The variables in itkConfig.sh don't get subtituted, here is a patch:
diff -ru Itk_-_the__incr_Tk__extension-72c13a0b6ef7e0a9/configure.in itk-new/configure.in
--- Itk_-_the__incr_Tk__extension-72c13a0b6ef7e0a9/configure.in 2011-04-20 14:56:16 +0000
+++ itk-new/configure.in 2011-10-25 08:27:36 +0000
@@ -195,6 +195,8 @@
# library.
#--------------------------------------------------------------------
+itkstub_LIB_FILE=${PKG_STUB_LIB_FILE}
+itk_LIB_FILE=${PKG_LIB_FILE}
AC_SUBST(itkstub_LIB_FILE)
AC_SUBST(itk_LIB_FILE)
@@ -210,6 +212,17 @@
TEA_PROG_WISH
#--------------------------------------------------------------------
+# These are for itkConfig.sh
+#--------------------------------------------------------------------
+
+TEA_EXPORT_CONFIG([itk])
+
+# itk_SRC_DIR must be a fully qualified path
+eval itk_SRC_DIR="$srcdir"
+itk_SRC_DIR=`cd "${itk_SRC_DIR}"; pwd`
+AC_SUBST(itk_SRC_DIR)
+
+#--------------------------------------------------------------------
# Finally, substitute all of the various values into the Makefile.
#--------------------------------------------------------------------
diff -ru Itk_-_the__incr_Tk__extension-72c13a0b6ef7e0a9/itkConfig.sh.in itk-new/itkConfig.sh.in
--- Itk_-_the__incr_Tk__extension-72c13a0b6ef7e0a9/itkConfig.sh.in 2011-04-20 14:56:16 +0000
+++ itk-new/itkConfig.sh.in 2011-10-25 08:25:30 +0000
@@ -12,29 +12,29 @@
# The information in this file is specific to a single platform.
# Itcl's version number.
-ITCL_VERSION='@ITCL_VERSION@'
+ITCL_VERSION='@itcl_VERSION@'
# The name of the Itk library (may be either a .a file or a shared library):
-ITK_LIB_FILE=@ITK_LIB_FILE@
+ITK_LIB_FILE=@itk_LIB_FILE@
# String to pass to linker to pick up the Itk library from its
# build directory.
-ITK_BUILD_LIB_SPEC='@ITK_BUILD_LIB_SPEC@'
+ITK_BUILD_LIB_SPEC='@itk_BUILD_LIB_SPEC@'
# String to pass to linker to pick up the Itk library from its
# installed directory.
-ITK_LIB_SPEC='@ITK_LIB_SPEC@'
+ITK_LIB_SPEC='@itk_LIB_SPEC@'
# The name of the Itk stub library (a .a file):
-ITK_STUB_LIB_FILE=@ITK_STUB_LIB_FILE@
+ITK_STUB_LIB_FILE=@itkstub_LIB_FILE@
# String to pass to linker to pick up the Itk stub library from its
# build directory.
-ITK_BUILD_STUB_LIB_SPEC='@ITK_BUILD_STUB_LIB_SPEC@'
+ITK_BUILD_STUB_LIB_SPEC='@itk_BUILD_STUB_LIB_SPEC@'
# String to pass to linker to pick up the Itk stub library from its
# installed directory.
-ITK_STUB_LIB_SPEC='@ITK_STUB_LIB_SPEC@'
+ITK_STUB_LIB_SPEC='@itk_STUB_LIB_SPEC@'
# Location of the top-level source directories from which [incr Tk]
# was built. This is the directory that contains a README file as well
@@ -42,4 +42,4 @@
# compiled in a different place than the directory containing the source
# files, this points to the location of the sources, not the location
# where [incr Tk] was compiled.
-ITK_SRC_DIR='@ITK_SRC_DIR@'
+ITK_SRC_DIR='@itk_SRC_DIR@'
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