Index: trunk/psLib/configure.ac
===================================================================
--- trunk/psLib/configure.ac	(revision 9799)
+++ trunk/psLib/configure.ac	(revision 9800)
@@ -115,6 +115,10 @@
 dnl ----------------- MYSQL options --------------------
 
-dnl MYSQL_LDFLAGS="-L${libdir}/mysql"
-dnl MYSQL_CFLAGS="-I${includedir}/mysql"
+dnl save LIBS/CFLAGS/LDFLAGS
+TMP_LIBS=${LIBS}
+TMP_CFLAGS=${CFLAGS}
+TMP_LDFLAGS=${LDFLAGS}
+TMP_CPPFLAGS=${CPPFLAGS}
+
 AC_ARG_ENABLE(mysql,
  [AS_HELP_STRING(--disable-mysql,Disable MySQL functionality)],
@@ -144,6 +148,5 @@
 
 dnl AC_RUN_IFELSE() uses CFLAGS to find mysql_version.h
-  TMP_CFLAGS=${CFLAGS}
-  CFLAGS=${MYSQL_CFLAGS}
+  CFLAGS="${CFLAGS} ${MYSQL_CFLAGS}"
   AC_RUN_IFELSE([AC_LANG_PROGRAM(
 [[#include <stdlib.h>
@@ -157,8 +160,5 @@
     }
 ]])], [], [AC_MSG_ERROR([MySQL 4.1.2 or newer is required.  Obtain it at  http://www.mysql.com or use --with-mysql to specify location.])])
-  CFLAGS=${TMP_CFLAGS}
 else
-  dnl FIXME
-  CFLAGS="${CFLAGS=} -DOMIT_PSDB"
   PSLIB_CFLAGS="${PSLIB_CFLAGS=} -DOMIT_PSDB"
   AC_MSG_RESULT([disable building MySQL functionality])
@@ -167,5 +167,18 @@
 AC_SUBST([MYSQL_CFLAGS])
 
+dnl restore the CFLAGS/LDFLAGS
+LIBS=${TMP_LIBS}
+CFLAGS=${TMP_CFLAGS}
+LDFLAGS=${TMP_LDFLAGS}
+CPPFLAGS=${TMP_CPPFLAGS}
+
 dnl ----------------- CFITSIO options --------------------
+
+dnl save LIBS/CFLAGS/LDFLAGS
+TMP_LIBS=${LIBS}
+TMP_CFLAGS=${CFLAGS}
+TMP_LDFLAGS=${LDFLAGS}
+TMP_CPPFLAGS=${CPPFLAGS}
+
 AC_ARG_WITH(cfitsio,
 [AS_HELP_STRING(--with-cfitsio=DIR,Specify location of CFITSIO.)],
@@ -181,12 +194,7 @@
 PSLIB_LIBS="${PSLIB_LIBS=} $CFITSIO_LDFLAGS -lcfitsio -lm"
 
-dnl Store off CFLAGS/LDFLAGS so that they can be restored after tests
-TMP_CFLAGS=${CPPFLAGS}
-TMP_CFLAGS=${CFLAGS}
-TMP_LDFLAGS=${LDFLAGS}
-
-CPPFLAGS=${PSLIB_CFLAGS}
-CFLAGS=${PSLIB_CFLAGS}
-LDFLAGS=${PSLIB_LIBS}
+CFLAGS=${CFLAGS} ${CFITSIO_CFLAGS}
+LDFLAGS=${LDFLAGS} ${CFITSIO_LDFLAGS}
+
 AC_CHECK_HEADERS([fitsio.h],[],
    [AC_MSG_ERROR([CFITSIO headers not found.  Obtain CFITSIO at  http://heasarc.gsfc.nasa.gov/docs/software/fitsio or use --with-cfitsio to specify location.])]
@@ -202,15 +210,22 @@
    CFITSIO_DISKFILE=0],[-lm]
 )
-LIBS=${TMP_LIBS}
-
-dnl restore the CFLAGS/LDFLAGS
-CPPFLAGS=${TMP_CPPFLAGS}
-CFLAGS=${TMP_CFLAGS}
-LDFLAGS=${TMP_LDFLAGS}
 
 AC_DEFINE_UNQUOTED([CFITSIO_DISKFILE],${CFITSIO_DISKFILE},[Define to 1 if you have fits_open_diskfile in CFITSIO])
 AC_SUBST([CFITSIO_CFLAGS])
 
+dnl restore the LIBS/CFLAGS/LDFLAGS
+LIBS=${TMP_LIBS}
+CFLAGS=${TMP_CFLAGS}
+LDFLAGS=${TMP_LDFLAGS}
+CPPFLAGS=${TMP_CPPFLAGS}
+
 dnl ------------------ FFTW3 options ---------------------
+
+dnl save LIBS/CFLAGS/LDFLAGS
+TMP_LIBS=${LIBS}
+TMP_CFLAGS=${CFLAGS}
+TMP_LDFLAGS=${LDFLAGS}
+TMP_CPPFLAGS=${CPPFLAGS}
+
 AC_ARG_WITH(fftw3,
 [AS_HELP_STRING(--with-fftw3=DIR,Specify location of FFTW version 3.)],
@@ -226,12 +241,8 @@
 PSLIB_LIBS="${PSLIB_LIBS=} $FFTW3_LDFLAGS -lfftw3f"
 
-dnl Store off CPPFLAGS/CFLAGS/LDFLAGS so that they can be restored after tests
-TMP_CPPFLAGS=${CPPFLAGS}
-TMP_CFLAGS=${CFLAGS}
-TMP_LDFLAGS=${LDFLAGS}
-
-CFLAGS="${TMP_CFLAGS} ${PSLIB_CFLAGS}"
-CPPFLAGS="$CFLAGS"
-LDFLAGS="${TMP_LDFLAGS} ${PSLIB_LIBS}"
+CFLAGS="${CFLAGS} ${FFTW3_CFLAGS}"
+CPPFLAGS=${CFLAGS}
+LDFLAGS="${LDFLAGS} ${FFTW3_LIBS}"
+
 AC_CHECK_HEADERS([fftw3.h],[],
   [AC_MSG_ERROR([FFTW version 3 (--enable-float) headers not found.  Obtain it at http://www.fftw.org/ or use --with-fftw3 to specify location.])]
@@ -240,14 +251,21 @@
   [AC_MSG_ERROR([FFTW version 3 (--enable-float) library not found.  Obtain it at http://www.fftw.org/ or use --with-fftw3 to specify location.])],[-lm]
 )
-LIBS=${TMP_LIBS}
-
-dnl restore the CFLAGS/LDFLAGS
-CPPFLAGS=${TMP_CPPFLAGS}
-CFLAGS=${TMP_CFLAGS}
-LDFLAGS=${TMP_LDFLAGS}
 
 AC_SUBST([FFTW3_CFLAGS])
 
+dnl restore the CFLAGS/LDFLAGS
+LIBS=${TMP_LIBS}
+CFLAGS=${TMP_CFLAGS}
+LDFLAGS=${TMP_LDFLAGS}
+CPPFLAGS=${TMP_CPPFLAGS}
+
 dnl -------------------- GSL options ---------------------
+
+dnl save LIBS/CFLAGS/LDFLAGS
+TMP_LIBS=${LIBS}
+TMP_CFLAGS=${CFLAGS}
+TMP_LDFLAGS=${LDFLAGS}
+TMP_CPPFLAGS=${CPPFLAGS}
+
 AC_ARG_WITH(gsl-config,
 [AS_HELP_STRING(--with-gsl-config=FILE,Specify location of gsl-config.)],
@@ -270,5 +288,17 @@
 AC_SUBST([GSL_CFLAGS])
 
+dnl restore the CFLAGS/LDFLAGS
+LIBS=${TMP_LIBS}
+CFLAGS=${TMP_CFLAGS}
+LDFLAGS=${TMP_LDFLAGS}
+CPPFLAGS=${TMP_CPPFLAGS}
+
 dnl ------------------ libjpeg options ---------------------
+
+dnl save LIBS/CFLAGS/LDFLAGS
+TMP_LIBS=${LIBS}
+TMP_CFLAGS=${CFLAGS}
+TMP_LDFLAGS=${LDFLAGS}
+TMP_CPPFLAGS=${CPPFLAGS}
 
 AC_ARG_WITH(jpeg,
@@ -283,12 +313,7 @@
 [JPEG_LDFLAGS="-L$withval"])
 
-dnl Store off CPPFLAGS/CFLAGS/LDFLAGS so that they can be restored after tests
-TMP_CPPFLAGS=${CPPFLAGS}
-TMP_CFLAGS=${CFLAGS}
-TMP_LDFLAGS=${LDFLAGS}
-
-CFLAGS="${TMP_CFLAGS} ${JPEG_CFLAGS}"
-CPPFLAGS="$CFLAGS"
-LDFLAGS="${TMP_LDFLAGS} ${JPEG_LDFLAGS}"
+CFLAGS="${CFLAGS} ${JPEG_CFLAGS}"
+CPPFLAGS=${CFLAGS}
+LDFLAGS="${LDFLAGS} ${JPEG_LDFLAGS}"
 
 AC_CHECK_HEADERS([jpeglib.h],[PSLIB_CFLAGS="$PSLIB_CFLAGS $JPEG_CFLAGS"
@@ -301,8 +326,9 @@
 )
 
-dnl restore the CFLAGS/LDFLAGS in case we decide to make missing libjpeg only a warning
-CPPFLAGS=${TMP_CPPFLAGS}
-CFLAGS=${TMP_CFLAGS}
-LDFLAGS=${TMP_LDFLAGS}
+dnl restore the CFLAGS/LDFLAGS
+LIBS=${TMP_LIBS}
+CFLAGS=${TMP_CFLAGS}
+LDFLAGS=${TMP_LDFLAGS}
+CPPFLAGS=${TMP_CPPFLAGS}
 
 dnl ------------------- XML2 options ---------------------
@@ -340,4 +366,11 @@
 
 dnl ------------------- SWIG options ---------------------
+
+dnl save LIBS/CFLAGS/LDFLAGS
+TMP_LIBS=${LIBS}
+TMP_CFLAGS=${CFLAGS}
+TMP_LDFLAGS=${LDFLAGS}
+TMP_CPPFLAGS=${CPPFLAGS}
+
 AC_ARG_ENABLE(perlmodule,
  [AS_HELP_STRING(--enable-perlmodule,Enables creation of perl module)],
@@ -358,5 +391,18 @@
   SUBDIR="${SUBDIR=} swig"
 
+dnl restore the CFLAGS/LDFLAGS
+LIBS=${TMP_LIBS}
+CFLAGS=${TMP_CFLAGS}
+LDFLAGS=${TMP_LDFLAGS}
+CPPFLAGS=${TMP_CPPFLAGS}
+
 dnl ---------------- PERLPREFIX option -------------------
+
+dnl save LIBS/CFLAGS/LDFLAGS
+TMP_LIBS=${LIBS}
+TMP_CFLAGS=${CFLAGS}
+TMP_LDFLAGS=${LDFLAGS}
+TMP_CPPFLAGS=${CPPFLAGS}
+
   AC_ARG_WITH(perlprefix,
     [AS_HELP_STRING(--with-perlprefix=DIR,Specify prefix of Perl Module's installation. (default=PREFIX))],
@@ -370,6 +416,18 @@
 fi
 
+dnl restore the CFLAGS/LDFLAGS
+LIBS=${TMP_LIBS}
+CFLAGS=${TMP_CFLAGS}
+LDFLAGS=${TMP_LDFLAGS}
+CPPFLAGS=${TMP_CPPFLAGS}
+
 dnl for MacOSX suppport -- check if sqrtf is in mx library.
-TMP_LIBS=${LIBS}
+
+dnl save LIBS/CFLAGS/LDFLAGS
+TMP_LIBS=${LIBS}
+TMP_CFLAGS=${CFLAGS}
+TMP_LDFLAGS=${LDFLAGS}
+TMP_CPPFLAGS=${CPPFLAGS}
+
 AC_CHECK_LIB(mx,sqrtf,
   [PSLIB_LIBS="${PSLIB_LIBS=} -lmx"])
@@ -378,6 +436,18 @@
   [AC_MSG_ERROR([The C99 function, atoll, is required; update your compiler version?])])
 
+dnl restore the CFLAGS/LDFLAGS
+LIBS=${TMP_LIBS}
+CFLAGS=${TMP_CFLAGS}
+LDFLAGS=${TMP_LDFLAGS}
+CPPFLAGS=${TMP_CPPFLAGS}
 
 dnl doxygen doc generation is very, very slow so we're turing it off by default
+
+dnl save LIBS/CFLAGS/LDFLAGS
+TMP_LIBS=${LIBS}
+TMP_CFLAGS=${CFLAGS}
+TMP_LDFLAGS=${LDFLAGS}
+TMP_CPPFLAGS=${CPPFLAGS}
+
 AC_ARG_ENABLE(doxygen,
   [AS_HELP_STRING(--enable-doxygen ,enable manpage generation)],
@@ -391,6 +461,11 @@
 AM_CONDITIONAL([HAVE_DOXYGEN], test -n "$DOXYGEN" -a "x$doxygen" != "xoff")
 
-
-dnl ------- restore CFLAGS / LDFLAGS (tests done) --------
+dnl restore the CFLAGS/LDFLAGS
+LIBS=${TMP_LIBS}
+CFLAGS=${TMP_CFLAGS}
+LDFLAGS=${TMP_LDFLAGS}
+CPPFLAGS=${TMP_CPPFLAGS}
+
+dnl ------- enable -Werror after all of the probes have run ---------
 CFLAGS="${CFLAGS} -Wall -Werror"