Follow-up Comment #6, bug #29291 (project gnustep):

I mean the configure script runs GNUstep.sh to set up the header/library
info.
If you can reproduce the problem, perhaps you can check the logs to see what
is actually being done in your case.

The relevant part of configure.ac follows.

GNUSTEP_MAKEFILES="$CURRENT_GNUSTEP_MAKEFILES"
GNUSTEP_SH_EXPORT_ALL_VARIABLES=yes
. "$CURRENT_GNUSTEP_MAKEFILES/GNUstep.sh"
unset GNUSTEP_SH_EXPORT_ALL_VARIABLES

# For backwards compatibility, define GNUSTEP_SYSTEM_HEADERS from
# GNUSTEP_SYSTEM_ROOT if not set yet.
if test x"$GNUSTEP_SYSTEM_HEADERS" = x""; then
  GNUSTEP_SYSTEM_HEADERS="$GNUSTEP_SYSTEM_ROOT/Library/Headers"
fi

if test x"$GNUSTEP_SYSTEM_LIBRARIES" = x""; then
  GNUSTEP_SYSTEM_LIBRARIES="$GNUSTEP_SYSTEM_ROOT/Library/Libraries"
fi

#
# Add standard library and header directories for configure to use to locate
# plain C developer headers/libraries which haver been installed in the
# GNUstep hierarchy.
#
CPPFLAGS="$CPPFLAGS -I$GNUSTEP_SYSTEM_HEADERS -I$GNUSTEP_LOCAL_HEADERS"
LDFLAGS="$LDFLAGS -L$GNUSTEP_SYSTEM_LIBRARIES -L$GNUSTEP_LOCAL_LIBRARIES"


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