvi-am html html-am info info-am \
install install-am install-binPROGRAMS install-data \
install-data-am install-dvi install-dvi-am install-exec \
install-exec-am install-foo2DATA install-fooDATA install-html \
install-html-am install-info install-info-am install-man \
install-pdf install-pdf-am install-ps install-ps-am \
install-strip installcheck installcheck-am installdirs \
maintainer-clean maintainer-clean-generic mostlyclean \
mostlyclean-compile mostlyclean-generic mostlyclean-libtool \
pdf pdf-am ps ps-am tags tags-am uninstall uninstall-am \
uninstall-binPROGRAMS uninstall-foo2DATA uninstall-fooDATA
.PHONY: release
# A rule for making the release.
# It just creates a list of files for later removal from files in an exclude list.
release: install
list=( $(EXCLUDE_FILES) ); for p in $${list[@]}; do \
echo "rm -fv $(prefix)/$(subdir)/$$p" >> $(prefix)/EXCLUDE_FILES_rm_cmds \;; \
done; \
list=( $(SUBDIRS) ); for subdir in $${list[@]}; do \
echo "Making release in $$subdir"; \
(cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) release) \
|| exit 1; \
done;
# A rule for making the source tarball. It removes files declared in a
# Makefile.am's EXCLUDE_FILES list (stuff that should not go outside the
# NMR Center).
dist-hook:
list=( $(EXCLUDE_FILES) ); for p in $${list[@]}; do \
find $(distdir) -follow -name $$p -exec rm -Rf {} \;; \
done; \
extra_dist=( $(EXTRA_DIST) );
# A rule to create a header from an xml file in order to
# include the file as a string at compilation time (see ProjectHelp wiki page)
#%.xml.h : %.xml
# xxd -i $< $@
# A rule to create an html file from an xml file (see ProjectHelp wiki page)
%.xml.html : %.xml
$(top_builddir)/utils/xmlToHtml $< $@
clean-local:
rm -f $(BUILT_SOURCES)
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
.NOEXPORT:
* Oct 04, 2017, at 02:01:13 AM, Hoopes, Andrew <AHOOPES@mgh.harvard.edu> wrote:
If you cd into BUILD/freesurfer-6.0.0/lta_convert, does the file lta_convert.help.xml.h exist?
Also, run ‘make' while in the lta_convert directory to see if the error output provides more details. If not, can you send me the contents of BUILD/freesurfer-6.0.0/lta_convert/Makefile?
thanks
Andrew
On Oct 3, 2017, at 1:16 PM, Sol Jerome <solj@utdallas.edu<mailto:solj@utdallas.edu>> wrote:
I think so. I am actually attempting to build an RPM. Here is my spec
file:
Name: freesurfer
Version: 6.0.0
Release: 1%{?dist}
Summary: FreeSurfer Software Suite
License: Proprietary
URL: https://surfer.nmr.mgh.harvard.edu/
Source0: https://github.com/freesurfer/freesurfer#/%{name}-%{version}.tar.gz
Source1: centos6-x86_64-packages.tar.gz
BuildRequires: freetype-devel, gcc-gfortran, libtool, libuuid-devel, libXaw-devel, libXi-devel, mesa-libGLU-devel, netcdf-devel, tcsh
BuildRequires: uuid-c++-devel, libXmu-devel, libpng-devel, lapack-static, blas-static
#Requires:
%description
An open source software suite for processing and analyzing (human)
brain MRI images.
%prep
%setup -q -a1
%build
./setup_configure
%configure --disable-Werror --with-pkgs-dir=$(pwd)/centos6-x86_64-packages --prefix=/opt/%{name}/%{version} --with-mni-dir=$(pwd)/centos6-x86_64-packages/mni/1.5
%install
make install DESTDIR=%{buildroot}
%files
%doc
%changelog
* Thu Sep 28 2017 Sol Jerome <solj@utdallas.edu<mailto:solj@utdallas.edu>> - 6.0.0-1
- Initial freesurfer RPM
Thanks,
Sol
* Oct 03, 2017, at 15:42:12 PM, Hoopes, Andrew <AHOOPES@mgh.harvard.edu<mailto:AHOOPES@mgh.harvard.edu>> wrote:
Hi Sol,
I don't recognize this error, but will look into it. Have you set up the required system libraries and library dependencies described in https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page ?
Andrew
On Oct 2, 2017, at 5:55 PM, Sol Jerome <solj@utdallas.edu<mailto:solj@utdallas.edu><mailto:solj@utdallas.edu>> wrote:
Hi,
I'm trying to build freesurfer on centos7 and I'm pretty sure that this
failure is due to a missing build dependency. Can someone please help me
determine what I'm missing?
Making all in lta_convert
make[2]: Entering directory `/builddir/build/BUILD/freesurfer-6.0.0/lta_convert'
make[2]: Leaving directory `/builddir/build/BUILD/freesurfer-6.0.0/lta_convert'
make[2]: *** No rule to make target `lta_convert.help.xml.h', needed by `all'. Stop.
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/builddir/build/BUILD/freesurfer-6.0.0'
make: *** [all] Error 2
Thanks,
Sol
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer