Merge branch 'master' into tom/speed

Conflicts: .gitignore
author: Thomas White <taw@physics.org> 2012-05-31 13:48:42 +0200
committer: Thomas White <taw@physics.org> 2012-05-31 13:48:42 +0200
commit: 13770d8553f9696c1c4c0c56703717524c028d86 (patch)
tree: 23c9f11f0407207ad24a8f7a4f6c72d52d0e7822
parent: 6ff1bbbd0deeac54175fc862a6e1b53374ae6306 (diff)
parent: b6e0b7972e3dbdace0034d439b992faf3ac8c454 (diff)
47 files changed, 871 insertions, 477 deletions
diff --git a/.gitignore b/.gitignore
index fba1c515..30a8bdee 100644
--- a/.gitignore
+++ b/.gitignore
@@ -46,4 +46,7 @@ build-aux/missing
 build-aux/config.guess
 build-aux/depcomp
 build-aux/ltmain.sh
-/nbproject/private/
-\ No newline at end of file
+/nbproject/private/
+lib/.libs/
+lib/dummy.lo
+lib/libgnu.la
diff --git a/Makefile.am b/Makefile.am
index 6460d8fb..f093d39a 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -28,7 +28,7 @@ endif
 AM_CFLAGS = -Wall @MAIN_CFLAGS@
 AM_CPPFLAGS = -DDATADIR=\""$(datadir)"\" -I$(top_builddir)/lib
 AM_CPPFLAGS += -I$(top_srcdir)/lib
-LDADD = $(top_builddir)/lib/libgnu.a @IGNORE_UNUSED_LIBRARIES_CFLAGS@
+LDADD = $(top_builddir)/lib/libgnu.la @IGNORE_UNUSED_LIBRARIES_CFLAGS@
 LDADD += $(top_builddir)/libcrystfel/libcrystfel.la @MAIN_LIBS@
 
 src_partial_sim_SOURCES = src/partial_sim.c
diff --git a/build-aux/arg-nonnull.h b/build-aux/snippet/arg-nonnull.h
index 6c2f1e82..3a9dd266 100644
--- a/build-aux/arg-nonnull.h
+++ b/build-aux/snippet/arg-nonnull.h
@@ -1,5 +1,5 @@
 /* A C macro for declaring that specific arguments must not be NULL.
-   Copyright (C) 2009-2011 Free Software Foundation, Inc.
+   Copyright (C) 2009-2012 Free Software Foundation, Inc.
 
    This program is free software: you can redistribute it and/or modify it
    under the terms of the GNU General Public License as published
diff --git a/build-aux/c++defs.h b/build-aux/snippet/c++defs.h
index b6821a64..96da94b9 100644
--- a/build-aux/c++defs.h
+++ b/build-aux/snippet/c++defs.h
@@ -1,5 +1,5 @@
 /* C++ compatible function declaration macros.
-   Copyright (C) 2010-2011 Free Software Foundation, Inc.
+   Copyright (C) 2010-2012 Free Software Foundation, Inc.
 
    This program is free software: you can redistribute it and/or modify it
    under the terms of the GNU General Public License as published
diff --git a/build-aux/warn-on-use.h b/build-aux/snippet/warn-on-use.h
index 2cdeec3e..d4cb94f3 100644
--- a/build-aux/warn-on-use.h
+++ b/build-aux/snippet/warn-on-use.h
@@ -1,5 +1,5 @@
 /* A C macro for emitting warnings if a function is used.
-   Copyright (C) 2010-2011 Free Software Foundation, Inc.
+   Copyright (C) 2010-2012 Free Software Foundation, Inc.
 
    This program is free software: you can redistribute it and/or modify it
    under the terms of the GNU General Public License as published
diff --git a/doc/twin-calculator.odt b/doc/twin-calculator.odt
index 16e43495..108aac55 100644
--- a/doc/twin-calculator.odt
+++ b/doc/twin-calculator.odt
diff --git a/doc/twin-calculator.pdf b/doc/twin-calculator.pdf
index 9f4735a7..1559fc96 100644
--- a/doc/twin-calculator.pdf
+++ b/doc/twin-calculator.pdf
diff --git a/lib/Makefile.am b/lib/Makefile.am
index 835dc32b..238cd918 100644
--- a/lib/Makefile.am
+++ b/lib/Makefile.am
@@ -1,15 +1,27 @@
 ## DO NOT EDIT! GENERATED AUTOMATICALLY!
 ## Process this file with automake to produce Makefile.in.
-# Copyright (C) 2002-2011 Free Software Foundation, Inc.
+# Copyright (C) 2002-2012 Free Software Foundation, Inc.
 #
-# This file is free software, distributed under the terms of the GNU
-# General Public License.  As a special exception to the GNU General
-# Public License, this file may be distributed as part of a program
-# that contains a configuration script generated by Autoconf, under
+# This file is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 3 of the License, or
+# (at your option) any later version.
+#
+# This file is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this file.  If not, see <http://www.gnu.org/licenses/>.
+#
+# As a special exception to the GNU General Public License,
+# this file may be distributed as part of a program that
+# contains a configuration script generated by Autoconf, under
 # the same distribution terms as the rest of that program.
 #
 # Generated by gnulib-tool.
-# Reproduce by: gnulib-tool --import --dir=. --lib=libgnu --source-base=lib --m4-base=m4 --doc-base=doc --tests-base=tests --aux-dir=build-aux --no-libtool --macro-prefix=gl lib-ignore strndup
+# Reproduce by: gnulib-tool --import --dir=. --lib=libgnu --source-base=lib --m4-base=m4 --doc-base=doc --tests-base=tests --aux-dir=build-aux --no-conditional-dependencies --libtool --macro-prefix=gl lib-ignore strndup
 
 AUTOMAKE_OPTIONS = 1.5 gnits
 
@@ -29,14 +41,16 @@ MAINTAINERCLEANFILES =
 AM_CPPFLAGS =
 AM_CFLAGS =
 
-noinst_LIBRARIES += libgnu.a
+noinst_LTLIBRARIES += libgnu.la
 
-libgnu_a_SOURCES =
-libgnu_a_LIBADD = $(gl_LIBOBJS)
-libgnu_a_DEPENDENCIES = $(gl_LIBOBJS)
-EXTRA_libgnu_a_SOURCES =
+libgnu_la_SOURCES =
+libgnu_la_LIBADD = $(gl_LTLIBOBJS)
+libgnu_la_DEPENDENCIES = $(gl_LTLIBOBJS)
+EXTRA_libgnu_la_SOURCES =
+libgnu_la_LDFLAGS = $(AM_LDFLAGS)
+libgnu_la_LDFLAGS += -no-undefined
 
-## begin gnulib module arg-nonnull
+## begin gnulib module snippet/arg-nonnull
 
 # The BUILT_SOURCES created by this Makefile snippet are not used via #include
 # statements but through direct file reference. Therefore this snippet must be
@@ -45,22 +59,23 @@ EXTRA_libgnu_a_SOURCES =
 
 BUILT_SOURCES += arg-nonnull.h
 # The arg-nonnull.h that gets inserted into generated .h files is the same as
-# build-aux/arg-nonnull.h, except that it has the copyright header cut off.
-arg-nonnull.h: $(top_srcdir)/build-aux/arg-nonnull.h
+# build-aux/snippet/arg-nonnull.h, except that it has the copyright header cut
+# off.
+arg-nonnull.h: $(top_srcdir)/build-aux/snippet/arg-nonnull.h
 	$(AM_V_GEN)rm -f $@-t $@ && \
 	sed -n -e '/GL_ARG_NONNULL/,$$p' \
-	  < $(top_srcdir)/build-aux/arg-nonnull.h \
+	  < $(top_srcdir)/build-aux/snippet/arg-nonnull.h \
 	  > $@-t && \
 	mv $@-t $@
 MOSTLYCLEANFILES += arg-nonnull.h arg-nonnull.h-t
 
 ARG_NONNULL_H=arg-nonnull.h
 
-EXTRA_DIST += $(top_srcdir)/build-aux/arg-nonnull.h
+EXTRA_DIST += $(top_srcdir)/build-aux/snippet/arg-nonnull.h
 
-## end   gnulib module arg-nonnull
+## end   gnulib module snippet/arg-nonnull
 
-## begin gnulib module c++defs
+## begin gnulib module snippet/c++defs
 
 # The BUILT_SOURCES created by this Makefile snippet are not used via #include
 # statements but through direct file reference. Therefore this snippet must be
@@ -69,20 +84,40 @@ EXTRA_DIST += $(top_srcdir)/build-aux/arg-nonnull.h
 
 BUILT_SOURCES += c++defs.h
 # The c++defs.h that gets inserted into generated .h files is the same as
-# build-aux/c++defs.h, except that it has the copyright header cut off.
-c++defs.h: $(top_srcdir)/build-aux/c++defs.h
+# build-aux/snippet/c++defs.h, except that it has the copyright header cut off.
+c++defs.h: $(top_srcdir)/build-aux/snippet/c++defs.h
 	$(AM_V_GEN)rm -f $@-t $@ && \
 	sed -n -e '/_GL_CXXDEFS/,$$p' \
-	  < $(top_srcdir)/build-aux/c++defs.h \
+	  < $(top_srcdir)/build-aux/snippet/c++defs.h \
 	  > $@-t && \
 	mv $@-t $@
 MOSTLYCLEANFILES += c++defs.h c++defs.h-t
 
 CXXDEFS_H=c++defs.h
 
-EXTRA_DIST += $(top_srcdir)/build-aux/c++defs.h
+EXTRA_DIST += $(top_srcdir)/build-aux/snippet/c++defs.h
+
+## end   gnulib module snippet/c++defs
+
+## begin gnulib module snippet/warn-on-use
+
+BUILT_SOURCES += warn-on-use.h
+# The warn-on-use.h that gets inserted into generated .h files is the same as
+# build-aux/snippet/warn-on-use.h, except that it has the copyright header cut
+# off.
+warn-on-use.h: $(top_srcdir)/build-aux/snippet/warn-on-use.h
+	$(AM_V_GEN)rm -f $@-t $@ && \
+	sed -n -e '/^.ifndef/,$$p' \
+	  < $(top_srcdir)/build-aux/snippet/warn-on-use.h \
+	  > $@-t && \
+	mv $@-t $@
+MOSTLYCLEANFILES += warn-on-use.h warn-on-use.h-t
+
+WARN_ON_USE_H=warn-on-use.h
 
-## end   gnulib module c++defs
+EXTRA_DIST += $(top_srcdir)/build-aux/snippet/warn-on-use.h
+
+## end   gnulib module snippet/warn-on-use
 
 ## begin gnulib module stddef
 
@@ -94,7 +129,8 @@ if GL_GENERATE_STDDEF_H
 stddef.h: stddef.in.h $(top_builddir)/config.status
 	$(AM_V_GEN)rm -f $@-t $@ && \
 	{ echo '/* DO NOT EDIT! GENERATED AUTOMATICALLY! */' && \
-	  sed -e 's|@''INCLUDE_NEXT''@|$(INCLUDE_NEXT)|g' \
+	  sed -e 's|@''GUARD_PREFIX''@|GL|g' \
+	      -e 's|@''INCLUDE_NEXT''@|$(INCLUDE_NEXT)|g' \
 	      -e 's|@''PRAGMA_SYSTEM_HEADER''@|@PRAGMA_SYSTEM_HEADER@|g' \
 	      -e 's|@''PRAGMA_COLUMNS''@|@PRAGMA_COLUMNS@|g' \
 	      -e 's|@''NEXT_STDDEF_H''@|$(NEXT_STDDEF_H)|g' \
@@ -122,47 +158,52 @@ BUILT_SOURCES += string.h
 string.h: string.in.h $(top_builddir)/config.status $(CXXDEFS_H) $(ARG_NONNULL_H) $(WARN_ON_USE_H)
 	$(AM_V_GEN)rm -f $@-t $@ && \
 	{ echo '/* DO NOT EDIT! GENERATED AUTOMATICALLY! */' && \
-	  sed -e 's|@''INCLUDE_NEXT''@|$(INCLUDE_NEXT)|g' \
+	  sed -e 's|@''GUARD_PREFIX''@|GL|g' \
+	      -e 's|@''INCLUDE_NEXT''@|$(INCLUDE_NEXT)|g' \
 	      -e 's|@''PRAGMA_SYSTEM_HEADER''@|@PRAGMA_SYSTEM_HEADER@|g' \
 	      -e 's|@''PRAGMA_COLUMNS''@|@PRAGMA_COLUMNS@|g' \
 	      -e 's|@''NEXT_STRING_H''@|$(NEXT_STRING_H)|g' \
-	      -e 's|@''GNULIB_MBSLEN''@|$(GNULIB_MBSLEN)|g' \
-	      -e 's|@''GNULIB_MBSNLEN''@|$(GNULIB_MBSNLEN)|g' \
-	      -e 's|@''GNULIB_MBSCHR''@|$(GNULIB_MBSCHR)|g' \
-	      -e 's|@''GNULIB_MBSRCHR''@|$(GNULIB_MBSRCHR)|g' \
-	      -e 's|@''GNULIB_MBSSTR''@|$(GNULIB_MBSSTR)|g' \
-	      -e 's|@''GNULIB_MBSCASECMP''@|$(GNULIB_MBSCASECMP)|g' \
-	      -e 's|@''GNULIB_MBSNCASECMP''@|$(GNULIB_MBSNCASECMP)|g' \
-	      -e 's|@''GNULIB_MBSPCASECMP''@|$(GNULIB_MBSPCASECMP)|g' \
-	      -e 's|@''GNULIB_MBSCASESTR''@|$(GNULIB_MBSCASESTR)|g' \
-	      -e 's|@''GNULIB_MBSCSPN''@|$(GNULIB_MBSCSPN)|g' \
-	      -e 's|@''GNULIB_MBSPBRK''@|$(GNULIB_MBSPBRK)|g' \
-	      -e 's|@''GNULIB_MBSSPN''@|$(GNULIB_MBSSPN)|g' \
-	      -e 's|@''GNULIB_MBSSEP''@|$(GNULIB_MBSSEP)|g' \
-	      -e 's|@''GNULIB_MBSTOK_R''@|$(GNULIB_MBSTOK_R)|g' \
-	      -e 's|@''GNULIB_MEMCHR''@|$(GNULIB_MEMCHR)|g' \
-	      -e 's|@''GNULIB_MEMMEM''@|$(GNULIB_MEMMEM)|g' \
-	      -e 's|@''GNULIB_MEMPCPY''@|$(GNULIB_MEMPCPY)|g' \
-	      -e 's|@''GNULIB_MEMRCHR''@|$(GNULIB_MEMRCHR)|g' \
-	      -e 's|@''GNULIB_RAWMEMCHR''@|$(GNULIB_RAWMEMCHR)|g' \
-	      -e 's|@''GNULIB_STPCPY''@|$(GNULIB_STPCPY)|g' \
-	      -e 's|@''GNULIB_STPNCPY''@|$(GNULIB_STPNCPY)|g' \
-	      -e 's|@''GNULIB_STRCHRNUL''@|$(GNULIB_STRCHRNUL)|g' \
-	      -e 's|@''GNULIB_STRDUP''@|$(GNULIB_STRDUP)|g' \
-	      -e 's|@''GNULIB_STRNCAT''@|$(GNULIB_STRNCAT)|g' \
-	      -e 's|@''GNULIB_STRNDUP''@|$(GNULIB_STRNDUP)|g' \
-	      -e 's|@''GNULIB_STRNLEN''@|$(GNULIB_STRNLEN)|g' \
-	      -e 's|@''GNULIB_STRPBRK''@|$(GNULIB_STRPBRK)|g' \
-	      -e 's|@''GNULIB_STRSEP''@|$(GNULIB_STRSEP)|g' \
-	      -e 's|@''GNULIB_STRSTR''@|$(GNULIB_STRSTR)|g' \
-	      -e 's|@''GNULIB_STRCASESTR''@|$(GNULIB_STRCASESTR)|g' \
-	      -e 's|@''GNULIB_STRTOK_R''@|$(GNULIB_STRTOK_R)|g' \
-	      -e 's|@''GNULIB_STRERROR''@|$(GNULIB_STRERROR)|g' \
-	      -e 's|@''GNULIB_STRERROR_R''@|$(GNULIB_STRERROR_R)|g' \
-	      -e 's|@''GNULIB_STRSIGNAL''@|$(GNULIB_STRSIGNAL)|g' \
-	      -e 's|@''GNULIB_STRVERSCMP''@|$(GNULIB_STRVERSCMP)|g' \
+	      -e 's/@''GNULIB_FFSL''@/$(GNULIB_FFSL)/g' \
+	      -e 's/@''GNULIB_FFSLL''@/$(GNULIB_FFSLL)/g' \
+	      -e 's/@''GNULIB_MBSLEN''@/$(GNULIB_MBSLEN)/g' \
+	      -e 's/@''GNULIB_MBSNLEN''@/$(GNULIB_MBSNLEN)/g' \
+	      -e 's/@''GNULIB_MBSCHR''@/$(GNULIB_MBSCHR)/g' \
+	      -e 's/@''GNULIB_MBSRCHR''@/$(GNULIB_MBSRCHR)/g' \
+	      -e 's/@''GNULIB_MBSSTR''@/$(GNULIB_MBSSTR)/g' \
+	      -e 's/@''GNULIB_MBSCASECMP''@/$(GNULIB_MBSCASECMP)/g' \
+	      -e 's/@''GNULIB_MBSNCASECMP''@/$(GNULIB_MBSNCASECMP)/g' \
+	      -e 's/@''GNULIB_MBSPCASECMP''@/$(GNULIB_MBSPCASECMP)/g' \
+	      -e 's/@''GNULIB_MBSCASESTR''@/$(GNULIB_MBSCASESTR)/g' \
+	      -e 's/@''GNULIB_MBSCSPN''@/$(GNULIB_MBSCSPN)/g' \
+	      -e 's/@''GNULIB_MBSPBRK''@/$(GNULIB_MBSPBRK)/g' \
+	      -e 's/@''GNULIB_MBSSPN''@/$(GNULIB_MBSSPN)/g' \
+	      -e 's/@''GNULIB_MBSSEP''@/$(GNULIB_MBSSEP)/g' \
+	      -e 's/@''GNULIB_MBSTOK_R''@/$(GNULIB_MBSTOK_R)/g' \
+	      -e 's/@''GNULIB_MEMCHR''@/$(GNULIB_MEMCHR)/g' \
+	      -e 's/@''GNULIB_MEMMEM''@/$(GNULIB_MEMMEM)/g' \
+	      -e 's/@''GNULIB_MEMPCPY''@/$(GNULIB_MEMPCPY)/g' \
+	      -e 's/@''GNULIB_MEMRCHR''@/$(GNULIB_MEMRCHR)/g' \
+	      -e 's/@''GNULIB_RAWMEMCHR''@/$(GNULIB_RAWMEMCHR)/g' \
+	      -e 's/@''GNULIB_STPCPY''@/$(GNULIB_STPCPY)/g' \
+	      -e 's/@''GNULIB_STPNCPY''@/$(GNULIB_STPNCPY)/g' \
+	      -e 's/@''GNULIB_STRCHRNUL''@/$(GNULIB_STRCHRNUL)/g' \
+	      -e 's/@''GNULIB_STRDUP''@/$(GNULIB_STRDUP)/g' \
+	      -e 's/@''GNULIB_STRNCAT''@/$(GNULIB_STRNCAT)/g' \
+	      -e 's/@''GNULIB_STRNDUP''@/$(GNULIB_STRNDUP)/g' \
+	      -e 's/@''GNULIB_STRNLEN''@/$(GNULIB_STRNLEN)/g' \
+	      -e 's/@''GNULIB_STRPBRK''@/$(GNULIB_STRPBRK)/g' \
+	      -e 's/@''GNULIB_STRSEP''@/$(GNULIB_STRSEP)/g' \
+	      -e 's/@''GNULIB_STRSTR''@/$(GNULIB_STRSTR)/g' \
+	      -e 's/@''GNULIB_STRCASESTR''@/$(GNULIB_STRCASESTR)/g' \
+	      -e 's/@''GNULIB_STRTOK_R''@/$(GNULIB_STRTOK_R)/g' \
+	      -e 's/@''GNULIB_STRERROR''@/$(GNULIB_STRERROR)/g' \
+	      -e 's/@''GNULIB_STRERROR_R''@/$(GNULIB_STRERROR_R)/g' \
+	      -e 's/@''GNULIB_STRSIGNAL''@/$(GNULIB_STRSIGNAL)/g' \
+	      -e 's/@''GNULIB_STRVERSCMP''@/$(GNULIB_STRVERSCMP)/g' \
 	      < $(srcdir)/string.in.h | \
-	  sed -e 's|@''HAVE_MBSLEN''@|$(HAVE_MBSLEN)|g' \
+	  sed -e 's|@''HAVE_FFSL''@|$(HAVE_FFSL)|g' \
+	      -e 's|@''HAVE_FFSLL''@|$(HAVE_FFSLL)|g' \
+	      -e 's|@''HAVE_MBSLEN''@|$(HAVE_MBSLEN)|g' \
 	      -e 's|@''HAVE_MEMCHR''@|$(HAVE_MEMCHR)|g' \
 	      -e 's|@''HAVE_DECL_MEMMEM''@|$(HAVE_DECL_MEMMEM)|g' \
 	      -e 's|@''HAVE_MEMPCPY''@|$(HAVE_MEMPCPY)|g' \
@@ -213,7 +254,7 @@ EXTRA_DIST += string.in.h
 
 EXTRA_DIST += strndup.c
 
-EXTRA_libgnu_a_SOURCES += strndup.c
+EXTRA_libgnu_la_SOURCES += strndup.c
 
 ## end   gnulib module strndup
 
@@ -222,32 +263,13 @@ EXTRA_libgnu_a_SOURCES += strndup.c
 
 EXTRA_DIST += strnlen.c
 
-EXTRA_libgnu_a_SOURCES += strnlen.c
+EXTRA_libgnu_la_SOURCES += strnlen.c
 
 ## end   gnulib module strnlen
 
-## begin gnulib module warn-on-use
-
-BUILT_SOURCES += warn-on-use.h
-# The warn-on-use.h that gets inserted into generated .h files is the same as
-# build-aux/warn-on-use.h, except that it has the copyright header cut off.
-warn-on-use.h: $(top_srcdir)/build-aux/warn-on-use.h
-	$(AM_V_GEN)rm -f $@-t $@ && \
-	sed -n -e '/^.ifndef/,$$p' \
-	  < $(top_srcdir)/build-aux/warn-on-use.h \
-	  > $@-t && \
-	mv $@-t $@
-MOSTLYCLEANFILES += warn-on-use.h warn-on-use.h-t
-
-WARN_ON_USE_H=warn-on-use.h
-
-EXTRA_DIST += $(top_srcdir)/build-aux/warn-on-use.h
-
-## end   gnulib module warn-on-use
-
 ## begin gnulib module dummy
 
-libgnu_a_SOURCES += dummy.c
+libgnu_la_SOURCES += dummy.c
 
 ## end   gnulib module dummy
 
diff --git a/lib/dummy.c b/lib/dummy.c
index c958ea05..6e4b76e0 100644
--- a/lib/dummy.c
+++ b/lib/dummy.c
@@ -1,5 +1,5 @@
 /* A dummy file, to prevent empty libraries from breaking builds.
-   Copyright (C) 2004, 2007, 2009-2011 Free Software Foundation, Inc.
+   Copyright (C) 2004, 2007, 2009-2012 Free Software Foundation, Inc.
 
    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
diff --git a/lib/stddef.in.h b/lib/stddef.in.h
index 62a91a7a..17fcaea2 100644
--- a/lib/stddef.in.h
+++ b/lib/stddef.in.h
@@ -1,6 +1,6 @@
 /* A substitute for POSIX 2008 <stddef.h>, for platforms that have issues.
 
-   Copyright (C) 2009-2011 Free Software Foundation, Inc.
+   Copyright (C) 2009-2012 Free Software Foundation, Inc.
 
    This program is free software; you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
@@ -13,8 +13,7 @@
    GNU General Public License for more details.
 
    You should have received a copy of the GNU General Public License
-   along with this program; if not, write to the Free Software Foundation,
-   Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.  */
+   along with this program; if not, see <http://www.gnu.org/licenses/>.  */
 
 /* Written by Eric Blake.  */
 
@@ -38,9 +37,9 @@
    remember if special invocation has ever been used to obtain wint_t,
    in which case we need to clean up NULL yet again.  */
 
-# if !(defined _GL_STDDEF_H && defined _GL_STDDEF_WINT_T)
+# if !(defined _@GUARD_PREFIX@_STDDEF_H && defined _GL_STDDEF_WINT_T)
 #  ifdef __need_wint_t
-#   undef _GL_STDDEF_H
+#   undef _@GUARD_PREFIX@_STDDEF_H
 #   define _GL_STDDEF_WINT_T
 #  endif
 #  @INCLUDE_NEXT@ @NEXT_STDDEF_H@
@@ -49,14 +48,14 @@
 #else
 /* Normal invocation convention.  */
 
-# ifndef _GL_STDDEF_H
+# ifndef _@GUARD_PREFIX@_STDDEF_H
 
 /* The include_next requires a split double-inclusion guard.  */
 
 #  @INCLUDE_NEXT@ @NEXT_STDDEF_H@
 
-#  ifndef _GL_STDDEF_H
-#   define _GL_STDDEF_H
+#  ifndef _@GUARD_PREFIX@_STDDEF_H
+#   define _@GUARD_PREFIX@_STDDEF_H
 
 /* On NetBSD 5.0, the definition of NULL lacks proper parentheses.  */
 #if @REPLACE_NULL@
@@ -82,6 +81,6 @@
 # define wchar_t int
 #endif
 
-#  endif /* _GL_STDDEF_H */
-# endif /* _GL_STDDEF_H */
+#  endif /* _@GUARD_PREFIX@_STDDEF_H */
+# endif /* _@GUARD_PREFIX@_STDDEF_H */
 #endif /* __need_XXX */
diff --git a/lib/string.in.h b/lib/string.in.h
index 76d26ed3..f8d7520e 100644
--- a/lib/string.in.h
+++ b/lib/string.in.h
@@ -1,6 +1,6 @@
 /* A GNU-like <string.h>.
 
-   Copyright (C) 1995-1996, 2001-2011 Free Software Foundation, Inc.
+   Copyright (C) 1995-1996, 2001-2012 Free Software Foundation, Inc.
 
    This program is free software; you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
@@ -13,10 +13,9 @@
    GNU General Public License for more details.
 
    You should have received a copy of the GNU General Public License
-   along with this program; if not, write to the Free Software Foundation,
-   Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.  */
+   along with this program; if not, see <http://www.gnu.org/licenses/>.  */
 
-#ifndef _GL_STRING_H
+#ifndef _@GUARD_PREFIX@_STRING_H
 
 #if __GNUC__ >= 3
 @PRAGMA_SYSTEM_HEADER@
@@ -26,8 +25,8 @@
 /* The include_next requires a split double-inclusion guard.  */
 #@INCLUDE_NEXT@ @NEXT_STRING_H@
 
-#ifndef _GL_STRING_H
-#define _GL_STRING_H
+#ifndef _@GUARD_PREFIX@_STRING_H
+#define _@GUARD_PREFIX@_STRING_H
 
 /* NetBSD 5.0 mis-defines NULL.  */
 #include <stddef.h>
@@ -59,6 +58,36 @@
 /* The definition of _GL_WARN_ON_USE is copied here.  */
 
 
+/* Find the index of the least-significant set bit.  */
+#if @GNULIB_FFSL@
+# if !@HAVE_FFSL@
+_GL_FUNCDECL_SYS (ffsl, int, (long int i));
+# endif
+_GL_CXXALIAS_SYS (ffsl, int, (long int i));
+_GL_CXXALIASWARN (ffsl);
+#elif defined GNULIB_POSIXCHECK
+# undef ffsl
+# if HAVE_RAW_DECL_FFSL
+_GL_WARN_ON_USE (ffsl, "ffsl is not portable - use the ffsl module");
+# endif
+#endif
+
+
+/* Find the index of the least-significant set bit.  */
+#if @GNULIB_FFSLL@
+# if !@HAVE_FFSLL@
+_GL_FUNCDECL_SYS (ffsll, int, (long long int i));
+# endif
+_GL_CXXALIAS_SYS (ffsll, int, (long long int i));
+_GL_CXXALIASWARN (ffsll);
+#elif defined GNULIB_POSIXCHECK
+# undef ffsll
+# if HAVE_RAW_DECL_FFSLL
+_GL_WARN_ON_USE (ffsll, "ffsll is not portable - use the ffsll module");
+# endif
+#endif
+
+
 /* Return the first instance of C within N bytes of S, or NULL.  */
 #if @GNULIB_MEMCHR@
 # if @REPLACE_MEMCHR@
@@ -695,10 +724,14 @@ _GL_WARN_ON_USE (strtok_r, "strtok_r is unportable - "
 #  if !(defined __cplusplus && defined GNULIB_NAMESPACE)
 #   define mbslen rpl_mbslen
 #  endif
-_GL_FUNCDECL_RPL (mbslen, size_t, (const char *string) _GL_ARG_NONNULL ((1)));
+_GL_FUNCDECL_RPL (mbslen, size_t, (const char *string)
+                                  _GL_ATTRIBUTE_PURE
+                                  _GL_ARG_NONNULL ((1)));
 _GL_CXXALIAS_RPL (mbslen, size_t, (const char *string));
 # else
-_GL_FUNCDECL_SYS (mbslen, size_t, (const char *string) _GL_ARG_NONNULL ((1)));
+_GL_FUNCDECL_SYS (mbslen, size_t, (const char *string)
+                                  _GL_ATTRIBUTE_PURE
+                                  _GL_ARG_NONNULL ((1)));
 _GL_CXXALIAS_SYS (mbslen, size_t, (const char *string));
 # endif
 _GL_CXXALIASWARN (mbslen);
@@ -708,6 +741,7 @@ _GL_CXXALIASWARN (mbslen);
 /* Return the number of multibyte characters in the character string starting
    at STRING and ending at STRING + LEN.  */
 _GL_EXTERN_C size_t mbsnlen (const char *string, size_t len)
+     _GL_ATTRIBUTE_PURE
      _GL_ARG_NONNULL ((1));
 #endif
 
@@ -721,10 +755,12 @@ _GL_EXTERN_C size_t mbsnlen (const char *string, size_t len)
 #   define mbschr rpl_mbschr /* avoid collision with HP-UX function */
 #  endif
 _GL_FUNCDECL_RPL (mbschr, char *, (const char *string, int c)
+                                  _GL_ATTRIBUTE_PURE
                                   _GL_ARG_NONNULL ((1)));
 _GL_CXXALIAS_RPL (mbschr, char *, (const char *string, int c));
 # else
 _GL_FUNCDECL_SYS (mbschr, char *, (const char *string, int c)
+                                  _GL_ATTRIBUTE_PURE
                                   _GL_ARG_NONNULL ((1)));
 _GL_CXXALIAS_SYS (mbschr, char *, (const char *string, int c));
 # endif
@@ -736,15 +772,17 @@ _GL_CXXALIASWARN (mbschr);
    and return a pointer to it.  Return NULL if C is not found in STRING.
    Unlike strrchr(), this function works correctly in multibyte locales with
    encodings such as GB18030.  */
-# if defined __hpux
+# if defined __hpux || defined __INTERIX
 #  if !(defined __cplusplus && defined GNULIB_NAMESPACE)
-#   define mbsrchr rpl_mbsrchr /* avoid collision with HP-UX function */
+#   define mbsrchr rpl_mbsrchr /* avoid collision with system function */
 #  endif
 _GL_FUNCDECL_RPL (mbsrchr, char *, (const char *string, int c)
+                                   _GL_ATTRIBUTE_PURE
                                    _GL_ARG_NONNULL ((1)));
 _GL_CXXALIAS_RPL (mbsrchr, char *, (const char *string, int c));
 # else
 _GL_FUNCDECL_SYS (mbsrchr, char *, (const char *string, int c)
+                                   _GL_ATTRIBUTE_PURE
                                    _GL_ARG_NONNULL ((1)));
 _GL_CXXALIAS_SYS (mbsrchr, char *, (const char *string, int c));
 # endif
@@ -757,6 +795,7 @@ _GL_CXXALIASWARN (mbsrchr);
    Unlike strstr(), this function works correctly in multibyte locales with
    encodings different from UTF-8.  */
 _GL_EXTERN_C char * mbsstr (const char *haystack, const char *needle)
+     _GL_ATTRIBUTE_PURE
      _GL_ARG_NONNULL ((1, 2));
 #endif
 
@@ -768,6 +807,7 @@ _GL_EXTERN_C char * mbsstr (const char *haystack, const char *needle)
    different lengths!
    Unlike strcasecmp(), this function works correctly in multibyte locales.  */
 _GL_EXTERN_C int mbscasecmp (const char *s1, const char *s2)
+     _GL_ATTRIBUTE_PURE
      _GL_ARG_NONNULL ((1, 2));
 #endif
 
@@ -782,6 +822,7 @@ _GL_EXTERN_C int mbscasecmp (const char *s1, const char *s2)
    Unlike strncasecmp(), this function works correctly in multibyte locales.
    But beware that N is not a byte count but a character count!  */
 _GL_EXTERN_C int mbsncasecmp (const char *s1, const char *s2, size_t n)
+     _GL_ATTRIBUTE_PURE
      _GL_ARG_NONNULL ((1, 2));
 #endif
 
@@ -795,6 +836,7 @@ _GL_EXTERN_C int mbsncasecmp (const char *s1, const char *s2, size_t n)
    Unlike strncasecmp(), this function works correctly in multibyte
    locales.  */
 _GL_EXTERN_C char * mbspcasecmp (const char *string, const char *prefix)
+     _GL_ATTRIBUTE_PURE
      _GL_ARG_NONNULL ((1, 2));
 #endif
 
@@ -805,6 +847,7 @@ _GL_EXTERN_C char * mbspcasecmp (const char *string, const char *prefix)
    strlen (haystack) < strlen (needle) !
    Unlike strcasestr(), this function works correctly in multibyte locales.  */
 _GL_EXTERN_C char * mbscasestr (const char *haystack, const char *needle)
+     _GL_ATTRIBUTE_PURE
      _GL_ARG_NONNULL ((1, 2));
 #endif
 
@@ -815,6 +858,7 @@ _GL_EXTERN_C char * mbscasestr (const char *haystack, const char *needle)
    if none exists.
    Unlike strcspn(), this function works correctly in multibyte locales.  */
 _GL_EXTERN_C size_t mbscspn (const char *string, const char *accept)
+     _GL_ATTRIBUTE_PURE
      _GL_ARG_NONNULL ((1, 2));
 #endif
 
@@ -828,10 +872,12 @@ _GL_EXTERN_C size_t mbscspn (const char *string, const char *accept)
 #   define mbspbrk rpl_mbspbrk /* avoid collision with HP-UX function */
 #  endif
 _GL_FUNCDECL_RPL (mbspbrk, char *, (const char *string, const char *accept)
+                                   _GL_ATTRIBUTE_PURE
                                    _GL_ARG_NONNULL ((1, 2)));
 _GL_CXXALIAS_RPL (mbspbrk, char *, (const char *string, const char *accept));
 # else
 _GL_FUNCDECL_SYS (mbspbrk, char *, (const char *string, const char *accept)
+                                   _GL_ATTRIBUTE_PURE
                                    _GL_ARG_NONNULL ((1, 2)));
 _GL_CXXALIAS_SYS (mbspbrk, char *, (const char *string, const char *accept));
 # endif
@@ -845,6 +891,7 @@ _GL_CXXALIASWARN (mbspbrk);
    if none exists.
    Unlike strspn(), this function works correctly in multibyte locales.  */
 _GL_EXTERN_C size_t mbsspn (const char *string, const char *reject)
+     _GL_ATTRIBUTE_PURE
      _GL_ARG_NONNULL ((1, 2));
 #endif
 
@@ -964,6 +1011,7 @@ _GL_WARN_ON_USE (strsignal, "strsignal is unportable - "
 #if @GNULIB_STRVERSCMP@
 # if !@HAVE_STRVERSCMP@
 _GL_FUNCDECL_SYS (strverscmp, int, (const char *, const char *)
+                                   _GL_ATTRIBUTE_PURE
                                    _GL_ARG_NONNULL ((1, 2)));
 # endif
 _GL_CXXALIAS_SYS (strverscmp, int, (const char *, const char *));
@@ -977,5 +1025,5 @@ _GL_WARN_ON_USE (strverscmp, "strverscmp is unportable - "
 #endif
 
 
-#endif /* _GL_STRING_H */
-#endif /* _GL_STRING_H */
+#endif /* _@GUARD_PREFIX@_STRING_H */
+#endif /* _@GUARD_PREFIX@_STRING_H */
diff --git a/lib/strndup.c b/lib/strndup.c
index 4a3bece4..40538711 100644
--- a/lib/strndup.c
+++ b/lib/strndup.c
@@ -1,6 +1,6 @@
 /* A replacement function, for systems that lack strndup.
 
-   Copyright (C) 1996-1998, 2001-2003, 2005-2007, 2009-2011 Free Software
+   Copyright (C) 1996-1998, 2001-2003, 2005-2007, 2009-2012 Free Software
    Foundation, Inc.
 
    This program is free software; you can redistribute it and/or modify it
@@ -14,8 +14,7 @@
    GNU General Public License for more details.
 
    You should have received a copy of the GNU General Public License
-   along with this program; if not, write to the Free Software Foundation,
-   Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.  */
+   along with this program; if not, see <http://www.gnu.org/licenses/>.  */
 
 #include <config.h>
 
diff --git a/lib/strnlen.c b/lib/strnlen.c
index 3cefa978..d36180dc 100644
--- a/lib/strnlen.c
+++ b/lib/strnlen.c
@@ -1,5 +1,5 @@
 /* Find the length of STRING, but scan at most MAXLEN characters.
-   Copyright (C) 2005-2007, 2009-2011 Free Software Foundation, Inc.
+   Copyright (C) 2005-2007, 2009-2012 Free Software Foundation, Inc.
    Written by Simon Josefsson.
 
    This program is free software; you can redistribute it and/or modify
@@ -13,8 +13,7 @@
    GNU General Public License for more details.
 
    You should have received a copy of the GNU General Public License
-   along with this program; if not, write to the Free Software Foundation,
-   Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.  */
+   along with this program; if not, see <http://www.gnu.org/licenses/>.  */
 
 #include <config.h>
 
diff --git a/libcrystfel/Makefile.am b/libcrystfel/Makefile.am
index d13bbc93..bd84ceff 100644
--- a/libcrystfel/Makefile.am
+++ b/libcrystfel/Makefile.am
@@ -1,5 +1,5 @@
 lib_LTLIBRARIES = libcrystfel.la
-libcrystfel_la_LIBADD = @LIBCRYSTFEL_LIBS@
+libcrystfel_la_LIBADD = ../lib/libgnu.la @LIBCRYSTFEL_LIBS@
 libcrystfel_la_LDFLAGS = -version-info=0:0:0
 
 libcrystfel_la_SOURCES = src/reflist.c src/utils.c src/cell.c src/detector.c \
diff --git a/libcrystfel/src/cell.c b/libcrystfel/src/cell.c
index 2e87b770..b6ea010b 100644
--- a/libcrystfel/src/cell.c
+++ b/libcrystfel/src/cell.c
@@ -424,7 +424,7 @@ int cell_get_parameters(UnitCell *cell, double *a, double *b, double *c,
 
 	switch ( cell->rep ) {
 
-	case CELL_REP_CRYST:
+		case CELL_REP_CRYST:
 		/* Direct response */
 		*a = cell->a;
 		*b = cell->b;
@@ -434,7 +434,7 @@ int cell_get_parameters(UnitCell *cell, double *a, double *b, double *c,
 		*gamma = cell->gamma;
 		return 0;
 
-	case CELL_REP_CART:
+		case CELL_REP_CART:
 		/* Convert cartesian -> crystallographic */
 		*a = modulus(cell->ax, cell->ay, cell->az);
 		*b = modulus(cell->bx, cell->by, cell->bz);
@@ -448,7 +448,7 @@ int cell_get_parameters(UnitCell *cell, double *a, double *b, double *c,
 		                       cell->bx, cell->by, cell->bz);
 		return 0;
 
-	case CELL_REP_RECIP:
+		case CELL_REP_RECIP:
 		/* Convert reciprocal -> crystallographic.
                  * Start by converting reciprocal -> cartesian */
 		cell_invert(cell->axs, cell->ays, cell->azs,
@@ -480,21 +480,21 @@ int cell_get_cartesian(UnitCell *cell,
 
 	switch ( cell->rep ) {
 
-	case CELL_REP_CRYST:
+		case CELL_REP_CRYST:
 		/* Convert crystallographic -> cartesian. */
 		return cell_crystallographic_to_cartesian(cell,
 		                                          ax, ay, az,
 		                                          bx, by, bz,
 		                                          cx, cy, cz);
 
-	case CELL_REP_CART:
+		case CELL_REP_CART:
 		/* Direct response */
 		*ax = cell->ax;  *ay = cell->ay;  *az = cell->az;
 		*bx = cell->bx;  *by = cell->by;  *bz = cell->bz;
 		*cx = cell->cx;  *cy = cell->cy;  *cz = cell->cz;
 		return 0;
 
-	case CELL_REP_RECIP:
+		case CELL_REP_RECIP:
 		/* Convert reciprocal -> cartesian */
 		return cell_invert(cell->axs, cell->ays, cell->azs,
 		                   cell->bxs, cell->bys, cell->bzs,
@@ -518,7 +518,7 @@ int cell_get_reciprocal(UnitCell *cell,
 
 	switch ( cell->rep ) {
 
-	case CELL_REP_CRYST:
+		case CELL_REP_CRYST:
 		/* Convert crystallographic -> reciprocal */
 		r = cell_crystallographic_to_cartesian(cell,
 		                                       &ax, &ay, &az,
@@ -528,7 +528,7 @@ int cell_get_reciprocal(UnitCell *cell,
 		return cell_invert(ax, ay, az,bx, by, bz, cx, cy, cz,
 		                   asx, asy, asz, bsx, bsy, bsz, csx, csy, csz);
 
-	case CELL_REP_CART:
+		case CELL_REP_CART:
 		/* Convert cartesian -> reciprocal */
 		cell_invert(cell->ax, cell->ay, cell->az,
 		            cell->bx, cell->by, cell->bz,
@@ -536,7 +536,7 @@ int cell_get_reciprocal(UnitCell *cell,
 		            asx, asy, asz, bsx, bsy, bsz, csx, csy, csz);
 		return 0;
 
-	case CELL_REP_RECIP:
+		case CELL_REP_RECIP:
 		/* Direct response */
 		*asx = cell->axs;  *asy = cell->ays;  *asz = cell->azs;
 		*bsx = cell->bxs;  *bsy = cell->bys;  *bsz = cell->bzs;
@@ -569,12 +569,16 @@ const char *cell_get_spacegroup(UnitCell *cell)
 static const char *cell_rep(UnitCell *cell)
 {
 	switch ( cell->rep ) {
-	case CELL_REP_CRYST:
+
+		case CELL_REP_CRYST:
 		return "crystallographic, direct space";
-	case CELL_REP_CART:
+
+		case CELL_REP_CART:
 		return "cartesian, direct space";
-	case CELL_REP_RECIP:
+
+		case CELL_REP_RECIP:
 		return "cartesian, reciprocal space";
+
 	}
 
 	return "unknown";
diff --git a/libcrystfel/src/dirax.c b/libcrystfel/src/dirax.c
index 20f48bd3..43de6c6e 100644
--- a/libcrystfel/src/dirax.c
+++ b/libcrystfel/src/dirax.c
@@ -226,37 +226,37 @@ static void dirax_send_next(struct image *image, struct dirax_data *dirax)
 
 	switch ( dirax->step ) {
 
-	case 1 :
+		case 1 :
 		dirax_sendline("\\echo off\n", dirax);
 		break;
 
-	case 2 :
+		case 2 :
 		snprintf(tmp, 31, "read xfel-%i.drx\n", image->id);
 		dirax_sendline(tmp, dirax);
 		break;
 
-	case 3 :
+		case 3 :
 		dirax_sendline("dmax 1000\n", dirax);
 		break;
 
-	case 4 :
+		case 4 :
 		dirax_sendline("indexfit 2\n", dirax);
 		break;
 
-	case 5 :
+		case 5 :
 		dirax_sendline("levelfit 1000\n", dirax);
 		break;
 
-	case 6 :
+		case 6 :
 		dirax_sendline("go\n", dirax);
 		dirax->finished_ok = 1;
 		break;
 
-	case 7 :
+		case 7 :
 		dirax_sendline("acl\n", dirax);
 		break;
 
-	case 8 :
+		case 8 :
 		if ( dirax->best_acl_nh == 0 ) {
 			/* At this point, DirAx is presenting its ACL prompt
 			 * and waiting for a single number.  Use an extra
@@ -270,11 +270,11 @@ static void dirax_send_next(struct image *image, struct dirax_data *dirax)
 		dirax_sendline(tmp, dirax);
 		break;
 
-	case 9 :
+		case 9 :
 		dirax_sendline("cell\n", dirax);
 		break;
 
-	case 10 :
+		case 10 :
 		if ( dirax->n_acls_tried == MAX_DIRAX_CELL_CANDIDATES ) {
 			dirax_sendline("exit\n", dirax);
 		} else {
@@ -285,7 +285,7 @@ static void dirax_send_next(struct image *image, struct dirax_data *dirax)
 		}
 		break;
 
-	default:
+		default:
 		dirax_sendline("exit\n", dirax);
 		return;
 
diff --git a/libcrystfel/src/hdf5-file.c b/libcrystfel/src/hdf5-file.c
index 88d11bff..af06c1b4 100644
--- a/libcrystfel/src/hdf5-file.c
+++ b/libcrystfel/src/hdf5-file.c
@@ -719,6 +719,10 @@ char *hdfile_get_string_value(struct hdfile *f, const char *name)
 	hsize_t max_size;
 	hid_t type;
 	hid_t class;
+	herr_t r;
+	int buf_i;
+	double buf_f;
+	char *tmp;
 
 	dh = H5Dopen2(f->fh, name, H5P_DEFAULT);
 	if ( dh < 0 ) return NULL;
@@ -761,40 +765,33 @@ char *hdfile_get_string_value(struct hdfile *f, const char *name)
 	}
 
 	switch ( class ) {
-	case H5T_FLOAT : {
 
-		herr_t r;
-		double buf;
-		char *tmp;
+		case H5T_FLOAT :
 
 		r = H5Dread(dh, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL,
-		            H5P_DEFAULT, &buf);
+		            H5P_DEFAULT, &buf_f);
 		if ( r < 0 ) goto fail;
 
 		tmp = malloc(256);
-		snprintf(tmp, 255, "%f", buf);
+		snprintf(tmp, 255, "%f", buf_f);
 
 		return tmp;
 
-	}
-	case H5T_INTEGER : {
+		case H5T_INTEGER :
 
-		herr_t r;
-		int buf;
-		char *tmp;
 
 		r = H5Dread(dh, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
-		            H5P_DEFAULT, &buf);
+		            H5P_DEFAULT, &buf_i);
 		if ( r < 0 ) goto fail;
 
 		tmp = malloc(256);
-		snprintf(tmp, 255, "%d", buf);
+		snprintf(tmp, 255, "%d", buf_i);
 
 		return tmp;
-	}
-	default : {
+
+		default :
 		goto fail;
-	}
+
 	}
 
 fail:
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 2baa2644..102a5312 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -83,18 +83,23 @@ IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
 	for ( n=0; n<nm; n++ ) {
 
 		switch ( indm[n] ) {
-		case INDEXING_NONE :
+
+			case INDEXING_NONE :
 			ERROR("Tried to prepare INDEXING_NONE!\n");
 			break;
-		case INDEXING_DIRAX :
+
+			case INDEXING_DIRAX :
 			iprivs[n] = indexing_private(indm[n]);
 			break;
-		case INDEXING_MOSFLM :
+
+			case INDEXING_MOSFLM :
 			iprivs[n] = indexing_private(indm[n]);
 			break;
-		case INDEXING_REAX :
+
+			case INDEXING_REAX :
 			iprivs[n] = reax_prepare();
 			break;
+
 		}
 
 	}
@@ -113,18 +118,23 @@ void cleanup_indexing(IndexingPrivate **priv)
 	while ( priv[n] != NULL ) {
 
 		switch ( priv[n]->indm ) {
-		case INDEXING_NONE :
+
+			case INDEXING_NONE :
 			free(priv[n]);
 			break;
-		case INDEXING_DIRAX :
+
+			case INDEXING_DIRAX :
 			free(priv[n]);
 			break;
-		case INDEXING_MOSFLM :
+
+			case INDEXING_MOSFLM :
 			free(priv[n]);
 			break;
-		case INDEXING_REAX :
+
+			case INDEXING_REAX :
 			reax_cleanup(priv[n]);
 			break;
+
 		}
 
 		n++;
@@ -173,17 +183,22 @@ void index_pattern(struct image *image, UnitCell *cell, IndexingMethod *indm,
 
 		/* Index as appropriate */
 		switch ( indm[n] ) {
-		case INDEXING_NONE :
+
+			case INDEXING_NONE :
 			return;
-		case INDEXING_DIRAX :
+
+			case INDEXING_DIRAX :
 			run_dirax(image);
 			break;
-		case INDEXING_MOSFLM :
+
+			case INDEXING_MOSFLM :
 			run_mosflm(image, cell);
 			break;
-		case INDEXING_REAX :
+
+			case INDEXING_REAX :
 			reax_index(ipriv[n], image, cell);
 			break;
+
 		}
 		if ( image->ncells == 0 ) {
 			n++;
@@ -205,20 +220,25 @@ void index_pattern(struct image *image, UnitCell *cell, IndexingMethod *indm,
 
 			/* Match or reduce the cell as appropriate */
 			switch ( cellr ) {
-			case CELLR_NONE :
+
+				case CELLR_NONE :
 				new_cell = cell_new_from_cell(cand);
 				break;
-			case CELLR_REDUCE :
+
+				case CELLR_REDUCE :
 				new_cell = match_cell(cand, cell, verbose,
 				                      ltl, 1);
 				break;
-			case CELLR_COMPARE :
+
+				case CELLR_COMPARE :
 				new_cell = match_cell(cand, cell, verbose,
 				                      ltl, 0);
 				break;
-			case CELLR_COMPARE_AB :
+
+				case CELLR_COMPARE_AB :
 				new_cell = match_cell_ab(cand, cell);
 				break;
+
 			}
 
 			/* No cell?  Move on to the next candidate */
diff --git a/libcrystfel/src/mosflm.c b/libcrystfel/src/mosflm.c
index 0032a095..ed118aa4 100644
--- a/libcrystfel/src/mosflm.c
+++ b/libcrystfel/src/mosflm.c
@@ -283,13 +283,13 @@ static void mosflm_send_next(struct image *image, struct mosflm_data *mosflm)
 
 	switch ( mosflm->step ) {
 
-	case 1 :
+		case 1 :
 		mosflm_sendline("DETECTOR ROTATION HORIZONTAL"
 		                " ANTICLOCKWISE ORIGIN LL FAST HORIZONTAL"
 		                " RECTANGULAR\n", mosflm);
 		break;
 
-	case 2 :
+		case 2 :
 		if ( mosflm->target_cell != NULL ) {
 			cell_get_parameters(mosflm->target_cell, &a, &b, &c,
 				            &alpha, &beta, &gamma);
@@ -303,7 +303,7 @@ static void mosflm_send_next(struct image *image, struct mosflm_data *mosflm)
 		}
 		break;
 
-	case 3 :
+		case 3 :
 		if ( mosflm->target_cell != NULL ) {
 			sg = cell_get_spacegroup(mosflm->target_cell);
 			/* Remove white space from space group */
@@ -321,31 +321,31 @@ static void mosflm_send_next(struct image *image, struct mosflm_data *mosflm)
 		}
 		break;
 
-	case 4 :
+		case 4 :
 		mosflm_sendline("DISTANCE 67.8\n", mosflm);
 		break;
 
-	case 5 :
+		case 5 :
 		mosflm_sendline("BEAM 0.0 0.0\n", mosflm);
 		break;
 
-	case 6 :
+		case 6 :
 		wavelength = image->lambda*1e10;
 		snprintf(tmp, 255, "WAVELENGTH %10.5f\n", wavelength);
 		mosflm_sendline(tmp, mosflm);
 		break;
 
-	case 7 :
+		case 7 :
 		snprintf(tmp, 255, "NEWMAT %s\n", mosflm->newmatfile);
 		mosflm_sendline(tmp, mosflm);
 		break;
 
-	case 8 :
+		case 8 :
 		snprintf(tmp, 255, "IMAGE %s phi 0 0\n", mosflm->imagefile);
 		mosflm_sendline(tmp, mosflm);
 		break;
 
-	case 9 :
+		case 9 :
 		snprintf(tmp, 255, "AUTOINDEX DPS FILE %s"
 		                   " IMAGE 1 MAXCELL 1000 REFINE\n",
 		         mosflm->sptfile);
@@ -357,7 +357,7 @@ static void mosflm_send_next(struct image *image, struct mosflm_data *mosflm)
 		mosflm_sendline(tmp, mosflm);
 		break;
 
-	case 10 :
+		case 10 :
 		mosflm_sendline("GO\n", mosflm);
 		mosflm->finished_ok = 1;
 		break;
diff --git a/libcrystfel/src/render.c b/libcrystfel/src/render.c
index c9e1f01e..5d0cf9e8 100644
--- a/libcrystfel/src/render.c
+++ b/libcrystfel/src/render.c
@@ -64,34 +64,35 @@ static void render_rgb(double val, double max,
 		s = 6;
 	}
 	switch ( s ) {
-		case 0 : {	/* Black to blue */
-			r = 0;  g = 0;  b = p;
-			break;
-		}
-		case 1 : {	/* Blue to pink */
-			r = p;  g = 0;  b = 1.0;
-			break;
-		}
-		case 2 : {	/* Pink to red */
-			r = 1.0;  g = 0;  b = (1.0-p)*1.0;
-			break;
-		}
-		case 3 : {	/* Red to Orange */
-			r = 1.0;  g = 0.5*p;  b = 0;
-			break;
-		}
-		case 4 : {	/* Orange to Yellow */
-			r = 1.0;  g = 0.5 + 0.5*p;  b = 0;
-			break;
-		}
-		case 5 : {	/* Yellow to White */
-			r = 1.0;  g = 1.0;  b = 1.0*p;
-			break;
-		}
-		case 6 : {	/* Pixel has hit the maximum value */
-			r = 1.0;  g = 1.0;  b = 1.0;
-			break;
-		}
+
+		case 0 :	/* Black to blue */
+		r = 0;  g = 0;  b = p;
+		break;
+
+		case 1 :	/* Blue to pink */
+		r = p;  g = 0;  b = 1.0;
+		break;
+
+		case 2 :	/* Pink to red */
+		r = 1.0;  g = 0;  b = (1.0-p)*1.0;
+		break;
+
+		case 3 :	/* Red to Orange */
+		r = 1.0;  g = 0.5*p;  b = 0;
+		break;
+
+		case 4 :	/* Orange to Yellow */
+		r = 1.0;  g = 0.5 + 0.5*p;  b = 0;
+		break;
+
+		case 5 :	/* Yellow to White */
+		r = 1.0;  g = 1.0;  b = 1.0*p;
+		break;
+
+		case 6 :	/* Pixel has hit the maximum value */
+		r = 1.0;  g = 1.0;  b = 1.0;
+		break;
+
 	}
 
 	*rp = r;
@@ -144,16 +145,20 @@ void render_scale(double val, double max, int scale,
                   double *rp, double *gp, double *bp)
 {
 	switch ( scale ) {
-	case SCALE_COLOUR :
+
+		case SCALE_COLOUR :
 		render_rgb(val, max, rp, gp, bp);
 		break;
-	case SCALE_MONO :
+
+		case SCALE_MONO :
 		render_mono(val, max, rp, gp, bp);
 		break;
-	case SCALE_INVMONO :
+
+		case SCALE_INVMONO :
 		render_invmono(val, max, rp, gp, bp);
 		break;
-	case SCALE_RATIO :
+
+		case SCALE_RATIO :
 		render_ratio(val, max, rp, gp, bp);
 		break;
 	}
diff --git a/libcrystfel/src/statistics.c b/libcrystfel/src/statistics.c
index 6ddf2850..56273fdb 100644
--- a/libcrystfel/src/statistics.c
+++ b/libcrystfel/src/statistics.c
@@ -407,22 +407,28 @@ static double calc_r(double scale, void *params)
 	struct r_params *rp = params;
 
 	switch ( rp->fom ) {
-	case R_1_ZERO :
+
+		case R_1_ZERO :
 		return internal_r1_negstozero(rp->list1, rp->list2, scale);
-	case R_1_IGNORE :
+
+		case R_1_IGNORE :
 		return internal_r1_ignorenegs(rp->list1, rp->list2, scale);
-	case R_2 :
+
+		case R_2 :
 		return internal_r2(rp->list1, rp->list2, scale);
 
-	case R_1_I :
+		case R_1_I :
 		return internal_r_i(rp->list1, rp->list2, scale);
 
-	case R_DIFF_ZERO :
+		case R_DIFF_ZERO :
 		return internal_rdiff_negstozero(rp->list1, rp->list2,scale);
-	case R_DIFF_IGNORE :
+
+		case R_DIFF_IGNORE :
 		return internal_rdiff_ignorenegs(rp->list1, rp->list2, scale);
-	case R_DIFF_INTENSITY :
+
+		case R_DIFF_INTENSITY :
 		return internal_rdiff_intensity(rp->list1, rp->list2, scale);
+
 	}
 
 	ERROR("No such FoM!\n");
@@ -457,17 +463,20 @@ static double r_minimised(RefList *list1, RefList *list2, double *scalep, int fo
 
 		/* Initial guess */
 		switch ( fom ) {
-		case R_1_ZERO :
-		case R_1_IGNORE :
-		case R_DIFF_ZERO :
-		case R_DIFF_IGNORE :
+
+			case R_1_ZERO :
+			case R_1_IGNORE :
+			case R_DIFF_ZERO :
+			case R_DIFF_IGNORE :
 			scale = stat_scale_sqrti(list1, list2);
 			break;
-		case R_2 :
-		case R_1_I :
-		case R_DIFF_INTENSITY :
+
+			case R_2 :
+			case R_1_I :
+			case R_DIFF_INTENSITY :
 			scale = stat_scale_intensity(list1, list2);
 			break;
+
 		}
 		//STATUS("Initial scale factor estimate: %5.2e\n", scale);
 
diff --git a/m4/00gnulib.m4 b/m4/00gnulib.m4
index 7feed466..d978cb89 100644
--- a/m4/00gnulib.m4
+++ b/m4/00gnulib.m4
@@ -1,5 +1,5 @@
 # 00gnulib.m4 serial 2
-dnl Copyright (C) 2009-2011 Free Software Foundation, Inc.
+dnl Copyright (C) 2009-2012 Free Software Foundation, Inc.
 dnl This file is free software; the Free Software Foundation
 dnl gives unlimited permission to copy and/or distribute it,
 dnl with or without modifications, as long as this notice is preserved.
diff --git a/m4/extensions.m4 b/m4/extensions.m4
index 1330503f..0bfaef6f 100644
--- a/m4/extensions.m4
+++ b/m4/extensions.m4
@@ -1,7 +1,7 @@
-# serial 9  -*- Autoconf -*-
+# serial 11  -*- Autoconf -*-
 # Enable extensions on systems that normally disable them.
 
-# Copyright (C) 2003, 2006-2011 Free Software Foundation, Inc.
+# Copyright (C) 2003, 2006-2012 Free Software Foundation, Inc.
 # This file 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.
@@ -43,7 +43,7 @@ AC_BEFORE([$0], [AC_RUN_IFELSE])dnl
   AC_CHECK_HEADER([minix/config.h], [MINIX=yes], [MINIX=])
   if test "$MINIX" = yes; then
     AC_DEFINE([_POSIX_SOURCE], [1],
-      [Define to 1 if you need to in order for `stat' and other
+      [Define to 1 if you need to in order for 'stat' and other
        things to work.])
     AC_DEFINE([_POSIX_1_SOURCE], [2],
       [Define to 2 if the system does not provide POSIX.1 features
@@ -67,6 +67,10 @@ AC_BEFORE([$0], [AC_RUN_IFELSE])dnl
 #ifndef _ALL_SOURCE
 # undef _ALL_SOURCE
 #endif
+/* Enable general extensions on MacOS X.  */
+#ifndef _DARWIN_C_SOURCE
+# undef _DARWIN_C_SOURCE
+#endif
 /* Enable GNU extensions on systems that have them.  */
 #ifndef _GNU_SOURCE
 # undef _GNU_SOURCE
@@ -95,6 +99,7 @@ AC_BEFORE([$0], [AC_RUN_IFELSE])dnl
   test $ac_cv_safe_to_define___extensions__ = yes &&
     AC_DEFINE([__EXTENSIONS__])
   AC_DEFINE([_ALL_SOURCE])
+  AC_DEFINE([_DARWIN_C_SOURCE])
   AC_DEFINE([_GNU_SOURCE])
   AC_DEFINE([_POSIX_PTHREAD_SEMANTICS])
   AC_DEFINE([_TANDEM_SOURCE])
diff --git a/m4/gnulib-cache.m4 b/m4/gnulib-cache.m4
index c93243e0..acc9a4c9 100644
--- a/m4/gnulib-cache.m4
+++ b/m4/gnulib-cache.m4
@@ -1,9 +1,21 @@
-# Copyright (C) 2002-2011 Free Software Foundation, Inc.
+# Copyright (C) 2002-2012 Free Software Foundation, Inc.
 #
-# This file is free software, distributed under the terms of the GNU
-# General Public License.  As a special exception to the GNU General
-# Public License, this file may be distributed as part of a program
-# that contains a configuration script generated by Autoconf, under
+# This file is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 3 of the License, or
+# (at your option) any later version.
+#
+# This file is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this file.  If not, see <http://www.gnu.org/licenses/>.
+#
+# As a special exception to the GNU General Public License,
+# this file may be distributed as part of a program that
+# contains a configuration script generated by Autoconf, under
 # the same distribution terms as the rest of that program.
 #
 # Generated by gnulib-tool.
@@ -15,7 +27,7 @@
 
 
 # Specification in the form of a command-line invocation:
-#   gnulib-tool --import --dir=. --lib=libgnu --source-base=lib --m4-base=m4 --doc-base=doc --tests-base=tests --aux-dir=build-aux --no-libtool --macro-prefix=gl lib-ignore strndup
+#   gnulib-tool --import --dir=. --lib=libgnu --source-base=lib --m4-base=m4 --doc-base=doc --tests-base=tests --aux-dir=build-aux --no-conditional-dependencies --libtool --macro-prefix=gl lib-ignore strndup
 
 # Specification in the form of a few gnulib-tool.m4 macro invocations:
 gl_LOCAL_DIR([])
@@ -31,5 +43,7 @@ gl_DOC_BASE([doc])
 gl_TESTS_BASE([tests])
 gl_LIB([libgnu])
 gl_MAKEFILE_NAME([])
+gl_LIBTOOL
 gl_MACRO_PREFIX([gl])
 gl_PO_DOMAIN([])
+gl_WITNESS_C_DOMAIN([])
diff --git a/m4/gnulib-common.m4 b/m4/gnulib-common.m4
index c4d7a20e..d62b7677 100644
--- a/m4/gnulib-common.m4
+++ b/m4/gnulib-common.m4
@@ -1,5 +1,5 @@
-# gnulib-common.m4 serial 24
-dnl Copyright (C) 2007-2011 Free Software Foundation, Inc.
+# gnulib-common.m4 serial 32
+dnl Copyright (C) 2007-2012 Free Software Foundation, Inc.
 dnl This file is free software; the Free Software Foundation
 dnl gives unlimited permission to copy and/or distribute it,
 dnl with or without modifications, as long as this notice is preserved.
@@ -12,6 +12,20 @@ AC_DEFUN([gl_COMMON], [
   AC_REQUIRE([gl_COMMON_BODY])
 ])
 AC_DEFUN([gl_COMMON_BODY], [
+  AH_VERBATIM([_Noreturn],
+[/* The _Noreturn keyword of C11.  */
+#if ! (defined _Noreturn \
+       || (defined __STDC_VERSION__ && 201112 <= __STDC_VERSION__))
+# if (3 <= __GNUC__ || (__GNUC__ == 2 && 8 <= __GNUC_MINOR__) \
+      || 0x5110 <= __SUNPRO_C)
+#  define _Noreturn __attribute__ ((__noreturn__))
+# elif defined _MSC_VER && 1200 <= _MSC_VER
+#  define _Noreturn __declspec (noreturn)
+# else
+#  define _Noreturn
+# endif
+#endif
+])
   AH_VERBATIM([isoc99_inline],
 [/* Work around a bug in Apple GCC 4.0.1 build 5465: In C99 mode, it supports
    the ISO C 99 semantics of 'extern inline' (unlike the GNU C semantics of
@@ -34,6 +48,20 @@ AC_DEFUN([gl_COMMON_BODY], [
 /* The name _UNUSED_PARAMETER_ is an earlier spelling, although the name
    is a misnomer outside of parameter lists.  */
 #define _UNUSED_PARAMETER_ _GL_UNUSED
+
+/* The __pure__ attribute was added in gcc 2.96.  */
+#if __GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ >= 96)
+# define _GL_ATTRIBUTE_PURE __attribute__ ((__pure__))
+#else
+# define _GL_ATTRIBUTE_PURE /* empty */
+#endif
+
+/* The __const__ attribute was added in gcc 2.95.  */
+#if __GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ >= 95)
+# define _GL_ATTRIBUTE_CONST __attribute__ ((__const__))
+#else
+# define _GL_ATTRIBUTE_CONST /* empty */
+#endif
 ])
   dnl Preparation for running test programs:
   dnl Tell glibc to write diagnostics from -D_FORTIFY_SOURCE=2 to stderr, not
@@ -47,16 +75,49 @@ AC_DEFUN([gl_COMMON_BODY], [
 # expands to a C preprocessor expression that evaluates to 1 or 0, depending
 # whether a gnulib module that has been requested shall be considered present
 # or not.
-AC_DEFUN([gl_MODULE_INDICATOR_CONDITION], [1])
+m4_define([gl_MODULE_INDICATOR_CONDITION], [1])
 
 # gl_MODULE_INDICATOR_SET_VARIABLE([modulename])
 # sets the shell variable that indicates the presence of the given module to
 # a C preprocessor expression that will evaluate to 1.
 AC_DEFUN([gl_MODULE_INDICATOR_SET_VARIABLE],
 [
-  GNULIB_[]m4_translit([[$1]],
-    [abcdefghijklmnopqrstuvwxyz./-],
-    [ABCDEFGHIJKLMNOPQRSTUVWXYZ___])=gl_MODULE_INDICATOR_CONDITION
+  gl_MODULE_INDICATOR_SET_VARIABLE_AUX(
+    [GNULIB_[]m4_translit([[$1]],
+                          [abcdefghijklmnopqrstuvwxyz./-],
+                          [ABCDEFGHIJKLMNOPQRSTUVWXYZ___])],
+    [gl_MODULE_INDICATOR_CONDITION])
+])
+
+# gl_MODULE_INDICATOR_SET_VARIABLE_AUX([variable])
+# modifies the shell variable to include the gl_MODULE_INDICATOR_CONDITION.
+# The shell variable's value is a C preprocessor expression that evaluates
+# to 0 or 1.
+AC_DEFUN([gl_MODULE_INDICATOR_SET_VARIABLE_AUX],
+[
+  m4_if(m4_defn([gl_MODULE_INDICATOR_CONDITION]), [1],
+    [
+     dnl Simplify the expression VALUE || 1 to 1.
+     $1=1
+    ],
+    [gl_MODULE_INDICATOR_SET_VARIABLE_AUX_OR([$1],
+                                             [gl_MODULE_INDICATOR_CONDITION])])
+])
+
+# gl_MODULE_INDICATOR_SET_VARIABLE_AUX_OR([variable], [condition])
+# modifies the shell variable to include the given condition.  The shell
+# variable's value is a C preprocessor expression that evaluates to 0 or 1.
+AC_DEFUN([gl_MODULE_INDICATOR_SET_VARIABLE_AUX_OR],
+[
+  dnl Simplify the expression 1 || CONDITION to 1.
+  if test "$[]$1" != 1; then
+    dnl Simplify the expression 0 || CONDITION to CONDITION.
+    if test "$[]$1" = 0; then
+      $1=$2
+    else
+      $1="($[]$1 || $2)"
+    fi
+  fi
 ])
 
 # gl_MODULE_INDICATOR([modulename])
@@ -151,6 +212,83 @@ m4_ifndef([AS_VAR_IF],
 [m4_define([AS_VAR_IF],
 [AS_IF([test x"AS_VAR_GET([$1])" = x""$2], [$3], [$4])])])
 
+# gl_PROG_CC_C99
+# Modifies the value of the shell variable CC in an attempt to make $CC
+# understand ISO C99 source code.
+# This is like AC_PROG_CC_C99, except that
+# - AC_PROG_CC_C99 did not exist in Autoconf versions < 2.60,
+# - AC_PROG_CC_C99 does not mix well with AC_PROG_CC_STDC
+#   <http://lists.gnu.org/archive/html/bug-gnulib/2011-09/msg00367.html>,
+#   but many more packages use AC_PROG_CC_STDC than AC_PROG_CC_C99
+#   <http://lists.gnu.org/archive/html/bug-gnulib/2011-09/msg00441.html>.
+# Remaining problems:
+# - When AC_PROG_CC_STDC is invoked twice, it adds the C99 enabling options
+#   to CC twice
+#   <http://lists.gnu.org/archive/html/bug-gnulib/2011-09/msg00431.html>.
+# - AC_PROG_CC_STDC is likely to change now that C11 is an ISO standard.
+AC_DEFUN([gl_PROG_CC_C99],
+[
+  dnl Change that version number to the minimum Autoconf version that supports
+  dnl mixing AC_PROG_CC_C99 calls with AC_PROG_CC_STDC calls.
+  m4_version_prereq([9.0],
+    [AC_REQUIRE([AC_PROG_CC_C99])],
+    [AC_REQUIRE([AC_PROG_CC_STDC])])
+])
+
+# gl_PROG_AR_RANLIB
+# Determines the values for AR, ARFLAGS, RANLIB that fit with the compiler.
+# The user can set the variables AR, ARFLAGS, RANLIB if he wants to override
+# the values.
+AC_DEFUN([gl_PROG_AR_RANLIB],
+[
+  dnl Minix 3 comes with two toolchains: The Amsterdam Compiler Kit compiler
+  dnl as "cc", and GCC as "gcc". They have different object file formats and
+  dnl library formats. In particular, the GNU binutils programs ar, ranlib
+  dnl produce libraries that work only with gcc, not with cc.
+  AC_REQUIRE([AC_PROG_CC])
+  AC_CACHE_CHECK([for Minix Amsterdam compiler], [gl_cv_c_amsterdam_compiler],
+    [
+      AC_EGREP_CPP([Amsterdam],
+        [
+#ifdef __ACK__
+Amsterdam
+#endif
+        ],
+        [gl_cv_c_amsterdam_compiler=yes],
+        [gl_cv_c_amsterdam_compiler=no])
+    ])
+  if test -z "$AR"; then
+    if test $gl_cv_c_amsterdam_compiler = yes; then
+      AR='cc -c.a'
+      if test -z "$ARFLAGS"; then
+        ARFLAGS='-o'
+      fi
+    else
+      dnl Use the Automake-documented default values for AR and ARFLAGS,
+      dnl but prefer ${host}-ar over ar (useful for cross-compiling).
+      AC_CHECK_TOOL([AR], [ar], [ar])
+      if test -z "$ARFLAGS"; then
+        ARFLAGS='cru'
+      fi
+    fi
+  else
+    if test -z "$ARFLAGS"; then
+      ARFLAGS='cru'
+    fi
+  fi
+  AC_SUBST([AR])
+  AC_SUBST([ARFLAGS])
+  if test -z "$RANLIB"; then
+    if test $gl_cv_c_amsterdam_compiler = yes; then
+      RANLIB=':'
+    else
+      dnl Use the ranlib program if it is available.
+      AC_PROG_RANLIB
+    fi
+  fi
+  AC_SUBST([RANLIB])
+])
+
 # AC_PROG_MKDIR_P
 # is a backport of autoconf-2.60's AC_PROG_MKDIR_P, with a fix
 # for interoperability with automake-1.9.6 from autoconf-2.62.
diff --git a/m4/gnulib-comp.m4 b/m4/gnulib-comp.m4
index 8c573e37..80d7893e 100644
--- a/m4/gnulib-comp.m4
+++ b/m4/gnulib-comp.m4
@@ -1,10 +1,22 @@
 # DO NOT EDIT! GENERATED AUTOMATICALLY!
-# Copyright (C) 2002-2011 Free Software Foundation, Inc.
+# Copyright (C) 2002-2012 Free Software Foundation, Inc.
 #
-# This file is free software, distributed under the terms of the GNU
-# General Public License.  As a special exception to the GNU General
-# Public License, this file may be distributed as part of a program
-# that contains a configuration script generated by Autoconf, under
+# This file is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 3 of the License, or
+# (at your option) any later version.
+#
+# This file is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this file.  If not, see <http://www.gnu.org/licenses/>.
+#
+# As a special exception to the GNU General Public License,
+# this file may be distributed as part of a program that
+# contains a configuration script generated by Autoconf, under
 # the same distribution terms as the rest of that program.
 #
 # Generated by gnulib-tool.
@@ -25,28 +37,26 @@ AC_DEFUN([gl_EARLY],
   m4_pattern_allow([^gl_ES$])dnl a valid locale name
   m4_pattern_allow([^gl_LIBOBJS$])dnl a variable
   m4_pattern_allow([^gl_LTLIBOBJS$])dnl a variable
-  AC_REQUIRE([AC_PROG_RANLIB])
-  # Code from module arg-nonnull:
-  # Code from module c++defs:
+  AC_REQUIRE([gl_PROG_AR_RANLIB])
   # Code from module extensions:
   AC_REQUIRE([gl_USE_SYSTEM_EXTENSIONS])
   # Code from module include_next:
   # Code from module lib-ignore:
+  # Code from module snippet/arg-nonnull:
+  # Code from module snippet/c++defs:
+  # Code from module snippet/warn-on-use:
   # Code from module stddef:
   # Code from module string:
   # Code from module strndup:
   # Code from module strnlen:
-  # Code from module warn-on-use:
 ])
 
 # This macro should be invoked from ./configure.ac, in the section
 # "Check for header files, types and library functions".
 AC_DEFUN([gl_INIT],
 [
-  AM_CONDITIONAL([GL_COND_LIBTOOL], [false])
-  gl_cond_libtool=false
-  gl_libdeps=
-  gl_ltlibdeps=
+  AM_CONDITIONAL([GL_COND_LIBTOOL], [true])
+  gl_cond_libtool=true
   gl_m4_base='m4'
   m4_pushdef([AC_LIBOBJ], m4_defn([gl_LIBOBJ]))
   m4_pushdef([AC_REPLACE_FUNCS], m4_defn([gl_REPLACE_FUNCS]))
@@ -59,8 +69,15 @@ gl_IGNORE_UNUSED_LIBRARIES
 gl_STDDEF_H
 gl_HEADER_STRING_H
 gl_FUNC_STRNDUP
+if test $HAVE_STRNDUP = 0 || test $REPLACE_STRNDUP = 1; then
+  AC_LIBOBJ([strndup])
+fi
 gl_STRING_MODULE_INDICATOR([strndup])
 gl_FUNC_STRNLEN
+if test $HAVE_DECL_STRNLEN = 0 || test $REPLACE_STRNLEN = 1; then
+  AC_LIBOBJ([strnlen])
+  gl_PREREQ_STRNLEN
+fi
 gl_STRING_MODULE_INDICATOR([strnlen])
   # End of code from modules
   m4_ifval(gl_LIBSOURCES_LIST, [
@@ -139,10 +156,6 @@ changequote([, ])dnl
     AC_SUBST([gltests_LIBOBJS], [$gltests_libobjs])
     AC_SUBST([gltests_LTLIBOBJS], [$gltests_ltlibobjs])
   ])
-  LIBGNU_LIBDEPS="$gl_libdeps"
-  AC_SUBST([LIBGNU_LIBDEPS])
-  LIBGNU_LTLIBDEPS="$gl_ltlibdeps"
-  AC_SUBST([LIBGNU_LTLIBDEPS])
 ])
 
 # Like AC_LIBOBJ, except that the module name goes
@@ -202,9 +215,9 @@ AC_DEFUN([gltests_LIBSOURCES], [
 # This macro records the list of files which have been installed by
 # gnulib-tool and may be removed by future gnulib-tool invocations.
 AC_DEFUN([gl_FILE_LIST], [
-  build-aux/arg-nonnull.h
-  build-aux/c++defs.h
-  build-aux/warn-on-use.h
+  build-aux/snippet/arg-nonnull.h
+  build-aux/snippet/c++defs.h
+  build-aux/snippet/warn-on-use.h
   lib/dummy.c
   lib/stddef.in.h
   lib/string.in.h
diff --git a/m4/gnulib-tool.m4 b/m4/gnulib-tool.m4
index ed41e9d4..a09ffc1d 100644
--- a/m4/gnulib-tool.m4
+++ b/m4/gnulib-tool.m4
@@ -1,5 +1,5 @@
 # gnulib-tool.m4 serial 2
-dnl Copyright (C) 2004-2005, 2009-2011 Free Software Foundation, Inc.
+dnl Copyright (C) 2004-2005, 2009-2012 Free Software Foundation, Inc.
 dnl This file is free software; the Free Software Foundation
 dnl gives unlimited permission to copy and/or distribute it,
 dnl with or without modifications, as long as this notice is preserved.
diff --git a/m4/include_next.m4 b/m4/include_next.m4
index b3c78491..a60a2614 100644
--- a/m4/include_next.m4
+++ b/m4/include_next.m4
@@ -1,5 +1,5 @@
-# include_next.m4 serial 18
-dnl Copyright (C) 2006-2011 Free Software Foundation, Inc.
+# include_next.m4 serial 23
+dnl Copyright (C) 2006-2012 Free Software Foundation, Inc.
 dnl This file is free software; the Free Software Foundation
 dnl gives unlimited permission to copy and/or distribute it,
 dnl with or without modifications, as long as this notice is preserved.
@@ -143,7 +143,7 @@ choke me
 # even if the compiler does not support include_next.
 # The three "///" are to pacify Sun C 5.8, which otherwise would say
 # "warning: #include of /usr/include/... may be non-portable".
-# Use `""', not `<>', so that the /// cannot be confused with a C99 comment.
+# Use '""', not '<>', so that the /// cannot be confused with a C99 comment.
 # Note: This macro assumes that the header file is not empty after
 # preprocessing, i.e. it does not only define preprocessor macros but also
 # provides some type/enum definitions or function/variable declarations.
@@ -175,11 +175,13 @@ AC_DEFUN([gl_NEXT_HEADERS_INTERNAL],
     [AC_CHECK_HEADERS_ONCE([$1])
     ])
 
+dnl FIXME: gl_next_header and gl_header_exists must be used unquoted
+dnl until we can assume autoconf 2.64 or newer.
   m4_foreach_w([gl_HEADER_NAME], [$1],
     [AS_VAR_PUSHDEF([gl_next_header],
                     [gl_cv_next_]m4_defn([gl_HEADER_NAME]))
      if test $gl_cv_have_include_next = yes; then
-       AS_VAR_SET([gl_next_header], ['<'gl_HEADER_NAME'>'])
+       AS_VAR_SET(gl_next_header, ['<'gl_HEADER_NAME'>'])
      else
        AC_CACHE_CHECK(
          [absolute name of <]m4_defn([gl_HEADER_NAME])[>],
@@ -205,33 +207,57 @@ AC_DEFUN([gl_NEXT_HEADERS_INTERNAL],
                  aix*) gl_absname_cpp="$ac_cpp -C" ;;
                  *)    gl_absname_cpp="$ac_cpp" ;;
                esac
+changequote(,)
+               case "$host_os" in
+                 mingw*)
+                   dnl For the sake of native Windows compilers (excluding gcc),
+                   dnl treat backslash as a directory separator, like /.
+                   dnl Actually, these compilers use a double-backslash as
+                   dnl directory separator, inside the
+                   dnl   # line "filename"
+                   dnl directives.
+                   gl_dirsep_regex='[/\\]'
+                   ;;
+                 *)
+                   gl_dirsep_regex='\/'
+                   ;;
+               esac
+               dnl A sed expression that turns a string into a basic regular
+               dnl expression, for use within "/.../".
+               gl_make_literal_regex_sed='s,[]$^\\.*/[],\\&,g'
+changequote([,])
+               gl_header_literal_regex=`echo ']m4_defn([gl_HEADER_NAME])[' \
+                                        | sed -e "$gl_make_literal_regex_sed"`
+               gl_absolute_header_sed="/${gl_dirsep_regex}${gl_header_literal_regex}/"'{
+                   s/.*"\(.*'"${gl_dirsep_regex}${gl_header_literal_regex}"'\)".*/\1/
+changequote(,)dnl
+                   s|^/[^/]|//&|
+changequote([,])dnl
+                   p
+                   q
+                 }'
                dnl eval is necessary to expand gl_absname_cpp.
                dnl Ultrix and Pyramid sh refuse to redirect output of eval,
                dnl so use subshell.
-               AS_VAR_SET([gl_next_header],
+               AS_VAR_SET(gl_next_header,
                  ['"'`(eval "$gl_absname_cpp conftest.$ac_ext") 2>&AS_MESSAGE_LOG_FD |
-                  sed -n '\#/]m4_defn([gl_HEADER_NAME])[#{
-                    s#.*"\(.*/]m4_defn([gl_HEADER_NAME])[\)".*#\1#
-                    s#^/[^/]#//&#
-                    p
-                    q
-                  }'`'"'])
+                      sed -n "$gl_absolute_header_sed"`'"'])
           m4_if([$2], [check],
             [else
-               AS_VAR_SET([gl_next_header], ['<'gl_HEADER_NAME'>'])
+               AS_VAR_SET(gl_next_header, ['<'gl_HEADER_NAME'>'])
              fi
             ])
          ])
      fi
      AC_SUBST(
        AS_TR_CPP([NEXT_]m4_defn([gl_HEADER_NAME])),
-       [AS_VAR_GET([gl_next_header])])
+       [AS_VAR_GET(gl_next_header)])
      if test $gl_cv_have_include_next = yes || test $gl_cv_have_include_next = buggy; then
        # INCLUDE_NEXT_AS_FIRST_DIRECTIVE='include_next'
        gl_next_as_first_directive='<'gl_HEADER_NAME'>'
      else
        # INCLUDE_NEXT_AS_FIRST_DIRECTIVE='include'
-       gl_next_as_first_directive=AS_VAR_GET([gl_next_header])
+       gl_next_as_first_directive=AS_VAR_GET(gl_next_header)
      fi
      AC_SUBST(
        AS_TR_CPP([NEXT_AS_FIRST_DIRECTIVE_]m4_defn([gl_HEADER_NAME])),
diff --git a/m4/lib-ignore.m4 b/m4/lib-ignore.m4
index 1fdfdc07..292c4691 100644
--- a/m4/lib-ignore.m4
+++ b/m4/lib-ignore.m4
@@ -1,6 +1,6 @@
 # If possible, ignore libraries that are not depended on.
 
-dnl Copyright (C) 2006, 2009-2011 Free Software Foundation, Inc.
+dnl Copyright (C) 2006, 2009-2012 Free Software Foundation, Inc.
 dnl This file is free software; the Free Software Foundation
 dnl gives unlimited permission to copy and/or distribute it,
 dnl with or without modifications, as long as this notice is preserved.
diff --git a/m4/onceonly.m4 b/m4/onceonly.m4
index 223071a2..275d73c4 100644
--- a/m4/onceonly.m4
+++ b/m4/onceonly.m4
@@ -1,9 +1,22 @@
-# onceonly.m4 serial 7
-dnl Copyright (C) 2002-2003, 2005-2006, 2008-2011 Free Software Foundation,
+# onceonly.m4 serial 9
+dnl Copyright (C) 2002-2003, 2005-2006, 2008-2012 Free Software Foundation,
 dnl Inc.
-dnl This file is free software, distributed under the terms of the GNU
-dnl General Public License.  As a special exception to the GNU General
-dnl Public License, this file may be distributed as part of a program
+dnl
+dnl This file is free software; you can redistribute it and/or modify
+dnl it under the terms of the GNU General Public License as published by
+dnl the Free Software Foundation; either version 3 of the License, or
+dnl (at your option) any later version.
+dnl
+dnl This file is distributed in the hope that it will be useful,
+dnl but WITHOUT ANY WARRANTY; without even the implied warranty of
+dnl MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+dnl GNU General Public License for more details.
+dnl
+dnl You should have received a copy of the GNU General Public License
+dnl along with this file.  If not, see <http://www.gnu.org/licenses/>.
+dnl
+dnl As a special exception to the GNU General Public License,
+dnl this file may be distributed as part of a program
 dnl that contains a configuration script generated by Autoconf, under
 dnl the same distribution terms as the rest of that program.
 
@@ -67,7 +80,7 @@ AC_DEFUN([AC_CHECK_FUNCS_ONCE], [
         [gl_func_list="$gl_func_list gl_FUNC_NAME"])
       gl_FUNCS_EXPANSION
       AH_TEMPLATE(AS_TR_CPP([HAVE_]m4_defn([gl_FUNC_NAME])),
-        [Define to 1 if you have the `]m4_defn([gl_FUNC_NAME])[' function.])
+        [Define to 1 if you have the ']m4_defn([gl_FUNC_NAME])[' function.])
     ])
     AC_REQUIRE([gl_CHECK_FUNC_]m4_defn([gl_FUNC_NAME]))
   ])
diff --git a/m4/stddef_h.m4 b/m4/stddef_h.m4
index 1ae23443..cc116096 100644
--- a/m4/stddef_h.m4
+++ b/m4/stddef_h.m4
@@ -1,6 +1,6 @@
 dnl A placeholder for POSIX 2008 <stddef.h>, for platforms that have issues.
 # stddef_h.m4 serial 4
-dnl Copyright (C) 2009-2011 Free Software Foundation, Inc.
+dnl Copyright (C) 2009-2012 Free Software Foundation, Inc.
 dnl This file is free software; the Free Software Foundation
 dnl gives unlimited permission to copy and/or distribute it,
 dnl with or without modifications, as long as this notice is preserved.
diff --git a/m4/string_h.m4 b/m4/string_h.m4
index df8c4035..5677e092 100644
--- a/m4/string_h.m4
+++ b/m4/string_h.m4
@@ -1,11 +1,11 @@
 # Configure a GNU-like replacement for <string.h>.
 
-# Copyright (C) 2007-2011 Free Software Foundation, Inc.
+# Copyright (C) 2007-2012 Free Software Foundation, Inc.
 # This file 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.
 
-# serial 20
+# serial 21
 
 # Written by Paul Eggert.
 
@@ -27,9 +27,9 @@ AC_DEFUN([gl_HEADER_STRING_H_BODY],
   dnl guaranteed by C89.
   gl_WARN_ON_USE_PREPARE([[#include <string.h>
     ]],
-    [memmem mempcpy memrchr rawmemchr stpcpy stpncpy strchrnul strdup
-     strncat strndup strnlen strpbrk strsep strcasestr strtok_r strerror_r
-     strsignal strverscmp])
+    [ffsl ffsll memmem mempcpy memrchr rawmemchr stpcpy stpncpy strchrnul
+     strdup strncat strndup strnlen strpbrk strsep strcasestr strtok_r
+     strerror_r strsignal strverscmp])
 ])
 
 AC_DEFUN([gl_STRING_MODULE_INDICATOR],
@@ -43,6 +43,8 @@ AC_DEFUN([gl_STRING_MODULE_INDICATOR],
 
 AC_DEFUN([gl_HEADER_STRING_H_DEFAULTS],
 [
+  GNULIB_FFSL=0;        AC_SUBST([GNULIB_FFSL])
+  GNULIB_FFSLL=0;       AC_SUBST([GNULIB_FFSLL])
   GNULIB_MEMCHR=0;      AC_SUBST([GNULIB_MEMCHR])
   GNULIB_MEMMEM=0;      AC_SUBST([GNULIB_MEMMEM])
   GNULIB_MEMPCPY=0;     AC_SUBST([GNULIB_MEMPCPY])
@@ -80,6 +82,8 @@ AC_DEFUN([gl_HEADER_STRING_H_DEFAULTS],
   GNULIB_STRVERSCMP=0;  AC_SUBST([GNULIB_STRVERSCMP])
   HAVE_MBSLEN=0;        AC_SUBST([HAVE_MBSLEN])
   dnl Assume proper GNU behavior unless another module says otherwise.
+  HAVE_FFSL=1;                  AC_SUBST([HAVE_FFSL])
+  HAVE_FFSLL=1;                 AC_SUBST([HAVE_FFSLL])
   HAVE_MEMCHR=1;                AC_SUBST([HAVE_MEMCHR])
   HAVE_DECL_MEMMEM=1;           AC_SUBST([HAVE_DECL_MEMMEM])
   HAVE_MEMPCPY=1;               AC_SUBST([HAVE_MEMPCPY])
diff --git a/m4/strndup.m4 b/m4/strndup.m4
index d8f00cab..bdde5fe1 100644
--- a/m4/strndup.m4
+++ b/m4/strndup.m4
@@ -1,5 +1,5 @@
-# strndup.m4 serial 18
-dnl Copyright (C) 2002-2003, 2005-2011 Free Software Foundation, Inc.
+# strndup.m4 serial 20
+dnl Copyright (C) 2002-2003, 2005-2012 Free Software Foundation, Inc.
 dnl This file is free software; the Free Software Foundation
 dnl gives unlimited permission to copy and/or distribute it,
 dnl with or without modifications, as long as this notice is preserved.
@@ -18,13 +18,18 @@ AC_DEFUN([gl_FUNC_STRNDUP],
   fi
 
   if test $ac_cv_func_strndup = yes; then
+    HAVE_STRNDUP=1
     # AIX 4.3.3, AIX 5.1 have a function that fails to add the terminating '\0'.
     AC_CACHE_CHECK([for working strndup], [gl_cv_func_strndup_works],
       [AC_RUN_IFELSE([
          AC_LANG_PROGRAM([[#include <string.h>
                            #include <stdlib.h>]], [[
 #ifndef HAVE_DECL_STRNDUP
-  extern char *strndup (const char *, size_t);
+  extern
+  #ifdef __cplusplus
+  "C"
+  #endif
+  char *strndup (const char *, size_t);
 #endif
   char *s;
   s = strndup ("some longer string", 15);
@@ -42,12 +47,9 @@ changequote(,)dnl
 changequote([,])dnl
          ])])
     case $gl_cv_func_strndup_works in
-      *no)
-        REPLACE_STRNDUP=1
-        AC_LIBOBJ([strndup])
-        ;;
+      *no) REPLACE_STRNDUP=1 ;;
     esac
   else
-    AC_LIBOBJ([strndup])
+    HAVE_STRNDUP=0
   fi
 ])
diff --git a/m4/strnlen.m4 b/m4/strnlen.m4
index a1c59ac6..d97e3075 100644
--- a/m4/strnlen.m4
+++ b/m4/strnlen.m4
@@ -1,5 +1,5 @@
-# strnlen.m4 serial 12
-dnl Copyright (C) 2002-2003, 2005-2007, 2009-2011 Free Software Foundation,
+# strnlen.m4 serial 13
+dnl Copyright (C) 2002-2003, 2005-2007, 2009-2012 Free Software Foundation,
 dnl Inc.
 dnl This file is free software; the Free Software Foundation
 dnl gives unlimited permission to copy and/or distribute it,
@@ -16,16 +16,14 @@ AC_DEFUN([gl_FUNC_STRNLEN],
   if test $ac_cv_have_decl_strnlen = no; then
     HAVE_DECL_STRNLEN=0
   else
-    AC_FUNC_STRNLEN
+    m4_pushdef([AC_LIBOBJ], [:])
     dnl Note: AC_FUNC_STRNLEN does AC_LIBOBJ([strnlen]).
+    AC_FUNC_STRNLEN
+    m4_popdef([AC_LIBOBJ])
     if test $ac_cv_func_strnlen_working = no; then
       REPLACE_STRNLEN=1
     fi
   fi
-  if test $HAVE_DECL_STRNLEN = 0 || test $REPLACE_STRNLEN = 1; then
-    AC_LIBOBJ([strnlen])
-    gl_PREREQ_STRNLEN
-  fi
 ])
 
 # Prerequisites of lib/strnlen.c.
diff --git a/m4/warn-on-use.m4 b/m4/warn-on-use.m4
index e0d0f276..a77802eb 100644
--- a/m4/warn-on-use.m4
+++ b/m4/warn-on-use.m4
@@ -1,5 +1,5 @@
-# warn-on-use.m4 serial 2
-dnl Copyright (C) 2010-2011 Free Software Foundation, Inc.
+# warn-on-use.m4 serial 5
+dnl Copyright (C) 2010-2012 Free Software Foundation, Inc.
 dnl This file is free software; the Free Software Foundation
 dnl gives unlimited permission to copy and/or distribute it,
 dnl with or without modifications, as long as this notice is preserved.
@@ -18,8 +18,8 @@ dnl with or without modifications, as long as this notice is preserved.
 # some systems declare functions in the wrong header, then INCLUDES
 # should do likewise.
 #
-# If you assume C89, then it is generally safe to assume declarations
-# for functions declared in that standard (such as gets) without
+# It is generally safe to assume declarations for functions declared
+# in the intersection of C89 and C11 (such as printf) without
 # needing gl_WARN_ON_USE_PREPARE.
 AC_DEFUN([gl_WARN_ON_USE_PREPARE],
 [
@@ -27,6 +27,8 @@ AC_DEFUN([gl_WARN_ON_USE_PREPARE],
     [AH_TEMPLATE([HAVE_RAW_DECL_]AS_TR_CPP(m4_defn([gl_decl])),
       [Define to 1 if ]m4_defn([gl_decl])[ is declared even after
        undefining macros.])])dnl
+dnl FIXME: gl_Symbol must be used unquoted until we can assume
+dnl autoconf 2.64 or newer.
   for gl_func in m4_flatten([$2]); do
     AS_VAR_PUSHDEF([gl_Symbol], [gl_cv_have_raw_decl_$gl_func])dnl
     AC_CACHE_CHECK([whether $gl_func is declared without a macro],
@@ -35,8 +37,8 @@ AC_DEFUN([gl_WARN_ON_USE_PREPARE],
 [@%:@undef $gl_func
   (void) $gl_func;])],
         [AS_VAR_SET(gl_Symbol, [yes])], [AS_VAR_SET(gl_Symbol, [no])])])
-     AS_VAR_IF(gl_Symbol, [yes],
-       [AC_DEFINE_UNQUOTED(AS_TR_CPP([HAVE_RAW_DECL_$gl_func]), [1])
+    AS_VAR_IF(gl_Symbol, [yes],
+      [AC_DEFINE_UNQUOTED(AS_TR_CPP([HAVE_RAW_DECL_$gl_func]), [1])
        dnl shortcut - if the raw declaration exists, then set a cache
        dnl variable to allow skipping any later AC_CHECK_DECL efforts
        eval ac_cv_have_decl_$gl_func=yes])
diff --git a/m4/wchar_t.m4 b/m4/wchar_t.m4
index d2c03c42..534735d8 100644
--- a/m4/wchar_t.m4
+++ b/m4/wchar_t.m4
@@ -1,5 +1,5 @@
 # wchar_t.m4 serial 4 (gettext-0.18.2)
-dnl Copyright (C) 2002-2003, 2008-2011 Free Software Foundation, Inc.
+dnl Copyright (C) 2002-2003, 2008-2012 Free Software Foundation, Inc.
 dnl This file is free software; the Free Software Foundation
 dnl gives unlimited permission to copy and/or distribute it,
 dnl with or without modifications, as long as this notice is preserved.
diff --git a/src/check_hkl.c b/src/check_hkl.c
index 649b86af..4927e60e 100644
--- a/src/check_hkl.c
+++ b/src/check_hkl.c
@@ -339,43 +339,44 @@ int main(int argc, char *argv[])
 	while ((c = getopt_long(argc, argv, "hy:p:", longopts, NULL)) != -1) {
 
 		switch (c) {
-		case 'h' :
+
+			case 'h' :
 			show_help(argv[0]);
 			return 0;
 
-		case 'y' :
+			case 'y' :
 			sym_str = strdup(optarg);
 			break;
 
-		case 'p' :
+			case 'p' :
 			pdb = strdup(optarg);
 			break;
 
-		case 0 :
+			case 0 :
 			break;
 
-		case 2 :
+			case 2 :
 			if ( sscanf(optarg, "%e", &rmin_fix) != 1 ) {
 				ERROR("Invalid value for --rmin\n");
 				return 1;
 			}
 			break;
 
-		case 3 :
+			case 3 :
 			if ( sscanf(optarg, "%e", &rmax_fix) != 1 ) {
 				ERROR("Invalid value for --rmax\n");
 				return 1;
 			}
 			break;
 
-		case 4 :
+			case 4 :
 			if ( sscanf(optarg, "%f", &sigma_cutoff) != 1 ) {
 				ERROR("Invalid value for --sigma-cutoff\n");
 				return 1;
 			}
 			break;
 
-		default :
+			default :
 			return 1;
 		}
 
diff --git a/src/cl-utils.c b/src/cl-utils.c
index ae146ed0..71ff25b5 100644
--- a/src/cl-utils.c
+++ b/src/cl-utils.c
@@ -46,28 +46,71 @@
 const char *clError(cl_int err)
 {
 	switch ( err ) {
-	case CL_SUCCESS : return "no error";
-	case CL_INVALID_PLATFORM : return "invalid platform";
-	case CL_INVALID_KERNEL : return "invalid kernel";
-	case CL_INVALID_ARG_INDEX : return "invalid argument index";
-	case CL_INVALID_ARG_VALUE : return "invalid argument value";
-	case CL_INVALID_MEM_OBJECT : return "invalid memory object";
-	case CL_INVALID_SAMPLER : return "invalid sampler";
-	case CL_INVALID_ARG_SIZE : return "invalid argument size";
-	case CL_INVALID_COMMAND_QUEUE  : return "invalid command queue";
-	case CL_INVALID_CONTEXT : return "invalid context";
-	case CL_INVALID_VALUE : return "invalid value";
-	case CL_INVALID_EVENT_WAIT_LIST : return "invalid wait list";
-	case CL_MAP_FAILURE : return "map failure";
-	case CL_MEM_OBJECT_ALLOCATION_FAILURE : return "object allocation failure";
-	case CL_OUT_OF_HOST_MEMORY : return "out of host memory";
-	case CL_OUT_OF_RESOURCES : return "out of resources";
-	case CL_INVALID_KERNEL_NAME : return "invalid kernel name";
-	case CL_INVALID_KERNEL_ARGS : return "invalid kernel arguments";
-	case CL_INVALID_WORK_GROUP_SIZE : return "invalid work group size";
-	case CL_IMAGE_FORMAT_NOT_SUPPORTED : return "image format not supported";
-	case CL_INVALID_WORK_DIMENSION : return "invalid work dimension";
-	default :
+
+		case CL_SUCCESS :
+		return "no error";
+
+		case CL_INVALID_PLATFORM :
+		return "invalid platform";
+
+		case CL_INVALID_KERNEL :
+		return "invalid kernel";
+
+		case CL_INVALID_ARG_INDEX :
+		return "invalid argument index";
+
+		case CL_INVALID_ARG_VALUE :
+		return "invalid argument value";
+
+		case CL_INVALID_MEM_OBJECT :
+		return "invalid memory object";
+
+		case CL_INVALID_SAMPLER :
+		return "invalid sampler";
+
+		case CL_INVALID_ARG_SIZE :
+		return "invalid argument size";
+
+		case CL_INVALID_COMMAND_QUEUE :
+		return "invalid command queue";
+
+		case CL_INVALID_CONTEXT :
+		return "invalid context";
+
+		case CL_INVALID_VALUE :
+		return "invalid value";
+
+		case CL_INVALID_EVENT_WAIT_LIST :
+		return "invalid wait list";
+
+		case CL_MAP_FAILURE :
+		return "map failure";
+
+		case CL_MEM_OBJECT_ALLOCATION_FAILURE :
+		return "object allocation failure";
+
+		case CL_OUT_OF_HOST_MEMORY :
+		return "out of host memory";
+
+		case CL_OUT_OF_RESOURCES :
+		return "out of resources";
+
+		case CL_INVALID_KERNEL_NAME :
+		return "invalid kernel name";
+
+		case CL_INVALID_KERNEL_ARGS :
+		return "invalid kernel arguments";
+
+		case CL_INVALID_WORK_GROUP_SIZE :
+		return "invalid work group size";
+
+		case CL_IMAGE_FORMAT_NOT_SUPPORTED :
+		return "image format not supported";
+
+		case CL_INVALID_WORK_DIMENSION :
+		return "invalid work dimension";
+
+		default :
 		return "unknown error";
 	}
 }
diff --git a/src/compare_hkl.c b/src/compare_hkl.c
index 5846682f..b926c3ae 100644
--- a/src/compare_hkl.c
+++ b/src/compare_hkl.c
@@ -331,49 +331,51 @@ int main(int argc, char *argv[])
 	{
 
 		switch (c) {
-		case 'h' :
+
+			case 'h' :
 			show_help(argv[0]);
 			return 0;
 
-		case 'o' :
+			case 'o' :
 			ratiofile = strdup(optarg);
 			break;
 
-		case 'y' :
+			case 'y' :
 			sym_str = strdup(optarg);
 			break;
 
-		case 'p' :
+			case 'p' :
 			pdb = strdup(optarg);
 			break;
 
-		case 'u' :
+			case 'u' :
 			config_unity = 1;
 			break;
 
-		case 0 :
+			case 0 :
 			break;
 
-		case 2 :
+			case 2 :
 			if ( sscanf(optarg, "%e", &rmin_fix) != 1 ) {
 				ERROR("Invalid value for --rmin\n");
 				return 1;
 			}
 			break;
 
-		case 3 :
+			case 3 :
 			if ( sscanf(optarg, "%e", &rmax_fix) != 1 ) {
 				ERROR("Invalid value for --rmax\n");
 				return 1;
 			}
 			break;
 
-		case 4 :
+			case 4 :
 			config_shells = get_r_shell(optarg);
 			break;
 
-		default :
+			default :
 			return 1;
+
 		}
 
 	}
diff --git a/src/get_hkl.c b/src/get_hkl.c
index 9f86f0f7..de5d74de 100644
--- a/src/get_hkl.c
+++ b/src/get_hkl.c
@@ -391,44 +391,46 @@ int main(int argc, char *argv[])
 	                        longopts, NULL)) != -1) {
 
 		switch (c) {
-		case 'h' :
+
+			case 'h' :
 			show_help(argv[0]);
 			return 0;
 
-		case 't' :
+			case 't' :
 			template = strdup(optarg);
 			break;
 
-		case 'o' :
+			case 'o' :
 			output = strdup(optarg);
 			break;
 
-		case 'i' :
+			case 'i' :
 			input_file = strdup(optarg);
 			break;
 
-		case 'y' :
+			case 'y' :
 			mero_str = strdup(optarg);
 			break;
 
-		case 'w' :
+			case 'w' :
 			holo_str = strdup(optarg);
 			break;
 
-		case 'e' :
+			case 'e' :
 			expand_str = strdup(optarg);
 			break;
 
-		case 2 :
+			case 2 :
 			adu_per_photon = strtof(optarg, NULL);
 			have_adu_per_photon = 1;
 			break;
 
-		case 0 :
+			case 0 :
 			break;
 
-		default :
+			default :
 			return 1;
+
 		}
 
 	}
diff --git a/src/hdfsee.c b/src/hdfsee.c
index 22302ec8..613572a2 100644
--- a/src/hdfsee.c
+++ b/src/hdfsee.c
@@ -151,15 +151,16 @@ int main(int argc, char *argv[])
 		char *test;
 
 		switch (c) {
-		case 'h' :
+
+			case 'h' :
 			show_help(argv[0]);
 			return 0;
 
-		case 'p' :
+			case 'p' :
 			peaks = strdup(optarg);
 			break;
 
-		case 'i' :
+			case 'i' :
 			boost = atoi(optarg);
 			if ( boost < 1 ) {
 				ERROR("Intensity boost must be a positive"
@@ -168,7 +169,7 @@ int main(int argc, char *argv[])
 			}
 			break;
 
-		case 'b' :
+			case 'b' :
 			binning = atoi(optarg);
 			if ( binning < 1 ) {
 				ERROR("Binning must be a positive integer.\n");
@@ -176,19 +177,19 @@ int main(int argc, char *argv[])
 			}
 			break;
 
-		case 'c' :
+			case 'c' :
 			cscale = strdup(optarg);
 			break;
 
-		case 'e' :
+			case 'e' :
 			element = strdup(optarg);
 			break;
 
-		case 'g' :
+			case 'g' :
 			geometry = strdup(optarg);
 			break;
 
-		case 2 :
+			case 2 :
 			ring_size = strtod(optarg, &test);
 			if ( test == optarg ) {
 				ERROR("Ring size must be numerical.\n");
@@ -196,7 +197,7 @@ int main(int argc, char *argv[])
 			}
 			break;
 
-		case 'r' :
+			case 'r' :
 			config_showrings = 1;
 			reslist = strdup(optarg);
 			int nchar = strlen(reslist);
@@ -219,10 +220,10 @@ int main(int argc, char *argv[])
 			}
 			break;
 
-		case 0 :
+			case 0 :
 			break;
 
-		default :
+			default :
 			return 1;
 		}
 
diff --git a/src/partial_sim.c b/src/partial_sim.c
index 31822eca..9e054675 100644
--- a/src/partial_sim.c
+++ b/src/partial_sim.c
@@ -341,47 +341,48 @@ int main(int argc, char *argv[])
 	                        longopts, NULL)) != -1)
 	{
 		switch (c) {
-		case 'h' :
+
+			case 'h' :
 			show_help(argv[0]);
 			return 0;
 
-		case 'o' :
+			case 'o' :
 			output_file = strdup(optarg);
 			break;
 
-		case 'i' :
+			case 'i' :
 			input_file = strdup(optarg);
 			break;
 
-		case 'b' :
+			case 'b' :
 			beamfile = strdup(optarg);
 			break;
 
-		case 'p' :
+			case 'p' :
 			cellfile = strdup(optarg);
 			break;
 
-		case 'g' :
+			case 'g' :
 			geomfile = strdup(optarg);
 			break;
 
-		case 'y' :
+			case 'y' :
 			sym_str = strdup(optarg);
 			break;
 
-		case 'n' :
+			case 'n' :
 			n = atoi(optarg);
 			break;
 
-		case 'r' :
+			case 'r' :
 			save_file = strdup(optarg);
 			break;
 
-		case 'j' :
+			case 'j' :
 			n_threads = atoi(optarg);
 			break;
 
-		case 'c' :
+			case 'c' :
 			cnoise = strtod(optarg, &rval);
 			if ( *rval != '\0' ) {
 				ERROR("Invalid cell noise value.\n");
@@ -389,15 +390,16 @@ int main(int argc, char *argv[])
 			}
 			break;
 
-		case 2 :
+			case 2 :
 			phist_file = strdup(optarg);
 			break;
 
-		case 0 :
+			case 0 :
 			break;
 
-		default :
+			default :
 			return 1;
+
 		}
 	}
 
diff --git a/src/partialator.c b/src/partialator.c
index 91f2ff99..4fa8c2bd 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -325,35 +325,36 @@ int main(int argc, char *argv[])
 	{
 
 		switch (c) {
-		case 'h' :
+
+			case 'h' :
 			show_help(argv[0]);
 			return 0;
 
-		case 'i' :
+			case 'i' :
 			infile = strdup(optarg);
 			break;
 
-		case 'g' :
+			case 'g' :
 			geomfile = strdup(optarg);
 			break;
 
-		case 'j' :
+			case 'j' :
 			nthreads = atoi(optarg);
 			break;
 
-		case 'y' :
+			case 'y' :
 			sym_str = strdup(optarg);
 			break;
 
-		case 'o' :
+			case 'o' :
 			outfile = strdup(optarg);
 			break;
 
-		case 'n' :
+			case 'n' :
 			n_iter = atoi(optarg);
 			break;
 
-		case 'b' :
+			case 'b' :
 			beam = get_beam_parameters(optarg);
 			if ( beam == NULL ) {
 				ERROR("Failed to load beam parameters"
@@ -362,15 +363,16 @@ int main(int argc, char *argv[])
 			}
 			break;
 
-		case 'r' :
+			case 'r' :
 			reference_file = strdup(optarg);
 			break;
 
-		case 0 :
+			case 0 :
 			break;
 
-		default :
+			default :
 			return 1;
+
 		}
 
 	}
diff --git a/src/pattern_sim.c b/src/pattern_sim.c
index c207e0dc..03b009b4 100644
--- a/src/pattern_sim.c
+++ b/src/pattern_sim.c
@@ -294,15 +294,16 @@ int main(int argc, char *argv[])
 	                        longopts, NULL)) != -1) {
 
 		switch (c) {
-		case 'h' :
+
+			case 'h' :
 			show_help(argv[0]);
 			return 0;
 
-		case 'r' :
+			case 'r' :
 			config_randomquat = 1;
 			break;
 
-		case 'n' :
+			case 'n' :
 			n_images = strtol(optarg, &rval, 10);
 			if ( *rval != '\0' ) {
 				ERROR("Invalid number of images.\n");
@@ -310,43 +311,43 @@ int main(int argc, char *argv[])
 			}
 			break;
 
-		case 'i' :
+			case 'i' :
 			intfile = strdup(optarg);
 			break;
 
-		case 't' :
+			case 't' :
 			grad_str = strdup(optarg);
 			break;
 
-		case 'p' :
+			case 'p' :
 			filename = strdup(optarg);
 			break;
 
-		case 'o' :
+			case 'o' :
 			outfile = strdup(optarg);
 			break;
 
-		case 'w' :
+			case 'w' :
 			powder_fn = strdup(optarg);
 			break;
 
-		case 'g' :
+			case 'g' :
 			geometry = strdup(optarg);
 			break;
 
-		case 'b' :
+			case 'b' :
 			beamfile = strdup(optarg);
 			break;
 
-		case 'y' :
+			case 'y' :
 			sym_str = strdup(optarg);
 			break;
 
-		case 2 :
+			case 2 :
 			gpu_dev = atoi(optarg);
 			break;
 
-		case 3 :
+			case 3 :
 			min_size = strtod(optarg, &rval);
 			if ( *rval != '\0' ) {
 				ERROR("Invalid minimum size.\n");
@@ -355,7 +356,7 @@ int main(int argc, char *argv[])
 			random_size++;
 			break;
 
-		case 4 :
+			case 4 :
 			max_size = strtod(optarg, &rval);
 			if ( *rval != '\0' ) {
 				ERROR("Invalid maximum size.\n");
@@ -364,11 +365,12 @@ int main(int argc, char *argv[])
 			random_size++;
 			break;
 
-		case 0 :
+			case 0 :
 			break;
 
-		default :
+			default :
 			return 1;
+
 		}
 
 	}
diff --git a/src/post-refinement.c b/src/post-refinement.c
index cf7b2576..78c47d07 100644
--- a/src/post-refinement.c
+++ b/src/post-refinement.c
@@ -241,7 +241,7 @@ static void apply_shift(struct image *image, int k, double shift)
 {
 	switch ( k ) {
 
-	case REF_DIV :
+		case REF_DIV :
 		if ( isnan(shift) ) {
 			ERROR("NaN divergence shift\n");
 		} else {
@@ -250,23 +250,23 @@ static void apply_shift(struct image *image, int k, double shift)
 		}
 		break;
 
-	case REF_R :
+		case REF_R :
 		image->profile_radius += shift;
 		break;
 
-	case REF_ASX :
-	case REF_ASY :
-	case REF_ASZ :
-	case REF_BSX :
-	case REF_BSY :
-	case REF_BSZ :
-	case REF_CSX :
-	case REF_CSY :
-	case REF_CSZ :
+		case REF_ASX :
+		case REF_ASY :
+		case REF_ASZ :
+		case REF_BSX :
+		case REF_BSY :
+		case REF_BSZ :
+		case REF_CSX :
+		case REF_CSY :
+		case REF_CSZ :
 		apply_cell_shift(image->indexed_cell, k, shift);
 		break;
 
-	default :
+		default :
 		ERROR("No shift defined for parameter %i\n", k);
 		abort();
 
diff --git a/src/powder_plot.c b/src/powder_plot.c
index 3f49695a..049b9c0e 100644
--- a/src/powder_plot.c
+++ b/src/powder_plot.c
@@ -775,51 +775,51 @@ int main(int argc, char *argv[])
 
 		switch (c) {
 
-		case 'h' :
+			case 'h' :
 			show_help(argv[0]);
 			return 0;
 
-		case 'i' :
+			case 'i' :
 			filename = strdup(optarg);
 			break;
 
-		case 'o' :
+			case 'o' :
 			output = strdup(optarg);
 			break;
 
-		case 'g' :
+			case 'g' :
 			geometry = strdup(optarg);
 			break;
 
-		case 'b' :
+			case 'b' :
 			beamf = strdup(optarg);
 			break;
 
-		case 'p' :
+			case 'p' :
 			pdb = strdup(optarg);
 			break;
 
-		case 'y' :
+			case 'y' :
 			sym_str = strdup(optarg);
 			break;
 
-		case 's' :
+			case 's' :
 			hist_info.histsize = atoi(optarg);
 			break;
 
-		case 'e' :
+			case 'e' :
 			element = strdup(optarg);
 			break;
 
-		case 1 :
+			case 1 :
 			hist_info.q_max = atof(optarg);
 			break;
 
-		case 2 :
+			case 2 :
 			hist_info.q_min = atof(optarg);
 			break;
 
-		case 3 :
+			case 3 :
 			if (strcmp(optarg, "linear") == 0 ) {
 				hist_info.spacing = LINEAR;
 			} else if (strcmp(optarg, "wilson") == 0 ) {
@@ -832,14 +832,14 @@ int main(int argc, char *argv[])
 			}
 			break;
 
-		case 'd' :
+			case 'd' :
 			datatype = strdup(optarg);
 			break;
 
-		case 0 :
+			case 0 :
 			break;
 
-		default :
+			default :
 			return 1;
 		}
 
@@ -1096,45 +1096,50 @@ int main(int argc, char *argv[])
 	}
 
 	/* Process reflections based on file type and data type */
-	switch (file_type) {
-	case FILE_H5 :
+	switch ( file_type ) {
+		case FILE_H5 :
 		n_patterns++;
 		n_peaks = process_h5(&image, &hist_info, histdata);
 		free(image.data);
 		break;
 
-	case FILE_HKL :
+		case FILE_HKL :
 		n_patterns++; //inc number of patterns used
 		n_peaks = process_hkl(&image, sym, cell, &hist_info, histdata,
                                       q_scaling, use_redundancy);
 		break;
 
-	case FILE_STREAM :
-		switch (data_type) {
-		case PLOT_REFL :
+		case FILE_STREAM :
+		switch ( data_type ) {
+
+			case PLOT_REFL :
 			n_peaks = process_stream_reflection(fh, &image,
 			             &hist_info, histdata, &n_patterns);
 			break;
-		case PLOT_HKL :
+
+			case PLOT_HKL :
 			n_peaks = process_stream_hkl(fh, &image, &hist_info,
+
 				     histdata, cell, &n_patterns);
 			break;
-		case PLOT_PEAKS :
+			case PLOT_PEAKS :
 			n_peaks = process_stream_peaks(fh, &image, &hist_info,
 			             histdata, &n_patterns, only_indexed);
 			break;
-		case PLOT_H5 :
+
+			case PLOT_H5 :
 			n_peaks =  process_stream_h5(fh, &image, &hist_info,
 			             histdata, config_satcorr, only_indexed,
 			             &n_patterns, element);
 			break;
-		default :
+
+			default :
 			break;
 		}
 		fclose(fh);
 		break;
 
-	default :
+		default :
 		break;
 
 	}
diff --git a/src/render_hkl.c b/src/render_hkl.c
index a63cbad3..a01e7609 100644
--- a/src/render_hkl.c
+++ b/src/render_hkl.c
@@ -118,23 +118,29 @@ static double max_value(RefList *list, int wght, const SymOpList *sym)
 		n = num_equivs(sym, m);
 
 		switch ( wght ) {
-		case WGHT_I :
+
+			case WGHT_I :
 			val = get_intensity(refl);
 			break;
-		case WGHT_SQRTI :
+
+			case WGHT_SQRTI :
 			val = get_intensity(refl);
 			val = (val>0.0) ? sqrt(val) : 0.0;
 			break;
-		case WGHT_COUNTS :
+
+			case WGHT_COUNTS :
 			val = get_redundancy(refl);
 			val /= (double)n;
 			break;
-		case WGHT_RAWCOUNTS :
+
+			case WGHT_RAWCOUNTS :
 			val = get_redundancy(refl);
 			break;
-		default :
+
+			default :
 			ERROR("Invalid weighting.\n");
 			abort();
+
 		}
 
 		if ( val > max ) max = val;
@@ -192,23 +198,29 @@ static void draw_circles(double xh, double xk, double xl,
 			yi = (h*yh + k*yk + l*yl) / ny;
 
 			switch ( wght) {
-			case WGHT_I :
+
+				case WGHT_I :
 				val = get_intensity(refl);
 				break;
-			case WGHT_SQRTI :
+
+				case WGHT_SQRTI :
 				val = get_intensity(refl);
 				val = (val>0.0) ? sqrt(val) : 0.0;
 				break;
-			case WGHT_COUNTS :
+
+				case WGHT_COUNTS :
 				val = get_redundancy(refl);
 				val /= (double)n;
 				break;
-			case WGHT_RAWCOUNTS :
+
+				case WGHT_RAWCOUNTS :
 				val = get_redundancy(refl);
 				break;
-			default :
+
+				default :
 				ERROR("Invalid weighting.\n");
 				abort();
+
 			}
 
 			/* Absolute location in image based on 2D basis */
@@ -621,43 +633,44 @@ int main(int argc, char *argv[])
 	                        longopts, NULL)) != -1) {
 
 		switch (c) {
-		case 'h' :
+
+			case 'h' :
 			show_help(argv[0]);
 			return 0;
 
-		case 'p' :
+			case 'p' :
 			pdb = strdup(optarg);
 			break;
 
-		case 'b' :
+			case 'b' :
 			boost = atof(optarg);
 			break;
 
-		case 'y' :
+			case 'y' :
 			sym_str = strdup(optarg);
 			break;
 
-		case 'w' :
+			case 'w' :
 			weighting = strdup(optarg);
 			break;
 
-		case 'c' :
+			case 'c' :
 			cscale = strdup(optarg);
 			break;
 
-		case 'd' :
+			case 'd' :
 			down = strdup(optarg);
 			break;
 
-		case 'r' :
+			case 'r' :
 			right = strdup(optarg);
 			break;
 
-		case 'o' :
+			case 'o' :
 			outfile = strdup(optarg);
 			break;
 
-		case 2 :
+			case 2 :
 			errno = 0;
 			scale_top = strtod(optarg, &endptr);
 			if ( !( (optarg[0] != '\0') && (endptr[0] == '\0') )
@@ -672,11 +685,12 @@ int main(int argc, char *argv[])
 			}
 			break;
 
-		case 0 :
+			case 0 :
 			break;
 
-		default :
+			default :
 			return 1;
+
 		}
 
 	}
author	Thomas White <taw@physics.org>	2012-05-31 13:48:42 +0200
committer	Thomas White <taw@physics.org>	2012-05-31 13:48:42 +0200
commit	13770d8553f9696c1c4c0c56703717524c028d86 (patch)
tree	23c9f11f0407207ad24a8f7a4f6c72d52d0e7822
parent	6ff1bbbd0deeac54175fc862a6e1b53374ae6306 (diff)
parent	b6e0b7972e3dbdace0034d439b992faf3ac8c454 (diff)