[mmdb] 01/08: Imported Upstream version 2.0.5
Frédéric-Emmanuel Picca
picca at moszumanska.debian.org
Tue Aug 16 11:24:54 UTC 2016
This is an automated email from the git hooks/post-receive script.
picca pushed a commit to branch master
in repository mmdb.
commit 855a8bf20ea3712eed7b73183921bcd2510a3ec1
Author: Picca Frédéric-Emmanuel <picca at debian.org>
Date: Tue Aug 16 09:21:51 2016 +0200
Imported Upstream version 2.0.5
---
Makefile.in | 63 ++++--
aclocal.m4 | 180 ++++++++++++---
build-aux/ar-lib | 2 +-
build-aux/compile | 347 +++++++++++++++++++++++++++++
build-aux/config.guess | 201 +++--------------
build-aux/config.sub | 53 +++--
build-aux/depcomp | 531 +++++++++++++++++++++++++++++---------------
build-aux/install-sh | 385 +++++++++++++++-----------------
build-aux/ltmain.sh | 0
build-aux/missing | 461 +++++++++++++-------------------------
config.h.in | 0
configure | 383 +++++++++++++++++++++++---------
configure.ac | 2 +-
m4/libtool.m4 | 277 ++++++++++++++++++-----
m4/ltoptions.m4 | 19 +-
m4/ltsugar.m4 | 0
m4/ltversion.m4 | 0
m4/lt~obsolete.m4 | 0
mmdb2/hybrid_36.cpp | 18 +-
mmdb2/hybrid_36.h | 23 ++
mmdb2/mmdb_atom.cpp | 185 ++++++++++++---
mmdb2/mmdb_atom.h | 14 +-
mmdb2/mmdb_chain.cpp | 76 ++++---
mmdb2/mmdb_coormngr.cpp | 155 +++++++++----
mmdb2/mmdb_coormngr.h | 70 ++++--
mmdb2/mmdb_defs.h | 8 +-
mmdb2/mmdb_io_file.cpp | 2 +-
mmdb2/mmdb_io_file.h | 1 +
mmdb2/mmdb_math_bfgsmin.cpp | 3 +-
mmdb2/mmdb_mattype.h | 6 +-
mmdb2/mmdb_mmcif_.cpp | 10 +-
mmdb2/mmdb_model.cpp | 106 ++++++---
mmdb2/mmdb_model.h | 7 +-
mmdb2/mmdb_root.cpp | 179 +++++++++------
mmdb2/mmdb_root.h | 12 +-
mmdb2/mmdb_rwbrook.cpp | 45 ++++
mmdb2/mmdb_rwbrook.h | 16 ++
mmdb2/mmdb_selmngr.cpp | 50 +++--
mmdb2/mmdb_selmngr.h | 2 +-
mmdb2/mmdb_tables.cpp | 32 ++-
mmdb2/mmdb_tables.h | 9 +-
mmdb2/mmdb_title.h | 2 +-
mmdb2/mmdb_utils.cpp | 5 +-
mmdb2/mmdb_utils.h | 2 +-
44 files changed, 2541 insertions(+), 1401 deletions(-)
diff --git a/Makefile.in b/Makefile.in
index bb9dde5..8691737 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -1,7 +1,7 @@
-# Makefile.in generated by automake 1.13.4 from Makefile.am.
+# Makefile.in generated by automake 1.15 from Makefile.am.
# @configure_input@
-# Copyright (C) 1994-2013 Free Software Foundation, Inc.
+# Copyright (C) 1994-2014 Free Software Foundation, Inc.
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -17,7 +17,17 @@
VPATH = @srcdir@
-am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+am__is_gnu_make = { \
+ if test -z '$(MAKELEVEL)'; then \
+ false; \
+ elif test -n '$(MAKE_HOST)'; then \
+ true; \
+ elif test -n '$(MAKE_VERSION)' && test -n '$(CURDIR)'; then \
+ true; \
+ else \
+ false; \
+ fi; \
+}
am__make_running_with_option = \
case $${target_option-} in \
?) ;; \
@@ -81,19 +91,6 @@ POST_UNINSTALL = :
build_triplet = @build@
host_triplet = @host@
subdir = .
-DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
- $(top_srcdir)/configure $(am__configure_deps) \
- $(srcdir)/config.h.in $(srcdir)/mmdb2.pc.in \
- $(top_srcdir)/build-aux/depcomp $(pkginclude_HEADERS) AUTHORS \
- COPYING COPYING.LESSER INSTALL README build-aux/ar-lib \
- build-aux/config.guess build-aux/config.sub build-aux/depcomp \
- build-aux/install-sh build-aux/missing build-aux/ltmain.sh \
- $(top_srcdir)/build-aux/ar-lib \
- $(top_srcdir)/build-aux/config.guess \
- $(top_srcdir)/build-aux/config.sub \
- $(top_srcdir)/build-aux/install-sh \
- $(top_srcdir)/build-aux/ltmain.sh \
- $(top_srcdir)/build-aux/missing
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/m4/libtool.m4 \
$(top_srcdir)/m4/ltoptions.m4 $(top_srcdir)/m4/ltsugar.m4 \
@@ -101,6 +98,8 @@ am__aclocal_m4_deps = $(top_srcdir)/m4/libtool.m4 \
$(top_srcdir)/configure.ac
am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
$(ACLOCAL_M4)
+DIST_COMMON = $(srcdir)/Makefile.am $(top_srcdir)/configure \
+ $(am__configure_deps) $(pkginclude_HEADERS) $(am__DIST_COMMON)
am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \
configure.lineno config.status.lineno
mkinstalldirs = $(install_sh) -d
@@ -228,6 +227,18 @@ ETAGS = etags
CTAGS = ctags
CSCOPE = cscope
AM_RECURSIVE_TARGETS = cscope
+am__DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/config.h.in \
+ $(srcdir)/mmdb2.pc.in $(top_srcdir)/build-aux/ar-lib \
+ $(top_srcdir)/build-aux/compile \
+ $(top_srcdir)/build-aux/config.guess \
+ $(top_srcdir)/build-aux/config.sub \
+ $(top_srcdir)/build-aux/depcomp \
+ $(top_srcdir)/build-aux/install-sh \
+ $(top_srcdir)/build-aux/ltmain.sh \
+ $(top_srcdir)/build-aux/missing AUTHORS COPYING COPYING.LESSER \
+ INSTALL README build-aux/ar-lib build-aux/compile \
+ build-aux/config.guess build-aux/config.sub build-aux/depcomp \
+ build-aux/install-sh build-aux/ltmain.sh build-aux/missing
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
distdir = $(PACKAGE)-$(VERSION)
top_distdir = $(distdir)
@@ -413,7 +424,6 @@ $(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(srcdir)/Makefile.am $(am__confi
echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign Makefile'; \
$(am__cd) $(top_srcdir) && \
$(AUTOMAKE) --foreign Makefile
-.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
*config.status*) \
@@ -434,8 +444,8 @@ $(ACLOCAL_M4): @MAINTAINER_MODE_TRUE@ $(am__aclocal_m4_deps)
$(am__aclocal_m4_deps):
config.h: stamp-h1
- @if test ! -f $@; then rm -f stamp-h1; else :; fi
- @if test ! -f $@; then $(MAKE) $(AM_MAKEFLAGS) stamp-h1; else :; fi
+ @test -f $@ || rm -f stamp-h1
+ @test -f $@ || $(MAKE) $(AM_MAKEFLAGS) stamp-h1
stamp-h1: $(srcdir)/config.h.in $(top_builddir)/config.status
@rm -f stamp-h1
@@ -793,10 +803,16 @@ dist-xz: distdir
$(am__post_remove_distdir)
dist-tarZ: distdir
+ @echo WARNING: "Support for distribution archives compressed with" \
+ "legacy program 'compress' is deprecated." >&2
+ @echo WARNING: "It will be removed altogether in Automake 2.0" >&2
tardir=$(distdir) && $(am__tar) | compress -c >$(distdir).tar.Z
$(am__post_remove_distdir)
dist-shar: distdir
+ @echo WARNING: "Support for shar distribution archives is" \
+ "deprecated." >&2
+ @echo WARNING: "It will be removed altogether in Automake 2.0" >&2
shar $(distdir) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).shar.gz
$(am__post_remove_distdir)
@@ -831,16 +847,17 @@ distcheck: dist
esac
chmod -R a-w $(distdir)
chmod u+w $(distdir)
- mkdir $(distdir)/_build $(distdir)/_inst
+ mkdir $(distdir)/_build $(distdir)/_build/sub $(distdir)/_inst
chmod a-w $(distdir)
test -d $(distdir)/_build || exit 0; \
dc_install_base=`$(am__cd) $(distdir)/_inst && pwd | sed -e 's,^[^:\\/]:[\\/],/,'` \
&& dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \
&& am__cwd=`pwd` \
- && $(am__cd) $(distdir)/_build \
- && ../configure --srcdir=.. --prefix="$$dc_install_base" \
+ && $(am__cd) $(distdir)/_build/sub \
+ && ../../configure \
$(AM_DISTCHECK_CONFIGURE_FLAGS) \
$(DISTCHECK_CONFIGURE_FLAGS) \
+ --srcdir=../.. --prefix="$$dc_install_base" \
&& $(MAKE) $(AM_MAKEFLAGS) \
&& $(MAKE) $(AM_MAKEFLAGS) dvi \
&& $(MAKE) $(AM_MAKEFLAGS) check \
@@ -1028,6 +1045,8 @@ uninstall-am: uninstall-libLTLIBRARIES uninstall-pkgconfigDATA \
uninstall-am uninstall-libLTLIBRARIES uninstall-pkgconfigDATA \
uninstall-pkgincludeHEADERS
+.PRECIOUS: Makefile
+
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
diff --git a/aclocal.m4 b/aclocal.m4
index 1efe2e1..e9f2cf8 100644
--- a/aclocal.m4
+++ b/aclocal.m4
@@ -1,6 +1,6 @@
-# generated automatically by aclocal 1.13.4 -*- Autoconf -*-
+# generated automatically by aclocal 1.15 -*- Autoconf -*-
-# Copyright (C) 1996-2013 Free Software Foundation, Inc.
+# Copyright (C) 1996-2014 Free Software Foundation, Inc.
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -20,7 +20,7 @@ You have another version of autoconf. It may work, but is not guaranteed to.
If you have problems, you may need to regenerate the build system entirely.
To do so, use the procedure documented by the package, typically 'autoreconf'.])])
-# Copyright (C) 2002-2013 Free Software Foundation, Inc.
+# Copyright (C) 2002-2014 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -32,10 +32,10 @@ To do so, use the procedure documented by the package, typically 'autoreconf'.])
# generated from the m4 files accompanying Automake X.Y.
# (This private macro should not be called outside this file.)
AC_DEFUN([AM_AUTOMAKE_VERSION],
-[am__api_version='1.13'
+[am__api_version='1.15'
dnl Some users find AM_AUTOMAKE_VERSION and mistake it for a way to
dnl require some minimum version. Point them to the right macro.
-m4_if([$1], [1.13.4], [],
+m4_if([$1], [1.15], [],
[AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl
])
@@ -51,12 +51,12 @@ m4_define([_AM_AUTOCONF_VERSION], [])
# Call AM_AUTOMAKE_VERSION and AM_AUTOMAKE_VERSION so they can be traced.
# This function is AC_REQUIREd by AM_INIT_AUTOMAKE.
AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION],
-[AM_AUTOMAKE_VERSION([1.13.4])dnl
+[AM_AUTOMAKE_VERSION([1.15])dnl
m4_ifndef([AC_AUTOCONF_VERSION],
[m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
_AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))])
-# Copyright (C) 2011-2013 Free Software Foundation, Inc.
+# Copyright (C) 2011-2014 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -76,7 +76,8 @@ AC_CHECK_TOOLS([AR], [ar lib "link -lib"], [false])
: ${AR=ar}
AC_CACHE_CHECK([the archiver ($AR) interface], [am_cv_ar_interface],
- [am_cv_ar_interface=ar
+ [AC_LANG_PUSH([C])
+ am_cv_ar_interface=ar
AC_COMPILE_IFELSE([AC_LANG_SOURCE([[int some_variable = 0;]])],
[am_ar_try='$AR cru libconftest.a conftest.$ac_objext >&AS_MESSAGE_LOG_FD'
AC_TRY_EVAL([am_ar_try])
@@ -93,7 +94,7 @@ AC_CACHE_CHECK([the archiver ($AR) interface], [am_cv_ar_interface],
fi
rm -f conftest.lib libconftest.a
])
- ])
+ AC_LANG_POP([C])])
case $am_cv_ar_interface in
ar)
@@ -117,7 +118,7 @@ AC_SUBST([AR])dnl
# AM_AUX_DIR_EXPAND -*- Autoconf -*-
-# Copyright (C) 2001-2013 Free Software Foundation, Inc.
+# Copyright (C) 2001-2014 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -162,15 +163,14 @@ AC_SUBST([AR])dnl
# configured tree to be moved without reconfiguration.
AC_DEFUN([AM_AUX_DIR_EXPAND],
-[dnl Rely on autoconf to set up CDPATH properly.
-AC_PREREQ([2.50])dnl
-# expand $ac_aux_dir to an absolute path
-am_aux_dir=`cd $ac_aux_dir && pwd`
+[AC_REQUIRE([AC_CONFIG_AUX_DIR_DEFAULT])dnl
+# Expand $ac_aux_dir to an absolute path.
+am_aux_dir=`cd "$ac_aux_dir" && pwd`
])
# AM_CONDITIONAL -*- Autoconf -*-
-# Copyright (C) 1997-2013 Free Software Foundation, Inc.
+# Copyright (C) 1997-2014 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -201,7 +201,7 @@ AC_CONFIG_COMMANDS_PRE(
Usually this means the macro was only invoked conditionally.]])
fi])])
-# Copyright (C) 1999-2013 Free Software Foundation, Inc.
+# Copyright (C) 1999-2014 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -392,7 +392,7 @@ _AM_SUBST_NOTMAKE([am__nodep])dnl
# Generate code to set up dependency tracking. -*- Autoconf -*-
-# Copyright (C) 1999-2013 Free Software Foundation, Inc.
+# Copyright (C) 1999-2014 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -468,7 +468,7 @@ AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS],
# Do all the work for Automake. -*- Autoconf -*-
-# Copyright (C) 1996-2013 Free Software Foundation, Inc.
+# Copyright (C) 1996-2014 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -477,6 +477,12 @@ AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS],
# This macro actually does too much. Some checks are only needed if
# your package does certain things. But this isn't really a big deal.
+dnl Redefine AC_PROG_CC to automatically invoke _AM_PROG_CC_C_O.
+m4_define([AC_PROG_CC],
+m4_defn([AC_PROG_CC])
+[_AM_PROG_CC_C_O
+])
+
# AM_INIT_AUTOMAKE(PACKAGE, VERSION, [NO-DEFINE])
# AM_INIT_AUTOMAKE([OPTIONS])
# -----------------------------------------------
@@ -552,8 +558,8 @@ AC_REQUIRE([AC_PROG_MKDIR_P])dnl
# <http://lists.gnu.org/archive/html/automake/2012-07/msg00001.html>
# <http://lists.gnu.org/archive/html/automake/2012-07/msg00014.html>
AC_SUBST([mkdir_p], ['$(MKDIR_P)'])
-# We need awk for the "check" target. The system "awk" is bad on
-# some platforms.
+# We need awk for the "check" target (and possibly the TAP driver). The
+# system "awk" is bad on some platforms.
AC_REQUIRE([AC_PROG_AWK])dnl
AC_REQUIRE([AC_PROG_MAKE_SET])dnl
AC_REQUIRE([AM_SET_LEADING_DOT])dnl
@@ -585,6 +591,51 @@ dnl macro is hooked onto _AC_COMPILER_EXEEXT early, see below.
AC_CONFIG_COMMANDS_PRE(dnl
[m4_provide_if([_AM_COMPILER_EXEEXT],
[AM_CONDITIONAL([am__EXEEXT], [test -n "$EXEEXT"])])])dnl
+
+# POSIX will say in a future version that running "rm -f" with no argument
+# is OK; and we want to be able to make that assumption in our Makefile
+# recipes. So use an aggressive probe to check that the usage we want is
+# actually supported "in the wild" to an acceptable degree.
+# See automake bug#10828.
+# To make any issue more visible, cause the running configure to be aborted
+# by default if the 'rm' program in use doesn't match our expectations; the
+# user can still override this though.
+if rm -f && rm -fr && rm -rf; then : OK; else
+ cat >&2 <<'END'
+Oops!
+
+Your 'rm' program seems unable to run without file operands specified
+on the command line, even when the '-f' option is present. This is contrary
+to the behaviour of most rm programs out there, and not conforming with
+the upcoming POSIX standard: <http://austingroupbugs.net/view.php?id=542>
+
+Please tell bug-automake at gnu.org about your system, including the value
+of your $PATH and any error possibly output before this message. This
+can help us improve future automake versions.
+
+END
+ if test x"$ACCEPT_INFERIOR_RM_PROGRAM" = x"yes"; then
+ echo 'Configuration will proceed anyway, since you have set the' >&2
+ echo 'ACCEPT_INFERIOR_RM_PROGRAM variable to "yes"' >&2
+ echo >&2
+ else
+ cat >&2 <<'END'
+Aborting the configuration process, to ensure you take notice of the issue.
+
+You can download and install GNU coreutils to get an 'rm' implementation
+that behaves properly: <http://www.gnu.org/software/coreutils/>.
+
+If you want to complete the configuration process using your problematic
+'rm' anyway, export the environment variable ACCEPT_INFERIOR_RM_PROGRAM
+to "yes", and re-run configure.
+
+END
+ AC_MSG_ERROR([Your 'rm' program is bad, sorry.])
+ fi
+fi
+dnl The trailing newline in this macro's definition is deliberate, for
+dnl backward compatibility and to allow trailing 'dnl'-style comments
+dnl after the AM_INIT_AUTOMAKE invocation. See automake bug#16841.
])
dnl Hook into '_AC_COMPILER_EXEEXT' early to learn its expansion. Do not
@@ -593,7 +644,6 @@ dnl mangled by Autoconf and run in a shell conditional statement.
m4_define([_AC_COMPILER_EXEEXT],
m4_defn([_AC_COMPILER_EXEEXT])[m4_provide([_AM_COMPILER_EXEEXT])])
-
# When config.status generates a header, we must update the stamp-h file.
# This file resides in the same directory as the config header
# that is generated. The stamp files are numbered to have different names.
@@ -615,7 +665,7 @@ for _am_header in $config_headers :; do
done
echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_count])
-# Copyright (C) 2001-2013 Free Software Foundation, Inc.
+# Copyright (C) 2001-2014 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -626,7 +676,7 @@ echo "timestamp for $_am_arg" >`AS_DIRNAME(["$_am_arg"])`/stamp-h[]$_am_stamp_co
# Define $install_sh.
AC_DEFUN([AM_PROG_INSTALL_SH],
[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
-if test x"${install_sh}" != xset; then
+if test x"${install_sh+set}" != xset; then
case $am_aux_dir in
*\ * | *\ *)
install_sh="\${SHELL} '$am_aux_dir/install-sh'" ;;
@@ -636,7 +686,7 @@ if test x"${install_sh}" != xset; then
fi
AC_SUBST([install_sh])])
-# Copyright (C) 2003-2013 Free Software Foundation, Inc.
+# Copyright (C) 2003-2014 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -658,7 +708,7 @@ AC_SUBST([am__leading_dot])])
# Add --enable-maintainer-mode option to configure. -*- Autoconf -*-
# From Jim Meyering
-# Copyright (C) 1996-2013 Free Software Foundation, Inc.
+# Copyright (C) 1996-2014 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -693,7 +743,7 @@ AC_MSG_CHECKING([whether to enable maintainer-specific portions of Makefiles])
# Check to see how 'make' treats includes. -*- Autoconf -*-
-# Copyright (C) 2001-2013 Free Software Foundation, Inc.
+# Copyright (C) 2001-2014 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -743,7 +793,7 @@ rm -f confinc confmf
# Fake the existence of programs that GNU maintainers use. -*- Autoconf -*-
-# Copyright (C) 1997-2013 Free Software Foundation, Inc.
+# Copyright (C) 1997-2014 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -782,7 +832,7 @@ fi
# Helper functions for option handling. -*- Autoconf -*-
-# Copyright (C) 2001-2013 Free Software Foundation, Inc.
+# Copyright (C) 2001-2014 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -811,9 +861,73 @@ AC_DEFUN([_AM_SET_OPTIONS],
AC_DEFUN([_AM_IF_OPTION],
[m4_ifset(_AM_MANGLE_OPTION([$1]), [$2], [$3])])
+# Copyright (C) 1999-2014 Free Software Foundation, Inc.
+#
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+
+# _AM_PROG_CC_C_O
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+# to automatically call this.
+AC_DEFUN([_AM_PROG_CC_C_O],
+[AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
+AC_REQUIRE_AUX_FILE([compile])dnl
+AC_LANG_PUSH([C])dnl
+AC_CACHE_CHECK(
+ [whether $CC understands -c and -o together],
+ [am_cv_prog_cc_c_o],
+ [AC_LANG_CONFTEST([AC_LANG_PROGRAM([])])
+ # Make sure it works both with $CC and with simple cc.
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+ # compilers refuse to overwrite an existing .o file with -o,
+ # though they will create one.
+ am_cv_prog_cc_c_o=yes
+ for am_i in 1 2; do
+ if AM_RUN_LOG([$CC -c conftest.$ac_ext -o conftest2.$ac_objext]) \
+ && test -f conftest2.$ac_objext; then
+ : OK
+ else
+ am_cv_prog_cc_c_o=no
+ break
+ fi
+ done
+ rm -f core conftest*
+ unset am_i])
+if test "$am_cv_prog_cc_c_o" != yes; then
+ # Losing compiler, so override with the script.
+ # FIXME: It is wrong to rewrite CC.
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+ # A longer-term fix would be to have automake use am__CC in this case,
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+# For backward compatibility.
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+# Copyright (C) 2001-2014 Free Software Foundation, Inc.
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+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
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+[{ echo "$as_me:$LINENO: $1" >&AS_MESSAGE_LOG_FD
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+ echo "$as_me:$LINENO: \$? = $ac_status" >&AS_MESSAGE_LOG_FD
+ (exit $ac_status); }])
+
# Check to make sure that the build environment is sane. -*- Autoconf -*-
-# Copyright (C) 1996-2013 Free Software Foundation, Inc.
+# Copyright (C) 1996-2014 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -894,7 +1008,7 @@ AC_CONFIG_COMMANDS_PRE(
rm -f conftest.file
])
-# Copyright (C) 2009-2013 Free Software Foundation, Inc.
+# Copyright (C) 2009-2014 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -954,7 +1068,7 @@ AC_SUBST([AM_BACKSLASH])dnl
_AM_SUBST_NOTMAKE([AM_BACKSLASH])dnl
])
-# Copyright (C) 2001-2013 Free Software Foundation, Inc.
+# Copyright (C) 2001-2014 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -982,7 +1096,7 @@ fi
INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
AC_SUBST([INSTALL_STRIP_PROGRAM])])
-# Copyright (C) 2006-2013 Free Software Foundation, Inc.
+# Copyright (C) 2006-2014 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
@@ -1001,7 +1115,7 @@ AC_DEFUN([AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE($@)])
# Check how to create a tarball. -*- Autoconf -*-
-# Copyright (C) 2004-2013 Free Software Foundation, Inc.
+# Copyright (C) 2004-2014 Free Software Foundation, Inc.
#
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
diff --git a/build-aux/ar-lib b/build-aux/ar-lib
index 67f5f36..463b9ec 100755
--- a/build-aux/ar-lib
+++ b/build-aux/ar-lib
@@ -4,7 +4,7 @@
me=ar-lib
scriptversion=2012-03-01.08; # UTC
-# Copyright (C) 2010-2012 Free Software Foundation, Inc.
+# Copyright (C) 2010-2014 Free Software Foundation, Inc.
# Written by Peter Rosin <peda at lysator.liu.se>.
#
# This program is free software; you can redistribute it and/or modify
diff --git a/build-aux/compile b/build-aux/compile
new file mode 100755
index 0000000..a85b723
--- /dev/null
+++ b/build-aux/compile
@@ -0,0 +1,347 @@
+#! /bin/sh
+# Wrapper for compilers which do not understand '-c -o'.
+
+scriptversion=2012-10-14.11; # UTC
+
+# Copyright (C) 1999-2014 Free Software Foundation, Inc.
+# Written by Tom Tromey <tromey at cygnus.com>.
+#
+# 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
+# the Free Software Foundation; either version 2, or (at your option)
+# any later version.
+#
+# This program 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 program. If not, see <http://www.gnu.org/licenses/>.
+
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+# This file is maintained in Automake, please report
+# bugs to <bug-automake at gnu.org> or send patches to
+# <automake-patches at gnu.org>.
+
+nl='
+'
+
+# We need space, tab and new line, in precisely that order. Quoting is
+# there to prevent tools from complaining about whitespace usage.
+IFS=" "" $nl"
+
+file_conv=
+
+# func_file_conv build_file lazy
+# Convert a $build file to $host form and store it in $file
+# Currently only supports Windows hosts. If the determined conversion
+# type is listed in (the comma separated) LAZY, no conversion will
+# take place.
+func_file_conv ()
+{
+ file=$1
+ case $file in
+ / | /[!/]*) # absolute file, and not a UNC file
+ if test -z "$file_conv"; then
+ # lazily determine how to convert abs files
+ case `uname -s` in
+ MINGW*)
+ file_conv=mingw
+ ;;
+ CYGWIN*)
+ file_conv=cygwin
+ ;;
+ *)
+ file_conv=wine
+ ;;
+ esac
+ fi
+ case $file_conv/,$2, in
+ *,$file_conv,*)
+ ;;
+ mingw/*)
+ file=`cmd //C echo "$file " | sed -e 's/"\(.*\) " *$/\1/'`
+ ;;
+ cygwin/*)
+ file=`cygpath -m "$file" || echo "$file"`
+ ;;
+ wine/*)
+ file=`winepath -w "$file" || echo "$file"`
+ ;;
+ esac
+ ;;
+ esac
+}
+
+# func_cl_dashL linkdir
+# Make cl look for libraries in LINKDIR
+func_cl_dashL ()
+{
+ func_file_conv "$1"
+ if test -z "$lib_path"; then
+ lib_path=$file
+ else
+ lib_path="$lib_path;$file"
+ fi
+ linker_opts="$linker_opts -LIBPATH:$file"
+}
+
+# func_cl_dashl library
+# Do a library search-path lookup for cl
+func_cl_dashl ()
+{
+ lib=$1
+ found=no
+ save_IFS=$IFS
+ IFS=';'
+ for dir in $lib_path $LIB
+ do
+ IFS=$save_IFS
+ if $shared && test -f "$dir/$lib.dll.lib"; then
+ found=yes
+ lib=$dir/$lib.dll.lib
+ break
+ fi
+ if test -f "$dir/$lib.lib"; then
+ found=yes
+ lib=$dir/$lib.lib
+ break
+ fi
+ if test -f "$dir/lib$lib.a"; then
+ found=yes
+ lib=$dir/lib$lib.a
+ break
+ fi
+ done
+ IFS=$save_IFS
+
+ if test "$found" != yes; then
+ lib=$lib.lib
+ fi
+}
+
+# func_cl_wrapper cl arg...
+# Adjust compile command to suit cl
+func_cl_wrapper ()
+{
+ # Assume a capable shell
+ lib_path=
+ shared=:
+ linker_opts=
+ for arg
+ do
+ if test -n "$eat"; then
+ eat=
+ else
+ case $1 in
+ -o)
+ # configure might choose to run compile as 'compile cc -o foo foo.c'.
+ eat=1
+ case $2 in
+ *.o | *.[oO][bB][jJ])
+ func_file_conv "$2"
+ set x "$@" -Fo"$file"
+ shift
+ ;;
+ *)
+ func_file_conv "$2"
+ set x "$@" -Fe"$file"
+ shift
+ ;;
+ esac
+ ;;
+ -I)
+ eat=1
+ func_file_conv "$2" mingw
+ set x "$@" -I"$file"
+ shift
+ ;;
+ -I*)
+ func_file_conv "${1#-I}" mingw
+ set x "$@" -I"$file"
+ shift
+ ;;
+ -l)
+ eat=1
+ func_cl_dashl "$2"
+ set x "$@" "$lib"
+ shift
+ ;;
+ -l*)
+ func_cl_dashl "${1#-l}"
+ set x "$@" "$lib"
+ shift
+ ;;
+ -L)
+ eat=1
+ func_cl_dashL "$2"
+ ;;
+ -L*)
+ func_cl_dashL "${1#-L}"
+ ;;
+ -static)
+ shared=false
+ ;;
+ -Wl,*)
+ arg=${1#-Wl,}
+ save_ifs="$IFS"; IFS=','
+ for flag in $arg; do
+ IFS="$save_ifs"
+ linker_opts="$linker_opts $flag"
+ done
+ IFS="$save_ifs"
+ ;;
+ -Xlinker)
+ eat=1
+ linker_opts="$linker_opts $2"
+ ;;
+ -*)
+ set x "$@" "$1"
+ shift
+ ;;
+ *.cc | *.CC | *.cxx | *.CXX | *.[cC]++)
+ func_file_conv "$1"
+ set x "$@" -Tp"$file"
+ shift
+ ;;
+ *.c | *.cpp | *.CPP | *.lib | *.LIB | *.Lib | *.OBJ | *.obj | *.[oO])
+ func_file_conv "$1" mingw
+ set x "$@" "$file"
+ shift
+ ;;
+ *)
+ set x "$@" "$1"
+ shift
+ ;;
+ esac
+ fi
+ shift
+ done
+ if test -n "$linker_opts"; then
+ linker_opts="-link$linker_opts"
+ fi
+ exec "$@" $linker_opts
+ exit 1
+}
+
+eat=
+
+case $1 in
+ '')
+ echo "$0: No command. Try '$0 --help' for more information." 1>&2
+ exit 1;
+ ;;
+ -h | --h*)
+ cat <<\EOF
+Usage: compile [--help] [--version] PROGRAM [ARGS]
+
+Wrapper for compilers which do not understand '-c -o'.
+Remove '-o dest.o' from ARGS, run PROGRAM with the remaining
+arguments, and rename the output as expected.
+
+If you are trying to build a whole package this is not the
+right script to run: please start by reading the file 'INSTALL'.
+
+Report bugs to <bug-automake at gnu.org>.
+EOF
+ exit $?
+ ;;
+ -v | --v*)
+ echo "compile $scriptversion"
+ exit $?
+ ;;
+ cl | *[/\\]cl | cl.exe | *[/\\]cl.exe )
+ func_cl_wrapper "$@" # Doesn't return...
+ ;;
+esac
+
+ofile=
+cfile=
+
+for arg
+do
+ if test -n "$eat"; then
+ eat=
+ else
+ case $1 in
+ -o)
+ # configure might choose to run compile as 'compile cc -o foo foo.c'.
+ # So we strip '-o arg' only if arg is an object.
+ eat=1
+ case $2 in
+ *.o | *.obj)
+ ofile=$2
+ ;;
+ *)
+ set x "$@" -o "$2"
+ shift
+ ;;
+ esac
+ ;;
+ *.c)
+ cfile=$1
+ set x "$@" "$1"
+ shift
+ ;;
+ *)
+ set x "$@" "$1"
+ shift
+ ;;
+ esac
+ fi
+ shift
+done
+
+if test -z "$ofile" || test -z "$cfile"; then
+ # If no '-o' option was seen then we might have been invoked from a
+ # pattern rule where we don't need one. That is ok -- this is a
+ # normal compilation that the losing compiler can handle. If no
+ # '.c' file was seen then we are probably linking. That is also
+ # ok.
+ exec "$@"
+fi
+
+# Name of file we expect compiler to create.
+cofile=`echo "$cfile" | sed 's|^.*[\\/]||; s|^[a-zA-Z]:||; s/\.c$/.o/'`
+
+# Create the lock directory.
+# Note: use '[/\\:.-]' here to ensure that we don't use the same name
+# that we are using for the .o file. Also, base the name on the expected
+# object file name, since that is what matters with a parallel build.
+lockdir=`echo "$cofile" | sed -e 's|[/\\:.-]|_|g'`.d
+while true; do
+ if mkdir "$lockdir" >/dev/null 2>&1; then
+ break
+ fi
+ sleep 1
+done
+# FIXME: race condition here if user kills between mkdir and trap.
+trap "rmdir '$lockdir'; exit 1" 1 2 15
+
+# Run the compile.
+"$@"
+ret=$?
+
+if test -f "$cofile"; then
+ test "$cofile" = "$ofile" || mv "$cofile" "$ofile"
+elif test -f "${cofile}bj"; then
+ test "${cofile}bj" = "$ofile" || mv "${cofile}bj" "$ofile"
+fi
+
+rmdir "$lockdir"
+exit $ret
+
+# Local Variables:
+# mode: shell-script
+# sh-indentation: 2
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
+# End:
diff --git a/build-aux/config.guess b/build-aux/config.guess
index b79252d..dbfb978 100755
--- a/build-aux/config.guess
+++ b/build-aux/config.guess
@@ -1,8 +1,8 @@
#! /bin/sh
# Attempt to guess a canonical system name.
-# Copyright 1992-2013 Free Software Foundation, Inc.
+# Copyright 1992-2015 Free Software Foundation, Inc.
-timestamp='2013-06-10'
+timestamp='2015-01-01'
# 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
@@ -24,12 +24,12 @@ timestamp='2013-06-10'
# program. This Exception is an additional permission under section 7
# of the GNU General Public License, version 3 ("GPLv3").
#
-# Originally written by Per Bothner.
+# Originally written by Per Bothner; maintained since 2000 by Ben Elliston.
#
# You can get the latest version of this script from:
# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD
#
-# Please send patches with a ChangeLog entry to config-patches at gnu.org.
+# Please send patches to <config-patches at gnu.org>.
me=`echo "$0" | sed -e 's,.*/,,'`
@@ -50,7 +50,7 @@ version="\
GNU config.guess ($timestamp)
Originally written by Per Bothner.
-Copyright 1992-2013 Free Software Foundation, Inc.
+Copyright 1992-2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
@@ -149,7 +149,7 @@ Linux|GNU|GNU/*)
LIBC=gnu
#endif
EOF
- eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^LIBC'`
+ eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^LIBC' | sed 's, ,,g'`
;;
esac
@@ -579,8 +579,9 @@ EOF
else
IBM_ARCH=powerpc
fi
- if [ -x /usr/bin/oslevel ] ; then
- IBM_REV=`/usr/bin/oslevel`
+ if [ -x /usr/bin/lslpp ] ; then
+ IBM_REV=`/usr/bin/lslpp -Lqc bos.rte.libc |
+ awk -F: '{ print $3 }' | sed s/[0-9]*$/0/`
else
IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE}
fi
@@ -826,7 +827,7 @@ EOF
*:MINGW*:*)
echo ${UNAME_MACHINE}-pc-mingw32
exit ;;
- i*:MSYS*:*)
+ *:MSYS*:*)
echo ${UNAME_MACHINE}-pc-msys
exit ;;
i*:windows32*:*)
@@ -969,10 +970,10 @@ EOF
eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^CPU'`
test x"${CPU}" != x && { echo "${CPU}-unknown-linux-${LIBC}"; exit; }
;;
- or1k:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+ openrisc*:Linux:*:*)
+ echo or1k-unknown-linux-${LIBC}
exit ;;
- or32:Linux:*:*)
+ or32:Linux:*:* | or1k*:Linux:*:*)
echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
exit ;;
padre:Linux:*:*)
@@ -1260,16 +1261,26 @@ EOF
if test "$UNAME_PROCESSOR" = unknown ; then
UNAME_PROCESSOR=powerpc
fi
- if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then
- if (echo '#ifdef __LP64__'; echo IS_64BIT_ARCH; echo '#endif') | \
- (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \
- grep IS_64BIT_ARCH >/dev/null
- then
- case $UNAME_PROCESSOR in
- i386) UNAME_PROCESSOR=x86_64 ;;
- powerpc) UNAME_PROCESSOR=powerpc64 ;;
- esac
+ if test `echo "$UNAME_RELEASE" | sed -e 's/\..*//'` -le 10 ; then
+ if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then
+ if (echo '#ifdef __LP64__'; echo IS_64BIT_ARCH; echo '#endif') | \
+ (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \
+ grep IS_64BIT_ARCH >/dev/null
+ then
+ case $UNAME_PROCESSOR in
+ i386) UNAME_PROCESSOR=x86_64 ;;
+ powerpc) UNAME_PROCESSOR=powerpc64 ;;
+ esac
+ fi
fi
+ elif test "$UNAME_PROCESSOR" = i386 ; then
+ # Avoid executing cc on OS X 10.9, as it ships with a stub
+ # that puts up a graphical alert prompting to install
+ # developer tools. Any system running Mac OS X 10.7 or
+ # later (Darwin 11 and later) is required to have a 64-bit
+ # processor. This is not true of the ARM version of Darwin
+ # that Apple uses in portable devices.
+ UNAME_PROCESSOR=x86_64
fi
echo ${UNAME_PROCESSOR}-apple-darwin${UNAME_RELEASE}
exit ;;
@@ -1361,154 +1372,6 @@ EOF
exit ;;
esac
-eval $set_cc_for_build
-cat >$dummy.c <<EOF
-#ifdef _SEQUENT_
-# include <sys/types.h>
-# include <sys/utsname.h>
-#endif
-main ()
-{
-#if defined (sony)
-#if defined (MIPSEB)
- /* BFD wants "bsd" instead of "newsos". Perhaps BFD should be changed,
- I don't know.... */
- printf ("mips-sony-bsd\n"); exit (0);
-#else
-#include <sys/param.h>
- printf ("m68k-sony-newsos%s\n",
-#ifdef NEWSOS4
- "4"
-#else
- ""
-#endif
- ); exit (0);
-#endif
-#endif
-
-#if defined (__arm) && defined (__acorn) && defined (__unix)
- printf ("arm-acorn-riscix\n"); exit (0);
-#endif
-
-#if defined (hp300) && !defined (hpux)
- printf ("m68k-hp-bsd\n"); exit (0);
-#endif
-
-#if defined (NeXT)
-#if !defined (__ARCHITECTURE__)
-#define __ARCHITECTURE__ "m68k"
-#endif
- int version;
- version=`(hostinfo | sed -n 's/.*NeXT Mach \([0-9]*\).*/\1/p') 2>/dev/null`;
- if (version < 4)
- printf ("%s-next-nextstep%d\n", __ARCHITECTURE__, version);
- else
- printf ("%s-next-openstep%d\n", __ARCHITECTURE__, version);
- exit (0);
-#endif
-
-#if defined (MULTIMAX) || defined (n16)
-#if defined (UMAXV)
- printf ("ns32k-encore-sysv\n"); exit (0);
-#else
-#if defined (CMU)
- printf ("ns32k-encore-mach\n"); exit (0);
-#else
- printf ("ns32k-encore-bsd\n"); exit (0);
-#endif
-#endif
-#endif
-
-#if defined (__386BSD__)
- printf ("i386-pc-bsd\n"); exit (0);
-#endif
-
-#if defined (sequent)
-#if defined (i386)
- printf ("i386-sequent-dynix\n"); exit (0);
-#endif
-#if defined (ns32000)
- printf ("ns32k-sequent-dynix\n"); exit (0);
-#endif
-#endif
-
-#if defined (_SEQUENT_)
- struct utsname un;
-
- uname(&un);
-
- if (strncmp(un.version, "V2", 2) == 0) {
- printf ("i386-sequent-ptx2\n"); exit (0);
- }
- if (strncmp(un.version, "V1", 2) == 0) { /* XXX is V1 correct? */
- printf ("i386-sequent-ptx1\n"); exit (0);
- }
- printf ("i386-sequent-ptx\n"); exit (0);
-
-#endif
-
-#if defined (vax)
-# if !defined (ultrix)
-# include <sys/param.h>
-# if defined (BSD)
-# if BSD == 43
- printf ("vax-dec-bsd4.3\n"); exit (0);
-# else
-# if BSD == 199006
- printf ("vax-dec-bsd4.3reno\n"); exit (0);
-# else
- printf ("vax-dec-bsd\n"); exit (0);
-# endif
-# endif
-# else
- printf ("vax-dec-bsd\n"); exit (0);
-# endif
-# else
- printf ("vax-dec-ultrix\n"); exit (0);
-# endif
-#endif
-
-#if defined (alliant) && defined (i860)
- printf ("i860-alliant-bsd\n"); exit (0);
-#endif
-
- exit (1);
-}
-EOF
-
-$CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null && SYSTEM_NAME=`$dummy` &&
- { echo "$SYSTEM_NAME"; exit; }
-
-# Apollos put the system type in the environment.
-
-test -d /usr/apollo && { echo ${ISP}-apollo-${SYSTYPE}; exit; }
-
-# Convex versions that predate uname can use getsysinfo(1)
-
-if [ -x /usr/convex/getsysinfo ]
-then
- case `getsysinfo -f cpu_type` in
- c1*)
- echo c1-convex-bsd
- exit ;;
- c2*)
- if getsysinfo -f scalar_acc
- then echo c32-convex-bsd
- else echo c2-convex-bsd
- fi
- exit ;;
- c34*)
- echo c34-convex-bsd
- exit ;;
- c38*)
- echo c38-convex-bsd
- exit ;;
- c4*)
- echo c4-convex-bsd
- exit ;;
- esac
-fi
-
cat >&2 <<EOF
$0: unable to guess system type
diff --git a/build-aux/config.sub b/build-aux/config.sub
index c765b34..6467c95 100755
--- a/build-aux/config.sub
+++ b/build-aux/config.sub
@@ -1,8 +1,8 @@
#! /bin/sh
# Configuration validation subroutine script.
-# Copyright 1992-2013 Free Software Foundation, Inc.
+# Copyright 1992-2015 Free Software Foundation, Inc.
-timestamp='2013-04-24'
+timestamp='2015-01-01'
# This file is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
@@ -25,7 +25,7 @@ timestamp='2013-04-24'
# of the GNU General Public License, version 3 ("GPLv3").
-# Please send patches with a ChangeLog entry to config-patches at gnu.org.
+# Please send patches to <config-patches at gnu.org>.
#
# Configuration subroutine to validate and canonicalize a configuration type.
# Supply the specified configuration type as an argument.
@@ -68,7 +68,7 @@ Report bugs and patches to <config-patches at gnu.org>."
version="\
GNU config.sub ($timestamp)
-Copyright 1992-2013 Free Software Foundation, Inc.
+Copyright 1992-2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
@@ -257,14 +257,15 @@ case $basic_machine in
| avr | avr32 \
| be32 | be64 \
| bfin \
- | c4x | clipper \
+ | c4x | c8051 | clipper \
| d10v | d30v | dlx | dsp16xx \
| epiphany \
- | fido | fr30 | frv \
+ | fido | fr30 | frv | ft32 \
| h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \
| hexagon \
| i370 | i860 | i960 | ia64 \
| ip2k | iq2000 \
+ | k1om \
| le32 | le64 \
| lm32 \
| m32c | m32r | m32rle | m68000 | m68k | m88k \
@@ -282,8 +283,10 @@ case $basic_machine in
| mips64vr5900 | mips64vr5900el \
| mipsisa32 | mipsisa32el \
| mipsisa32r2 | mipsisa32r2el \
+ | mipsisa32r6 | mipsisa32r6el \
| mipsisa64 | mipsisa64el \
| mipsisa64r2 | mipsisa64r2el \
+ | mipsisa64r6 | mipsisa64r6el \
| mipsisa64sb1 | mipsisa64sb1el \
| mipsisa64sr71k | mipsisa64sr71kel \
| mipsr5900 | mipsr5900el \
@@ -295,11 +298,11 @@ case $basic_machine in
| nds32 | nds32le | nds32be \
| nios | nios2 | nios2eb | nios2el \
| ns16k | ns32k \
- | open8 \
- | or1k | or32 \
+ | open8 | or1k | or1knd | or32 \
| pdp10 | pdp11 | pj | pjl \
| powerpc | powerpc64 | powerpc64le | powerpcle \
| pyramid \
+ | riscv32 | riscv64 \
| rl78 | rx \
| score \
| sh | sh[1234] | sh[24]a | sh[24]aeb | sh[23]e | sh[34]eb | sheb | shbe | shle | sh[1234]le | sh3ele \
@@ -310,6 +313,7 @@ case $basic_machine in
| tahoe | tic4x | tic54x | tic55x | tic6x | tic80 | tron \
| ubicom32 \
| v850 | v850e | v850e1 | v850e2 | v850es | v850e2v3 \
+ | visium \
| we32k \
| x86 | xc16x | xstormy16 | xtensa \
| z8k | z80)
@@ -324,7 +328,10 @@ case $basic_machine in
c6x)
basic_machine=tic6x-unknown
;;
- m6811 | m68hc11 | m6812 | m68hc12 | m68hcs12x | picochip)
+ leon|leon[3-9])
+ basic_machine=sparc-$basic_machine
+ ;;
+ m6811 | m68hc11 | m6812 | m68hc12 | m68hcs12x | nvptx | picochip)
basic_machine=$basic_machine-unknown
os=-none
;;
@@ -372,7 +379,7 @@ case $basic_machine in
| be32-* | be64-* \
| bfin-* | bs2000-* \
| c[123]* | c30-* | [cjt]90-* | c4x-* \
- | clipper-* | craynv-* | cydra-* \
+ | c8051-* | clipper-* | craynv-* | cydra-* \
| d10v-* | d30v-* | dlx-* \
| elxsi-* \
| f30[01]-* | f700-* | fido-* | fr30-* | frv-* | fx80-* \
@@ -381,6 +388,7 @@ case $basic_machine in
| hexagon-* \
| i*86-* | i860-* | i960-* | ia64-* \
| ip2k-* | iq2000-* \
+ | k1om-* \
| le32-* | le64-* \
| lm32-* \
| m32c-* | m32r-* | m32rle-* \
@@ -400,8 +408,10 @@ case $basic_machine in
| mips64vr5900-* | mips64vr5900el-* \
| mipsisa32-* | mipsisa32el-* \
| mipsisa32r2-* | mipsisa32r2el-* \
+ | mipsisa32r6-* | mipsisa32r6el-* \
| mipsisa64-* | mipsisa64el-* \
| mipsisa64r2-* | mipsisa64r2el-* \
+ | mipsisa64r6-* | mipsisa64r6el-* \
| mipsisa64sb1-* | mipsisa64sb1el-* \
| mipsisa64sr71k-* | mipsisa64sr71kel-* \
| mipsr5900-* | mipsr5900el-* \
@@ -413,6 +423,7 @@ case $basic_machine in
| nios-* | nios2-* | nios2eb-* | nios2el-* \
| none-* | np1-* | ns16k-* | ns32k-* \
| open8-* \
+ | or1k*-* \
| orion-* \
| pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \
| powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* \
@@ -430,6 +441,7 @@ case $basic_machine in
| ubicom32-* \
| v850-* | v850e-* | v850e1-* | v850es-* | v850e2-* | v850e2v3-* \
| vax-* \
+ | visium-* \
| we32k-* \
| x86-* | x86_64-* | xc16x-* | xps100-* \
| xstormy16-* | xtensa*-* \
@@ -767,6 +779,9 @@ case $basic_machine in
basic_machine=m68k-isi
os=-sysv
;;
+ leon-*|leon[3-9]-*)
+ basic_machine=sparc-`echo $basic_machine | sed 's/-.*//'`
+ ;;
m68knommu)
basic_machine=m68k-unknown
os=-linux
@@ -794,7 +809,7 @@ case $basic_machine in
os=-mingw64
;;
mingw32)
- basic_machine=i386-pc
+ basic_machine=i686-pc
os=-mingw32
;;
mingw32ce)
@@ -822,6 +837,10 @@ case $basic_machine in
basic_machine=powerpc-unknown
os=-morphos
;;
+ moxiebox)
+ basic_machine=moxie-unknown
+ os=-moxiebox
+ ;;
msdos)
basic_machine=i386-pc
os=-msdos
@@ -830,7 +849,7 @@ case $basic_machine in
basic_machine=`echo $basic_machine | sed -e 's/ms1-/mt-/'`
;;
msys)
- basic_machine=i386-pc
+ basic_machine=i686-pc
os=-msys
;;
mvs)
@@ -1367,14 +1386,14 @@ case $os in
| -cygwin* | -msys* | -pe* | -psos* | -moss* | -proelf* | -rtems* \
| -mingw32* | -mingw64* | -linux-gnu* | -linux-android* \
| -linux-newlib* | -linux-musl* | -linux-uclibc* \
- | -uxpv* | -beos* | -mpeix* | -udk* \
+ | -uxpv* | -beos* | -mpeix* | -udk* | -moxiebox* \
| -interix* | -uwin* | -mks* | -rhapsody* | -darwin* | -opened* \
| -openstep* | -oskit* | -conix* | -pw32* | -nonstopux* \
| -storm-chaos* | -tops10* | -tenex* | -tops20* | -its* \
| -os2* | -vos* | -palmos* | -uclinux* | -nucleus* \
| -morphos* | -superux* | -rtmk* | -rtmk-nova* | -windiss* \
| -powermax* | -dnix* | -nx6 | -nx7 | -sei* | -dragonfly* \
- | -skyos* | -haiku* | -rdos* | -toppers* | -drops* | -es*)
+ | -skyos* | -haiku* | -rdos* | -toppers* | -drops* | -es* | -tirtos*)
# Remember, each alternative MUST END IN *, to match a version number.
;;
-qnx*)
@@ -1546,6 +1565,9 @@ case $basic_machine in
c4x-* | tic4x-*)
os=-coff
;;
+ c8051-*)
+ os=-elf
+ ;;
hexagon-*)
os=-elf
;;
@@ -1589,9 +1611,6 @@ case $basic_machine in
mips*-*)
os=-elf
;;
- or1k-*)
- os=-elf
- ;;
or32-*)
os=-coff
;;
diff --git a/build-aux/depcomp b/build-aux/depcomp
index df8eea7..fc98710 100755
--- a/build-aux/depcomp
+++ b/build-aux/depcomp
@@ -1,10 +1,9 @@
#! /bin/sh
# depcomp - compile a program generating dependencies as side-effects
-scriptversion=2009-04-28.21; # UTC
+scriptversion=2013-05-30.07; # UTC
-# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007, 2009 Free
-# Software Foundation, Inc.
+# Copyright (C) 1999-2014 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
@@ -28,9 +27,9 @@ scriptversion=2009-04-28.21; # UTC
case $1 in
'')
- echo "$0: No command. Try \`$0 --help' for more information." 1>&2
- exit 1;
- ;;
+ echo "$0: No command. Try '$0 --help' for more information." 1>&2
+ exit 1;
+ ;;
-h | --h*)
cat <<\EOF
Usage: depcomp [--help] [--version] PROGRAM [ARGS]
@@ -40,11 +39,11 @@ as side-effects.
Environment variables:
depmode Dependency tracking mode.
- source Source file read by `PROGRAMS ARGS'.
- object Object file output by `PROGRAMS ARGS'.
+ source Source file read by 'PROGRAMS ARGS'.
+ object Object file output by 'PROGRAMS ARGS'.
DEPDIR directory where to store dependencies.
depfile Dependency file to output.
- tmpdepfile Temporary file to use when outputing dependencies.
+ tmpdepfile Temporary file to use when outputting dependencies.
libtool Whether libtool is used (yes/no).
Report bugs to <bug-automake at gnu.org>.
@@ -57,6 +56,66 @@ EOF
;;
esac
+# Get the directory component of the given path, and save it in the
+# global variables '$dir'. Note that this directory component will
+# be either empty or ending with a '/' character. This is deliberate.
+set_dir_from ()
+{
+ case $1 in
+ */*) dir=`echo "$1" | sed -e 's|/[^/]*$|/|'`;;
+ *) dir=;;
+ esac
+}
+
+# Get the suffix-stripped basename of the given path, and save it the
+# global variable '$base'.
+set_base_from ()
+{
+ base=`echo "$1" | sed -e 's|^.*/||' -e 's/\.[^.]*$//'`
+}
+
+# If no dependency file was actually created by the compiler invocation,
+# we still have to create a dummy depfile, to avoid errors with the
+# Makefile "include basename.Plo" scheme.
+make_dummy_depfile ()
+{
+ echo "#dummy" > "$depfile"
+}
+
+# Factor out some common post-processing of the generated depfile.
+# Requires the auxiliary global variable '$tmpdepfile' to be set.
+aix_post_process_depfile ()
+{
+ # If the compiler actually managed to produce a dependency file,
+ # post-process it.
+ if test -f "$tmpdepfile"; then
+ # Each line is of the form 'foo.o: dependency.h'.
+ # Do two passes, one to just change these to
+ # $object: dependency.h
+ # and one to simply output
+ # dependency.h:
+ # which is needed to avoid the deleted-header problem.
+ { sed -e "s,^.*\.[$lower]*:,$object:," < "$tmpdepfile"
+ sed -e "s,^.*\.[$lower]*:[$tab ]*,," -e 's,$,:,' < "$tmpdepfile"
+ } > "$depfile"
+ rm -f "$tmpdepfile"
+ else
+ make_dummy_depfile
+ fi
+}
+
+# A tabulation character.
+tab=' '
+# A newline character.
+nl='
+'
+# Character ranges might be problematic outside the C locale.
+# These definitions help.
+upper=ABCDEFGHIJKLMNOPQRSTUVWXYZ
+lower=abcdefghijklmnopqrstuvwxyz
+digits=0123456789
+alpha=${upper}${lower}
+
if test -z "$depmode" || test -z "$source" || test -z "$object"; then
echo "depcomp: Variables source, object and depmode must be set" 1>&2
exit 1
@@ -69,6 +128,9 @@ tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`}
rm -f "$tmpdepfile"
+# Avoid interferences from the environment.
+gccflag= dashmflag=
+
# Some modes work just like other modes, but use different flags. We
# parameterize here, but still list the modes in the big case below,
# to make depend.m4 easier to write. Note that we *cannot* use a case
@@ -80,18 +142,32 @@ if test "$depmode" = hp; then
fi
if test "$depmode" = dashXmstdout; then
- # This is just like dashmstdout with a different argument.
- dashmflag=-xM
- depmode=dashmstdout
+ # This is just like dashmstdout with a different argument.
+ dashmflag=-xM
+ depmode=dashmstdout
fi
cygpath_u="cygpath -u -f -"
if test "$depmode" = msvcmsys; then
- # This is just like msvisualcpp but w/o cygpath translation.
- # Just convert the backslash-escaped backslashes to single forward
- # slashes to satisfy depend.m4
- cygpath_u="sed s,\\\\\\\\,/,g"
- depmode=msvisualcpp
+ # This is just like msvisualcpp but w/o cygpath translation.
+ # Just convert the backslash-escaped backslashes to single forward
+ # slashes to satisfy depend.m4
+ cygpath_u='sed s,\\\\,/,g'
+ depmode=msvisualcpp
+fi
+
+if test "$depmode" = msvc7msys; then
+ # This is just like msvc7 but w/o cygpath translation.
+ # Just convert the backslash-escaped backslashes to single forward
+ # slashes to satisfy depend.m4
+ cygpath_u='sed s,\\\\,/,g'
+ depmode=msvc7
+fi
+
+if test "$depmode" = xlc; then
+ # IBM C/C++ Compilers xlc/xlC can output gcc-like dependency information.
+ gccflag=-qmakedep=gcc,-MF
+ depmode=gcc
fi
case "$depmode" in
@@ -114,8 +190,7 @@ gcc3)
done
"$@"
stat=$?
- if test $stat -eq 0; then :
- else
+ if test $stat -ne 0; then
rm -f "$tmpdepfile"
exit $stat
fi
@@ -123,13 +198,17 @@ gcc3)
;;
gcc)
+## Note that this doesn't just cater to obsosete pre-3.x GCC compilers.
+## but also to in-use compilers like IMB xlc/xlC and the HP C compiler.
+## (see the conditional assignment to $gccflag above).
## There are various ways to get dependency output from gcc. Here's
## why we pick this rather obscure method:
## - Don't want to use -MD because we'd like the dependencies to end
## up in a subdir. Having to rename by hand is ugly.
## (We might end up doing this anyway to support other compilers.)
## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like
-## -MM, not -M (despite what the docs say).
+## -MM, not -M (despite what the docs say). Also, it might not be
+## supported by the other compilers which use the 'gcc' depmode.
## - Using -M directly means running the compiler twice (even worse
## than renaming).
if test -z "$gccflag"; then
@@ -137,31 +216,31 @@ gcc)
fi
"$@" -Wp,"$gccflag$tmpdepfile"
stat=$?
- if test $stat -eq 0; then :
- else
+ if test $stat -ne 0; then
rm -f "$tmpdepfile"
exit $stat
fi
rm -f "$depfile"
echo "$object : \\" > "$depfile"
- alpha=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz
-## The second -e expression handles DOS-style file names with drive letters.
+ # The second -e expression handles DOS-style file names with drive
+ # letters.
sed -e 's/^[^:]*: / /' \
-e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile"
-## This next piece of magic avoids the `deleted header file' problem.
+## This next piece of magic avoids the "deleted header file" problem.
## The problem is that when a header file which appears in a .P file
## is deleted, the dependency causes make to die (because there is
## typically no way to rebuild the header). We avoid this by adding
## dummy dependencies for each header file. Too bad gcc doesn't do
## this for us directly.
- tr ' ' '
-' < "$tmpdepfile" |
-## Some versions of gcc put a space before the `:'. On the theory
+## Some versions of gcc put a space before the ':'. On the theory
## that the space means something, we add a space to the output as
-## well.
+## well. hp depmode also adds that space, but also prefixes the VPATH
+## to the object. Take care to not repeat it in the output.
## Some versions of the HPUX 10.20 sed can't process this invocation
## correctly. Breaking it into two sed invocations is a workaround.
- sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+ tr ' ' "$nl" < "$tmpdepfile" \
+ | sed -e 's/^\\$//' -e '/^$/d' -e "s|.*$object$||" -e '/:$/d' \
+ | sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
@@ -179,8 +258,7 @@ sgi)
"$@" -MDupdate "$tmpdepfile"
fi
stat=$?
- if test $stat -eq 0; then :
- else
+ if test $stat -ne 0; then
rm -f "$tmpdepfile"
exit $stat
fi
@@ -188,43 +266,41 @@ sgi)
if test -f "$tmpdepfile"; then # yes, the sourcefile depend on other files
echo "$object : \\" > "$depfile"
-
# Clip off the initial element (the dependent). Don't try to be
# clever and replace this with sed code, as IRIX sed won't handle
# lines with more than a fixed number of characters (4096 in
# IRIX 6.2 sed, 8192 in IRIX 6.5). We also remove comment lines;
- # the IRIX cc adds comments like `#:fec' to the end of the
+ # the IRIX cc adds comments like '#:fec' to the end of the
# dependency line.
- tr ' ' '
-' < "$tmpdepfile" \
- | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \
- tr '
-' ' ' >> "$depfile"
+ tr ' ' "$nl" < "$tmpdepfile" \
+ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' \
+ | tr "$nl" ' ' >> "$depfile"
echo >> "$depfile"
-
# The second pass generates a dummy entry for each header file.
- tr ' ' '
-' < "$tmpdepfile" \
- | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \
- >> "$depfile"
+ tr ' ' "$nl" < "$tmpdepfile" \
+ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \
+ >> "$depfile"
else
- # The sourcefile does not contain any dependencies, so just
- # store a dummy comment line, to avoid errors with the Makefile
- # "include basename.Plo" scheme.
- echo "#dummy" > "$depfile"
+ make_dummy_depfile
fi
rm -f "$tmpdepfile"
;;
+xlc)
+ # This case exists only to let depend.m4 do its work. It works by
+ # looking at the text of this script. This case will never be run,
+ # since it is checked for above.
+ exit 1
+ ;;
+
aix)
# The C for AIX Compiler uses -M and outputs the dependencies
# in a .u file. In older versions, this file always lives in the
- # current directory. Also, the AIX compiler puts `$object:' at the
+ # current directory. Also, the AIX compiler puts '$object:' at the
# start of each line; $object doesn't have directory information.
# Version 6 uses the directory in both cases.
- dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
- test "x$dir" = "x$object" && dir=
- base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
+ set_dir_from "$object"
+ set_base_from "$object"
if test "$libtool" = yes; then
tmpdepfile1=$dir$base.u
tmpdepfile2=$base.u
@@ -237,9 +313,7 @@ aix)
"$@" -M
fi
stat=$?
-
- if test $stat -eq 0; then :
- else
+ if test $stat -ne 0; then
rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
exit $stat
fi
@@ -248,44 +322,100 @@ aix)
do
test -f "$tmpdepfile" && break
done
- if test -f "$tmpdepfile"; then
- # Each line is of the form `foo.o: dependent.h'.
- # Do two passes, one to just change these to
- # `$object: dependent.h' and one to simply `dependent.h:'.
- sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
- # That's a tab and a space in the [].
- sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
- else
- # The sourcefile does not contain any dependencies, so just
- # store a dummy comment line, to avoid errors with the Makefile
- # "include basename.Plo" scheme.
- echo "#dummy" > "$depfile"
+ aix_post_process_depfile
+ ;;
+
+tcc)
+ # tcc (Tiny C Compiler) understand '-MD -MF file' since version 0.9.26
+ # FIXME: That version still under development at the moment of writing.
+ # Make that this statement remains true also for stable, released
+ # versions.
+ # It will wrap lines (doesn't matter whether long or short) with a
+ # trailing '\', as in:
+ #
+ # foo.o : \
+ # foo.c \
+ # foo.h \
+ #
+ # It will put a trailing '\' even on the last line, and will use leading
+ # spaces rather than leading tabs (at least since its commit 0394caf7
+ # "Emit spaces for -MD").
+ "$@" -MD -MF "$tmpdepfile"
+ stat=$?
+ if test $stat -ne 0; then
+ rm -f "$tmpdepfile"
+ exit $stat
fi
+ rm -f "$depfile"
+ # Each non-empty line is of the form 'foo.o : \' or ' dep.h \'.
+ # We have to change lines of the first kind to '$object: \'.
+ sed -e "s|.*:|$object :|" < "$tmpdepfile" > "$depfile"
+ # And for each line of the second kind, we have to emit a 'dep.h:'
+ # dummy dependency, to avoid the deleted-header problem.
+ sed -n -e 's|^ *\(.*\) *\\$|\1:|p' < "$tmpdepfile" >> "$depfile"
rm -f "$tmpdepfile"
;;
-icc)
- # Intel's C compiler understands `-MD -MF file'. However on
- # icc -MD -MF foo.d -c -o sub/foo.o sub/foo.c
- # ICC 7.0 will fill foo.d with something like
- # foo.o: sub/foo.c
- # foo.o: sub/foo.h
- # which is wrong. We want:
- # sub/foo.o: sub/foo.c
- # sub/foo.o: sub/foo.h
- # sub/foo.c:
- # sub/foo.h:
- # ICC 7.1 will output
+## The order of this option in the case statement is important, since the
+## shell code in configure will try each of these formats in the order
+## listed in this file. A plain '-MD' option would be understood by many
+## compilers, so we must ensure this comes after the gcc and icc options.
+pgcc)
+ # Portland's C compiler understands '-MD'.
+ # Will always output deps to 'file.d' where file is the root name of the
+ # source file under compilation, even if file resides in a subdirectory.
+ # The object file name does not affect the name of the '.d' file.
+ # pgcc 10.2 will output
# foo.o: sub/foo.c sub/foo.h
- # and will wrap long lines using \ :
+ # and will wrap long lines using '\' :
# foo.o: sub/foo.c ... \
# sub/foo.h ... \
# ...
+ set_dir_from "$object"
+ # Use the source, not the object, to determine the base name, since
+ # that's sadly what pgcc will do too.
+ set_base_from "$source"
+ tmpdepfile=$base.d
+
+ # For projects that build the same source file twice into different object
+ # files, the pgcc approach of using the *source* file root name can cause
+ # problems in parallel builds. Use a locking strategy to avoid stomping on
+ # the same $tmpdepfile.
+ lockdir=$base.d-lock
+ trap "
+ echo '$0: caught signal, cleaning up...' >&2
+ rmdir '$lockdir'
+ exit 1
+ " 1 2 13 15
+ numtries=100
+ i=$numtries
+ while test $i -gt 0; do
+ # mkdir is a portable test-and-set.
+ if mkdir "$lockdir" 2>/dev/null; then
+ # This process acquired the lock.
+ "$@" -MD
+ stat=$?
+ # Release the lock.
+ rmdir "$lockdir"
+ break
+ else
+ # If the lock is being held by a different process, wait
+ # until the winning process is done or we timeout.
+ while test -d "$lockdir" && test $i -gt 0; do
+ sleep 1
+ i=`expr $i - 1`
+ done
+ fi
+ i=`expr $i - 1`
+ done
+ trap - 1 2 13 15
+ if test $i -le 0; then
+ echo "$0: failed to acquire lock after $numtries attempts" >&2
+ echo "$0: check lockdir '$lockdir'" >&2
+ exit 1
+ fi
- "$@" -MD -MF "$tmpdepfile"
- stat=$?
- if test $stat -eq 0; then :
- else
+ if test $stat -ne 0; then
rm -f "$tmpdepfile"
exit $stat
fi
@@ -297,8 +427,8 @@ icc)
sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile"
# Some versions of the HPUX 10.20 sed can't process this invocation
# correctly. Breaking it into two sed invocations is a workaround.
- sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" |
- sed -e 's/$/ :/' >> "$depfile"
+ sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" \
+ | sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
@@ -309,9 +439,8 @@ hp2)
# 'foo.d', which lands next to the object file, wherever that
# happens to be.
# Much of this is similar to the tru64 case; see comments there.
- dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
- test "x$dir" = "x$object" && dir=
- base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
+ set_dir_from "$object"
+ set_base_from "$object"
if test "$libtool" = yes; then
tmpdepfile1=$dir$base.d
tmpdepfile2=$dir.libs/$base.d
@@ -322,8 +451,7 @@ hp2)
"$@" +Maked
fi
stat=$?
- if test $stat -eq 0; then :
- else
+ if test $stat -ne 0; then
rm -f "$tmpdepfile1" "$tmpdepfile2"
exit $stat
fi
@@ -333,77 +461,107 @@ hp2)
test -f "$tmpdepfile" && break
done
if test -f "$tmpdepfile"; then
- sed -e "s,^.*\.[a-z]*:,$object:," "$tmpdepfile" > "$depfile"
- # Add `dependent.h:' lines.
+ sed -e "s,^.*\.[$lower]*:,$object:," "$tmpdepfile" > "$depfile"
+ # Add 'dependent.h:' lines.
sed -ne '2,${
- s/^ *//
- s/ \\*$//
- s/$/:/
- p
- }' "$tmpdepfile" >> "$depfile"
+ s/^ *//
+ s/ \\*$//
+ s/$/:/
+ p
+ }' "$tmpdepfile" >> "$depfile"
else
- echo "#dummy" > "$depfile"
+ make_dummy_depfile
fi
rm -f "$tmpdepfile" "$tmpdepfile2"
;;
tru64)
- # The Tru64 compiler uses -MD to generate dependencies as a side
- # effect. `cc -MD -o foo.o ...' puts the dependencies into `foo.o.d'.
- # At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put
- # dependencies in `foo.d' instead, so we check for that too.
- # Subdirectories are respected.
- dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
- test "x$dir" = "x$object" && dir=
- base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
-
- if test "$libtool" = yes; then
- # With Tru64 cc, shared objects can also be used to make a
- # static library. This mechanism is used in libtool 1.4 series to
- # handle both shared and static libraries in a single compilation.
- # With libtool 1.4, dependencies were output in $dir.libs/$base.lo.d.
- #
- # With libtool 1.5 this exception was removed, and libtool now
- # generates 2 separate objects for the 2 libraries. These two
- # compilations output dependencies in $dir.libs/$base.o.d and
- # in $dir$base.o.d. We have to check for both files, because
- # one of the two compilations can be disabled. We should prefer
- # $dir$base.o.d over $dir.libs/$base.o.d because the latter is
- # automatically cleaned when .libs/ is deleted, while ignoring
- # the former would cause a distcleancheck panic.
- tmpdepfile1=$dir.libs/$base.lo.d # libtool 1.4
- tmpdepfile2=$dir$base.o.d # libtool 1.5
- tmpdepfile3=$dir.libs/$base.o.d # libtool 1.5
- tmpdepfile4=$dir.libs/$base.d # Compaq CCC V6.2-504
- "$@" -Wc,-MD
- else
- tmpdepfile1=$dir$base.o.d
- tmpdepfile2=$dir$base.d
- tmpdepfile3=$dir$base.d
- tmpdepfile4=$dir$base.d
- "$@" -MD
- fi
-
- stat=$?
- if test $stat -eq 0; then :
- else
- rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
- exit $stat
- fi
-
- for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
- do
- test -f "$tmpdepfile" && break
- done
- if test -f "$tmpdepfile"; then
- sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
- # That's a tab and a space in the [].
- sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
- else
- echo "#dummy" > "$depfile"
- fi
- rm -f "$tmpdepfile"
- ;;
+ # The Tru64 compiler uses -MD to generate dependencies as a side
+ # effect. 'cc -MD -o foo.o ...' puts the dependencies into 'foo.o.d'.
+ # At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put
+ # dependencies in 'foo.d' instead, so we check for that too.
+ # Subdirectories are respected.
+ set_dir_from "$object"
+ set_base_from "$object"
+
+ if test "$libtool" = yes; then
+ # Libtool generates 2 separate objects for the 2 libraries. These
+ # two compilations output dependencies in $dir.libs/$base.o.d and
+ # in $dir$base.o.d. We have to check for both files, because
+ # one of the two compilations can be disabled. We should prefer
+ # $dir$base.o.d over $dir.libs/$base.o.d because the latter is
+ # automatically cleaned when .libs/ is deleted, while ignoring
+ # the former would cause a distcleancheck panic.
+ tmpdepfile1=$dir$base.o.d # libtool 1.5
+ tmpdepfile2=$dir.libs/$base.o.d # Likewise.
+ tmpdepfile3=$dir.libs/$base.d # Compaq CCC V6.2-504
+ "$@" -Wc,-MD
+ else
+ tmpdepfile1=$dir$base.d
+ tmpdepfile2=$dir$base.d
+ tmpdepfile3=$dir$base.d
+ "$@" -MD
+ fi
+
+ stat=$?
+ if test $stat -ne 0; then
+ rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
+ exit $stat
+ fi
+
+ for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
+ do
+ test -f "$tmpdepfile" && break
+ done
+ # Same post-processing that is required for AIX mode.
+ aix_post_process_depfile
+ ;;
+
+msvc7)
+ if test "$libtool" = yes; then
+ showIncludes=-Wc,-showIncludes
+ else
+ showIncludes=-showIncludes
+ fi
+ "$@" $showIncludes > "$tmpdepfile"
+ stat=$?
+ grep -v '^Note: including file: ' "$tmpdepfile"
+ if test $stat -ne 0; then
+ rm -f "$tmpdepfile"
+ exit $stat
+ fi
+ rm -f "$depfile"
+ echo "$object : \\" > "$depfile"
+ # The first sed program below extracts the file names and escapes
+ # backslashes for cygpath. The second sed program outputs the file
+ # name when reading, but also accumulates all include files in the
+ # hold buffer in order to output them again at the end. This only
+ # works with sed implementations that can handle large buffers.
+ sed < "$tmpdepfile" -n '
+/^Note: including file: *\(.*\)/ {
+ s//\1/
+ s/\\/\\\\/g
+ p
+}' | $cygpath_u | sort -u | sed -n '
+s/ /\\ /g
+s/\(.*\)/'"$tab"'\1 \\/p
+s/.\(.*\) \\/\1:/
+H
+$ {
+ s/.*/'"$tab"'/
+ G
+ p
+}' >> "$depfile"
+ echo >> "$depfile" # make sure the fragment doesn't end with a backslash
+ rm -f "$tmpdepfile"
+ ;;
+
+msvc7msys)
+ # This case exists only to let depend.m4 do its work. It works by
+ # looking at the text of this script. This case will never be run,
+ # since it is checked for above.
+ exit 1
+ ;;
#nosideeffect)
# This comment above is used by automake to tell side-effect
@@ -422,7 +580,7 @@ dashmstdout)
shift
fi
- # Remove `-o $object'.
+ # Remove '-o $object'.
IFS=" "
for arg
do
@@ -442,18 +600,18 @@ dashmstdout)
done
test -z "$dashmflag" && dashmflag=-M
- # Require at least two characters before searching for `:'
+ # Require at least two characters before searching for ':'
# in the target name. This is to cope with DOS-style filenames:
- # a dependency such as `c:/foo/bar' could be seen as target `c' otherwise.
+ # a dependency such as 'c:/foo/bar' could be seen as target 'c' otherwise.
"$@" $dashmflag |
- sed 's:^[ ]*[^: ][^:][^:]*\:[ ]*:'"$object"'\: :' > "$tmpdepfile"
+ sed "s|^[$tab ]*[^:$tab ][^:][^:]*:[$tab ]*|$object: |" > "$tmpdepfile"
rm -f "$depfile"
cat < "$tmpdepfile" > "$depfile"
- tr ' ' '
-' < "$tmpdepfile" | \
-## Some versions of the HPUX 10.20 sed can't process this invocation
-## correctly. Breaking it into two sed invocations is a workaround.
- sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+ # Some versions of the HPUX 10.20 sed can't process this sed invocation
+ # correctly. Breaking it into two sed invocations is a workaround.
+ tr ' ' "$nl" < "$tmpdepfile" \
+ | sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' \
+ | sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
@@ -503,12 +661,15 @@ makedepend)
touch "$tmpdepfile"
${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@"
rm -f "$depfile"
- cat < "$tmpdepfile" > "$depfile"
- sed '1,2d' "$tmpdepfile" | tr ' ' '
-' | \
-## Some versions of the HPUX 10.20 sed can't process this invocation
-## correctly. Breaking it into two sed invocations is a workaround.
- sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+ # makedepend may prepend the VPATH from the source file name to the object.
+ # No need to regex-escape $object, excess matching of '.' is harmless.
+ sed "s|^.*\($object *:\)|\1|" "$tmpdepfile" > "$depfile"
+ # Some versions of the HPUX 10.20 sed can't process the last invocation
+ # correctly. Breaking it into two sed invocations is a workaround.
+ sed '1,2d' "$tmpdepfile" \
+ | tr ' ' "$nl" \
+ | sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' \
+ | sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile" "$tmpdepfile".bak
;;
@@ -525,7 +686,7 @@ cpp)
shift
fi
- # Remove `-o $object'.
+ # Remove '-o $object'.
IFS=" "
for arg
do
@@ -544,10 +705,10 @@ cpp)
esac
done
- "$@" -E |
- sed -n -e '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \
- -e '/^#line [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' |
- sed '$ s: \\$::' > "$tmpdepfile"
+ "$@" -E \
+ | sed -n -e '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \
+ -e '/^#line [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \
+ | sed '$ s: \\$::' > "$tmpdepfile"
rm -f "$depfile"
echo "$object : \\" > "$depfile"
cat < "$tmpdepfile" >> "$depfile"
@@ -579,23 +740,23 @@ msvisualcpp)
shift
;;
"-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI")
- set fnord "$@"
- shift
- shift
- ;;
+ set fnord "$@"
+ shift
+ shift
+ ;;
*)
- set fnord "$@" "$arg"
- shift
- shift
- ;;
+ set fnord "$@" "$arg"
+ shift
+ shift
+ ;;
esac
done
"$@" -E 2>/dev/null |
sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::\1:p' | $cygpath_u | sort -u > "$tmpdepfile"
rm -f "$depfile"
echo "$object : \\" > "$depfile"
- sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile"
- echo " " >> "$depfile"
+ sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::'"$tab"'\1 \\:p' >> "$depfile"
+ echo "$tab" >> "$depfile"
sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::\1\::p' >> "$depfile"
rm -f "$tmpdepfile"
;;
diff --git a/build-aux/install-sh b/build-aux/install-sh
index 6781b98..0b0fdcb 100755
--- a/build-aux/install-sh
+++ b/build-aux/install-sh
@@ -1,7 +1,7 @@
#!/bin/sh
# install - install a program, script, or datafile
-scriptversion=2009-04-28.21; # UTC
+scriptversion=2013-12-25.23; # UTC
# This originates from X11R5 (mit/util/scripts/install.sh), which was
# later released in X11R6 (xc/config/util/install.sh) with the
@@ -35,25 +35,21 @@ scriptversion=2009-04-28.21; # UTC
# FSF changes to this file are in the public domain.
#
# Calling this script install-sh is preferred over install.sh, to prevent
-# `make' implicit rules from creating a file called install from it
+# 'make' implicit rules from creating a file called install from it
# when there is no Makefile.
#
# This script is compatible with the BSD install script, but was written
# from scratch.
+tab=' '
nl='
'
-IFS=" "" $nl"
+IFS=" $tab$nl"
-# set DOITPROG to echo to test this script
+# Set DOITPROG to "echo" to test this script.
-# Don't use :- since 4.3BSD and earlier shells don't like it.
doit=${DOITPROG-}
-if test -z "$doit"; then
- doit_exec=exec
-else
- doit_exec=$doit
-fi
+doit_exec=${doit:-exec}
# Put in absolute file names if you don't have them in your path;
# or use environment vars.
@@ -68,17 +64,6 @@ mvprog=${MVPROG-mv}
rmprog=${RMPROG-rm}
stripprog=${STRIPPROG-strip}
-posix_glob='?'
-initialize_posix_glob='
- test "$posix_glob" != "?" || {
- if (set -f) 2>/dev/null; then
- posix_glob=
- else
- posix_glob=:
- fi
- }
-'
-
posix_mkdir=
# Desired mode of installed file.
@@ -97,7 +82,7 @@ dir_arg=
dst_arg=
copy_on_change=false
-no_target_directory=
+is_target_a_directory=possibly
usage="\
Usage: $0 [OPTION]... [-T] SRCFILE DSTFILE
@@ -137,42 +122,57 @@ while test $# -ne 0; do
-d) dir_arg=true;;
-g) chgrpcmd="$chgrpprog $2"
- shift;;
+ shift;;
--help) echo "$usage"; exit $?;;
-m) mode=$2
- case $mode in
- *' '* | *' '* | *'
-'* | *'*'* | *'?'* | *'['*)
- echo "$0: invalid mode: $mode" >&2
- exit 1;;
- esac
- shift;;
+ case $mode in
+ *' '* | *"$tab"* | *"$nl"* | *'*'* | *'?'* | *'['*)
+ echo "$0: invalid mode: $mode" >&2
+ exit 1;;
+ esac
+ shift;;
-o) chowncmd="$chownprog $2"
- shift;;
+ shift;;
-s) stripcmd=$stripprog;;
- -t) dst_arg=$2
- shift;;
+ -t)
+ is_target_a_directory=always
+ dst_arg=$2
+ # Protect names problematic for 'test' and other utilities.
+ case $dst_arg in
+ -* | [=\(\)!]) dst_arg=./$dst_arg;;
+ esac
+ shift;;
- -T) no_target_directory=true;;
+ -T) is_target_a_directory=never;;
--version) echo "$0 $scriptversion"; exit $?;;
- --) shift
- break;;
+ --) shift
+ break;;
- -*) echo "$0: invalid option: $1" >&2
- exit 1;;
+ -*) echo "$0: invalid option: $1" >&2
+ exit 1;;
*) break;;
esac
shift
done
+# We allow the use of options -d and -T together, by making -d
+# take the precedence; this is for compatibility with GNU install.
+
+if test -n "$dir_arg"; then
+ if test -n "$dst_arg"; then
+ echo "$0: target directory not allowed when installing a directory." >&2
+ exit 1
+ fi
+fi
+
if test $# -ne 0 && test -z "$dir_arg$dst_arg"; then
# When -d is used, all remaining arguments are directories to create.
# When -t is used, the destination is already specified.
@@ -186,6 +186,10 @@ if test $# -ne 0 && test -z "$dir_arg$dst_arg"; then
fi
shift # arg
dst_arg=$arg
+ # Protect names problematic for 'test' and other utilities.
+ case $dst_arg in
+ -* | [=\(\)!]) dst_arg=./$dst_arg;;
+ esac
done
fi
@@ -194,13 +198,26 @@ if test $# -eq 0; then
echo "$0: no input file specified." >&2
exit 1
fi
- # It's OK to call `install-sh -d' without argument.
+ # It's OK to call 'install-sh -d' without argument.
# This can happen when creating conditional directories.
exit 0
fi
if test -z "$dir_arg"; then
- trap '(exit $?); exit' 1 2 13 15
+ if test $# -gt 1 || test "$is_target_a_directory" = always; then
+ if test ! -d "$dst_arg"; then
+ echo "$0: $dst_arg: Is not a directory." >&2
+ exit 1
+ fi
+ fi
+fi
+
+if test -z "$dir_arg"; then
+ do_exit='(exit $ret); exit $ret'
+ trap "ret=129; $do_exit" 1
+ trap "ret=130; $do_exit" 2
+ trap "ret=141; $do_exit" 13
+ trap "ret=143; $do_exit" 15
# Set umask so as not to create temps with too-generous modes.
# However, 'strip' requires both read and write access to temps.
@@ -211,16 +228,16 @@ if test -z "$dir_arg"; then
*[0-7])
if test -z "$stripcmd"; then
- u_plus_rw=
+ u_plus_rw=
else
- u_plus_rw='% 200'
+ u_plus_rw='% 200'
fi
cp_umask=`expr '(' 777 - $mode % 1000 ')' $u_plus_rw`;;
*)
if test -z "$stripcmd"; then
- u_plus_rw=
+ u_plus_rw=
else
- u_plus_rw=,u+rw
+ u_plus_rw=,u+rw
fi
cp_umask=$mode$u_plus_rw;;
esac
@@ -228,9 +245,9 @@ fi
for src
do
- # Protect names starting with `-'.
+ # Protect names problematic for 'test' and other utilities.
case $src in
- -*) src=./$src;;
+ -* | [=\(\)!]) src=./$src;;
esac
if test -n "$dir_arg"; then
@@ -252,51 +269,20 @@ do
echo "$0: no destination specified." >&2
exit 1
fi
-
dst=$dst_arg
- # Protect names starting with `-'.
- case $dst in
- -*) dst=./$dst;;
- esac
# If destination is a directory, append the input filename; won't work
# if double slashes aren't ignored.
if test -d "$dst"; then
- if test -n "$no_target_directory"; then
- echo "$0: $dst_arg: Is a directory" >&2
- exit 1
+ if test "$is_target_a_directory" = never; then
+ echo "$0: $dst_arg: Is a directory" >&2
+ exit 1
fi
dstdir=$dst
dst=$dstdir/`basename "$src"`
dstdir_status=0
else
- # Prefer dirname, but fall back on a substitute if dirname fails.
- dstdir=`
- (dirname "$dst") 2>/dev/null ||
- expr X"$dst" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
- X"$dst" : 'X\(//\)[^/]' \| \
- X"$dst" : 'X\(//\)$' \| \
- X"$dst" : 'X\(/\)' \| . 2>/dev/null ||
- echo X"$dst" |
- sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
- s//\1/
- q
- }
- /^X\(\/\/\)[^/].*/{
- s//\1/
- q
- }
- /^X\(\/\/\)$/{
- s//\1/
- q
- }
- /^X\(\/\).*/{
- s//\1/
- q
- }
- s/.*/./; q'
- `
-
+ dstdir=`dirname "$dst"`
test -d "$dstdir"
dstdir_status=$?
fi
@@ -307,74 +293,74 @@ do
if test $dstdir_status != 0; then
case $posix_mkdir in
'')
- # Create intermediate dirs using mode 755 as modified by the umask.
- # This is like FreeBSD 'install' as of 1997-10-28.
- umask=`umask`
- case $stripcmd.$umask in
- # Optimize common cases.
- *[2367][2367]) mkdir_umask=$umask;;
- .*0[02][02] | .[02][02] | .[02]) mkdir_umask=22;;
-
- *[0-7])
- mkdir_umask=`expr $umask + 22 \
- - $umask % 100 % 40 + $umask % 20 \
- - $umask % 10 % 4 + $umask % 2
- `;;
- *) mkdir_umask=$umask,go-w;;
- esac
-
- # With -d, create the new directory with the user-specified mode.
- # Otherwise, rely on $mkdir_umask.
- if test -n "$dir_arg"; then
- mkdir_mode=-m$mode
- else
- mkdir_mode=
- fi
-
- posix_mkdir=false
- case $umask in
- *[123567][0-7][0-7])
- # POSIX mkdir -p sets u+wx bits regardless of umask, which
- # is incompatible with FreeBSD 'install' when (umask & 300) != 0.
- ;;
- *)
- tmpdir=${TMPDIR-/tmp}/ins$RANDOM-$$
- trap 'ret=$?; rmdir "$tmpdir/d" "$tmpdir" 2>/dev/null; exit $ret' 0
-
- if (umask $mkdir_umask &&
- exec $mkdirprog $mkdir_mode -p -- "$tmpdir/d") >/dev/null 2>&1
- then
- if test -z "$dir_arg" || {
- # Check for POSIX incompatibilities with -m.
- # HP-UX 11.23 and IRIX 6.5 mkdir -m -p sets group- or
- # other-writeable bit of parent directory when it shouldn't.
- # FreeBSD 6.1 mkdir -m -p sets mode of existing directory.
- ls_ld_tmpdir=`ls -ld "$tmpdir"`
- case $ls_ld_tmpdir in
- d????-?r-*) different_mode=700;;
- d????-?--*) different_mode=755;;
- *) false;;
- esac &&
- $mkdirprog -m$different_mode -p -- "$tmpdir" && {
- ls_ld_tmpdir_1=`ls -ld "$tmpdir"`
- test "$ls_ld_tmpdir" = "$ls_ld_tmpdir_1"
- }
- }
- then posix_mkdir=:
- fi
- rmdir "$tmpdir/d" "$tmpdir"
- else
- # Remove any dirs left behind by ancient mkdir implementations.
- rmdir ./$mkdir_mode ./-p ./-- 2>/dev/null
- fi
- trap '' 0;;
- esac;;
+ # Create intermediate dirs using mode 755 as modified by the umask.
+ # This is like FreeBSD 'install' as of 1997-10-28.
+ umask=`umask`
+ case $stripcmd.$umask in
+ # Optimize common cases.
+ *[2367][2367]) mkdir_umask=$umask;;
+ .*0[02][02] | .[02][02] | .[02]) mkdir_umask=22;;
+
+ *[0-7])
+ mkdir_umask=`expr $umask + 22 \
+ - $umask % 100 % 40 + $umask % 20 \
+ - $umask % 10 % 4 + $umask % 2
+ `;;
+ *) mkdir_umask=$umask,go-w;;
+ esac
+
+ # With -d, create the new directory with the user-specified mode.
+ # Otherwise, rely on $mkdir_umask.
+ if test -n "$dir_arg"; then
+ mkdir_mode=-m$mode
+ else
+ mkdir_mode=
+ fi
+
+ posix_mkdir=false
+ case $umask in
+ *[123567][0-7][0-7])
+ # POSIX mkdir -p sets u+wx bits regardless of umask, which
+ # is incompatible with FreeBSD 'install' when (umask & 300) != 0.
+ ;;
+ *)
+ tmpdir=${TMPDIR-/tmp}/ins$RANDOM-$$
+ trap 'ret=$?; rmdir "$tmpdir/d" "$tmpdir" 2>/dev/null; exit $ret' 0
+
+ if (umask $mkdir_umask &&
+ exec $mkdirprog $mkdir_mode -p -- "$tmpdir/d") >/dev/null 2>&1
+ then
+ if test -z "$dir_arg" || {
+ # Check for POSIX incompatibilities with -m.
+ # HP-UX 11.23 and IRIX 6.5 mkdir -m -p sets group- or
+ # other-writable bit of parent directory when it shouldn't.
+ # FreeBSD 6.1 mkdir -m -p sets mode of existing directory.
+ ls_ld_tmpdir=`ls -ld "$tmpdir"`
+ case $ls_ld_tmpdir in
+ d????-?r-*) different_mode=700;;
+ d????-?--*) different_mode=755;;
+ *) false;;
+ esac &&
+ $mkdirprog -m$different_mode -p -- "$tmpdir" && {
+ ls_ld_tmpdir_1=`ls -ld "$tmpdir"`
+ test "$ls_ld_tmpdir" = "$ls_ld_tmpdir_1"
+ }
+ }
+ then posix_mkdir=:
+ fi
+ rmdir "$tmpdir/d" "$tmpdir"
+ else
+ # Remove any dirs left behind by ancient mkdir implementations.
+ rmdir ./$mkdir_mode ./-p ./-- 2>/dev/null
+ fi
+ trap '' 0;;
+ esac;;
esac
if
$posix_mkdir && (
- umask $mkdir_umask &&
- $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir"
+ umask $mkdir_umask &&
+ $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir"
)
then :
else
@@ -384,53 +370,51 @@ do
# directory the slow way, step by step, checking for races as we go.
case $dstdir in
- /*) prefix='/';;
- -*) prefix='./';;
- *) prefix='';;
+ /*) prefix='/';;
+ [-=\(\)!]*) prefix='./';;
+ *) prefix='';;
esac
- eval "$initialize_posix_glob"
-
oIFS=$IFS
IFS=/
- $posix_glob set -f
+ set -f
set fnord $dstdir
shift
- $posix_glob set +f
+ set +f
IFS=$oIFS
prefixes=
for d
do
- test -z "$d" && continue
-
- prefix=$prefix$d
- if test -d "$prefix"; then
- prefixes=
- else
- if $posix_mkdir; then
- (umask=$mkdir_umask &&
- $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir") && break
- # Don't fail if two instances are running concurrently.
- test -d "$prefix" || exit 1
- else
- case $prefix in
- *\'*) qprefix=`echo "$prefix" | sed "s/'/'\\\\\\\\''/g"`;;
- *) qprefix=$prefix;;
- esac
- prefixes="$prefixes '$qprefix'"
- fi
- fi
- prefix=$prefix/
+ test X"$d" = X && continue
+
+ prefix=$prefix$d
+ if test -d "$prefix"; then
+ prefixes=
+ else
+ if $posix_mkdir; then
+ (umask=$mkdir_umask &&
+ $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir") && break
+ # Don't fail if two instances are running concurrently.
+ test -d "$prefix" || exit 1
+ else
+ case $prefix in
+ *\'*) qprefix=`echo "$prefix" | sed "s/'/'\\\\\\\\''/g"`;;
+ *) qprefix=$prefix;;
+ esac
+ prefixes="$prefixes '$qprefix'"
+ fi
+ fi
+ prefix=$prefix/
done
if test -n "$prefixes"; then
- # Don't fail if two instances are running concurrently.
- (umask $mkdir_umask &&
- eval "\$doit_exec \$mkdirprog $prefixes") ||
- test -d "$dstdir" || exit 1
- obsolete_mkdir_used=true
+ # Don't fail if two instances are running concurrently.
+ (umask $mkdir_umask &&
+ eval "\$doit_exec \$mkdirprog $prefixes") ||
+ test -d "$dstdir" || exit 1
+ obsolete_mkdir_used=true
fi
fi
fi
@@ -465,15 +449,12 @@ do
# If -C, don't bother to copy if it wouldn't change the file.
if $copy_on_change &&
- old=`LC_ALL=C ls -dlL "$dst" 2>/dev/null` &&
- new=`LC_ALL=C ls -dlL "$dsttmp" 2>/dev/null` &&
-
- eval "$initialize_posix_glob" &&
- $posix_glob set -f &&
+ old=`LC_ALL=C ls -dlL "$dst" 2>/dev/null` &&
+ new=`LC_ALL=C ls -dlL "$dsttmp" 2>/dev/null` &&
+ set -f &&
set X $old && old=:$2:$4:$5:$6 &&
set X $new && new=:$2:$4:$5:$6 &&
- $posix_glob set +f &&
-
+ set +f &&
test "$old" = "$new" &&
$cmpprog "$dst" "$dsttmp" >/dev/null 2>&1
then
@@ -486,24 +467,24 @@ do
# to itself, or perhaps because mv is so ancient that it does not
# support -f.
{
- # Now remove or move aside any old file at destination location.
- # We try this two ways since rm can't unlink itself on some
- # systems and the destination file might be busy for other
- # reasons. In this case, the final cleanup might fail but the new
- # file should still install successfully.
- {
- test ! -f "$dst" ||
- $doit $rmcmd -f "$dst" 2>/dev/null ||
- { $doit $mvcmd -f "$dst" "$rmtmp" 2>/dev/null &&
- { $doit $rmcmd -f "$rmtmp" 2>/dev/null; :; }
- } ||
- { echo "$0: cannot unlink or rename $dst" >&2
- (exit 1); exit 1
- }
- } &&
-
- # Now rename the file to the real destination.
- $doit $mvcmd "$dsttmp" "$dst"
+ # Now remove or move aside any old file at destination location.
+ # We try this two ways since rm can't unlink itself on some
+ # systems and the destination file might be busy for other
+ # reasons. In this case, the final cleanup might fail but the new
+ # file should still install successfully.
+ {
+ test ! -f "$dst" ||
+ $doit $rmcmd -f "$dst" 2>/dev/null ||
+ { $doit $mvcmd -f "$dst" "$rmtmp" 2>/dev/null &&
+ { $doit $rmcmd -f "$rmtmp" 2>/dev/null; :; }
+ } ||
+ { echo "$0: cannot unlink or rename $dst" >&2
+ (exit 1); exit 1
+ }
+ } &&
+
+ # Now rename the file to the real destination.
+ $doit $mvcmd "$dsttmp" "$dst"
}
fi || exit 1
diff --git a/build-aux/ltmain.sh b/build-aux/ltmain.sh
old mode 100755
new mode 100644
diff --git a/build-aux/missing b/build-aux/missing
index 28055d2..f62bbae 100755
--- a/build-aux/missing
+++ b/build-aux/missing
@@ -1,11 +1,10 @@
#! /bin/sh
-# Common stub for a few missing GNU programs while installing.
+# Common wrapper for a few potentially missing GNU programs.
-scriptversion=2009-04-28.21; # UTC
+scriptversion=2013-10-28.13; # UTC
-# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005, 2006,
-# 2008, 2009 Free Software Foundation, Inc.
-# Originally by Fran,cois Pinard <pinard at iro.umontreal.ca>, 1996.
+# Copyright (C) 1996-2014 Free Software Foundation, Inc.
+# Originally written by Fran,cois Pinard <pinard at iro.umontreal.ca>, 1996.
# 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
@@ -26,69 +25,40 @@ scriptversion=2009-04-28.21; # UTC
# the same distribution terms that you use for the rest of that program.
if test $# -eq 0; then
- echo 1>&2 "Try \`$0 --help' for more information"
+ echo 1>&2 "Try '$0 --help' for more information"
exit 1
fi
-run=:
-sed_output='s/.* --output[ =]\([^ ]*\).*/\1/p'
-sed_minuso='s/.* -o \([^ ]*\).*/\1/p'
-
-# In the cases where this matters, `missing' is being run in the
-# srcdir already.
-if test -f configure.ac; then
- configure_ac=configure.ac
-else
- configure_ac=configure.in
-fi
+case $1 in
-msg="missing on your system"
+ --is-lightweight)
+ # Used by our autoconf macros to check whether the available missing
+ # script is modern enough.
+ exit 0
+ ;;
-case $1 in
---run)
- # Try to run requested program, and just exit if it succeeds.
- run=
- shift
- "$@" && exit 0
- # Exit code 63 means version mismatch. This often happens
- # when the user try to use an ancient version of a tool on
- # a file that requires a minimum version. In this case we
- # we should proceed has if the program had been absent, or
- # if --run hadn't been passed.
- if test $? = 63; then
- run=:
- msg="probably too old"
- fi
- ;;
+ --run)
+ # Back-compat with the calling convention used by older automake.
+ shift
+ ;;
-h|--h|--he|--hel|--help)
echo "\
$0 [OPTION]... PROGRAM [ARGUMENT]...
-Handle \`PROGRAM [ARGUMENT]...' for when PROGRAM is missing, or return an
-error status if there is no known handling for PROGRAM.
+Run 'PROGRAM [ARGUMENT]...', returning a proper advice when this fails due
+to PROGRAM being missing or too old.
Options:
-h, --help display this help and exit
-v, --version output version information and exit
- --run try to run the given command, and emulate it if it fails
Supported PROGRAM values:
- aclocal touch file \`aclocal.m4'
- autoconf touch file \`configure'
- autoheader touch file \`config.h.in'
- autom4te touch the output file, or create a stub one
- automake touch all \`Makefile.in' files
- bison create \`y.tab.[ch]', if possible, from existing .[ch]
- flex create \`lex.yy.c', if possible, from existing .c
- help2man touch the output file
- lex create \`lex.yy.c', if possible, from existing .c
- makeinfo touch the output file
- tar try tar, gnutar, gtar, then tar without non-portable flags
- yacc create \`y.tab.[ch]', if possible, from existing .[ch]
+ aclocal autoconf autoheader autom4te automake makeinfo
+ bison yacc flex lex help2man
-Version suffixes to PROGRAM as well as the prefixes \`gnu-', \`gnu', and
-\`g' are ignored when checking the name.
+Version suffixes to PROGRAM as well as the prefixes 'gnu-', 'gnu', and
+'g' are ignored when checking the name.
Send bug reports to <bug-automake at gnu.org>."
exit $?
@@ -100,272 +70,141 @@ Send bug reports to <bug-automake at gnu.org>."
;;
-*)
- echo 1>&2 "$0: Unknown \`$1' option"
- echo 1>&2 "Try \`$0 --help' for more information"
+ echo 1>&2 "$0: unknown '$1' option"
+ echo 1>&2 "Try '$0 --help' for more information"
exit 1
;;
esac
-# normalize program name to check for.
-program=`echo "$1" | sed '
- s/^gnu-//; t
- s/^gnu//; t
- s/^g//; t'`
-
-# Now exit if we have it, but it failed. Also exit now if we
-# don't have it and --version was passed (most likely to detect
-# the program). This is about non-GNU programs, so use $1 not
-# $program.
-case $1 in
- lex*|yacc*)
- # Not GNU programs, they don't have --version.
- ;;
-
- tar*)
- if test -n "$run"; then
- echo 1>&2 "ERROR: \`tar' requires --run"
- exit 1
- elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
- exit 1
- fi
- ;;
-
- *)
- if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
- # We have it, but it failed.
- exit 1
- elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
- # Could not run --version or --help. This is probably someone
- # running `$TOOL --version' or `$TOOL --help' to check whether
- # $TOOL exists and not knowing $TOOL uses missing.
- exit 1
- fi
- ;;
-esac
-
-# If it does not exist, or fails to run (possibly an outdated version),
-# try to emulate it.
-case $program in
- aclocal*)
- echo 1>&2 "\
-WARNING: \`$1' is $msg. You should only need it if
- you modified \`acinclude.m4' or \`${configure_ac}'. You might want
- to install the \`Automake' and \`Perl' packages. Grab them from
- any GNU archive site."
- touch aclocal.m4
- ;;
-
- autoconf*)
- echo 1>&2 "\
-WARNING: \`$1' is $msg. You should only need it if
- you modified \`${configure_ac}'. You might want to install the
- \`Autoconf' and \`GNU m4' packages. Grab them from any GNU
- archive site."
- touch configure
- ;;
-
- autoheader*)
- echo 1>&2 "\
-WARNING: \`$1' is $msg. You should only need it if
- you modified \`acconfig.h' or \`${configure_ac}'. You might want
- to install the \`Autoconf' and \`GNU m4' packages. Grab them
- from any GNU archive site."
- files=`sed -n 's/^[ ]*A[CM]_CONFIG_HEADER(\([^)]*\)).*/\1/p' ${configure_ac}`
- test -z "$files" && files="config.h"
- touch_files=
- for f in $files; do
- case $f in
- *:*) touch_files="$touch_files "`echo "$f" |
- sed -e 's/^[^:]*://' -e 's/:.*//'`;;
- *) touch_files="$touch_files $f.in";;
- esac
- done
- touch $touch_files
- ;;
-
- automake*)
- echo 1>&2 "\
-WARNING: \`$1' is $msg. You should only need it if
- you modified \`Makefile.am', \`acinclude.m4' or \`${configure_ac}'.
- You might want to install the \`Automake' and \`Perl' packages.
- Grab them from any GNU archive site."
- find . -type f -name Makefile.am -print |
- sed 's/\.am$/.in/' |
- while read f; do touch "$f"; done
- ;;
-
- autom4te*)
- echo 1>&2 "\
-WARNING: \`$1' is needed, but is $msg.
- You might have modified some files without having the
- proper tools for further handling them.
- You can get \`$1' as part of \`Autoconf' from any GNU
- archive site."
-
- file=`echo "$*" | sed -n "$sed_output"`
- test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
- if test -f "$file"; then
- touch $file
- else
- test -z "$file" || exec >$file
- echo "#! /bin/sh"
- echo "# Created by GNU Automake missing as a replacement of"
- echo "# $ $@"
- echo "exit 0"
- chmod +x $file
- exit 1
- fi
- ;;
-
- bison*|yacc*)
- echo 1>&2 "\
-WARNING: \`$1' $msg. You should only need it if
- you modified a \`.y' file. You may need the \`Bison' package
- in order for those modifications to take effect. You can get
- \`Bison' from any GNU archive site."
- rm -f y.tab.c y.tab.h
- if test $# -ne 1; then
- eval LASTARG="\${$#}"
- case $LASTARG in
- *.y)
- SRCFILE=`echo "$LASTARG" | sed 's/y$/c/'`
- if test -f "$SRCFILE"; then
- cp "$SRCFILE" y.tab.c
- fi
- SRCFILE=`echo "$LASTARG" | sed 's/y$/h/'`
- if test -f "$SRCFILE"; then
- cp "$SRCFILE" y.tab.h
- fi
- ;;
- esac
- fi
- if test ! -f y.tab.h; then
- echo >y.tab.h
- fi
- if test ! -f y.tab.c; then
- echo 'main() { return 0; }' >y.tab.c
- fi
- ;;
-
- lex*|flex*)
- echo 1>&2 "\
-WARNING: \`$1' is $msg. You should only need it if
- you modified a \`.l' file. You may need the \`Flex' package
- in order for those modifications to take effect. You can get
- \`Flex' from any GNU archive site."
- rm -f lex.yy.c
- if test $# -ne 1; then
- eval LASTARG="\${$#}"
- case $LASTARG in
- *.l)
- SRCFILE=`echo "$LASTARG" | sed 's/l$/c/'`
- if test -f "$SRCFILE"; then
- cp "$SRCFILE" lex.yy.c
- fi
- ;;
- esac
- fi
- if test ! -f lex.yy.c; then
- echo 'main() { return 0; }' >lex.yy.c
- fi
- ;;
-
- help2man*)
- echo 1>&2 "\
-WARNING: \`$1' is $msg. You should only need it if
- you modified a dependency of a manual page. You may need the
- \`Help2man' package in order for those modifications to take
- effect. You can get \`Help2man' from any GNU archive site."
-
- file=`echo "$*" | sed -n "$sed_output"`
- test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
- if test -f "$file"; then
- touch $file
- else
- test -z "$file" || exec >$file
- echo ".ab help2man is required to generate this page"
- exit $?
- fi
- ;;
-
- makeinfo*)
- echo 1>&2 "\
-WARNING: \`$1' is $msg. You should only need it if
- you modified a \`.texi' or \`.texinfo' file, or any other file
- indirectly affecting the aspect of the manual. The spurious
- call might also be the consequence of using a buggy \`make' (AIX,
- DU, IRIX). You might want to install the \`Texinfo' package or
- the \`GNU make' package. Grab either from any GNU archive site."
- # The file to touch is that specified with -o ...
- file=`echo "$*" | sed -n "$sed_output"`
- test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
- if test -z "$file"; then
- # ... or it is the one specified with @setfilename ...
- infile=`echo "$*" | sed 's/.* \([^ ]*\) *$/\1/'`
- file=`sed -n '
- /^@setfilename/{
- s/.* \([^ ]*\) *$/\1/
- p
- q
- }' $infile`
- # ... or it is derived from the source name (dir/f.texi becomes f.info)
- test -z "$file" && file=`echo "$infile" | sed 's,.*/,,;s,.[^.]*$,,'`.info
- fi
- # If the file does not exist, the user really needs makeinfo;
- # let's fail without touching anything.
- test -f $file || exit 1
- touch $file
- ;;
-
- tar*)
- shift
-
- # We have already tried tar in the generic part.
- # Look for gnutar/gtar before invocation to avoid ugly error
- # messages.
- if (gnutar --version > /dev/null 2>&1); then
- gnutar "$@" && exit 0
- fi
- if (gtar --version > /dev/null 2>&1); then
- gtar "$@" && exit 0
- fi
- firstarg="$1"
- if shift; then
- case $firstarg in
- *o*)
- firstarg=`echo "$firstarg" | sed s/o//`
- tar "$firstarg" "$@" && exit 0
- ;;
- esac
- case $firstarg in
- *h*)
- firstarg=`echo "$firstarg" | sed s/h//`
- tar "$firstarg" "$@" && exit 0
- ;;
- esac
- fi
-
- echo 1>&2 "\
-WARNING: I can't seem to be able to run \`tar' with the given arguments.
- You may want to install GNU tar or Free paxutils, or check the
- command line arguments."
- exit 1
- ;;
-
- *)
- echo 1>&2 "\
-WARNING: \`$1' is needed, and is $msg.
- You might have modified some files without having the
- proper tools for further handling them. Check the \`README' file,
- it often tells you about the needed prerequisites for installing
- this package. You may also peek at any GNU archive site, in case
- some other package would contain this missing \`$1' program."
- exit 1
- ;;
-esac
+# Run the given program, remember its exit status.
+"$@"; st=$?
+
+# If it succeeded, we are done.
+test $st -eq 0 && exit 0
+
+# Also exit now if we it failed (or wasn't found), and '--version' was
+# passed; such an option is passed most likely to detect whether the
+# program is present and works.
+case $2 in --version|--help) exit $st;; esac
+
+# Exit code 63 means version mismatch. This often happens when the user
+# tries to use an ancient version of a tool on a file that requires a
+# minimum version.
+if test $st -eq 63; then
+ msg="probably too old"
+elif test $st -eq 127; then
+ # Program was missing.
+ msg="missing on your system"
+else
+ # Program was found and executed, but failed. Give up.
+ exit $st
+fi
-exit 0
+perl_URL=http://www.perl.org/
+flex_URL=http://flex.sourceforge.net/
+gnu_software_URL=http://www.gnu.org/software
+
+program_details ()
+{
+ case $1 in
+ aclocal|automake)
+ echo "The '$1' program is part of the GNU Automake package:"
+ echo "<$gnu_software_URL/automake>"
+ echo "It also requires GNU Autoconf, GNU m4 and Perl in order to run:"
+ echo "<$gnu_software_URL/autoconf>"
+ echo "<$gnu_software_URL/m4/>"
+ echo "<$perl_URL>"
+ ;;
+ autoconf|autom4te|autoheader)
+ echo "The '$1' program is part of the GNU Autoconf package:"
+ echo "<$gnu_software_URL/autoconf/>"
+ echo "It also requires GNU m4 and Perl in order to run:"
+ echo "<$gnu_software_URL/m4/>"
+ echo "<$perl_URL>"
+ ;;
+ esac
+}
+
+give_advice ()
+{
+ # Normalize program name to check for.
+ normalized_program=`echo "$1" | sed '
+ s/^gnu-//; t
+ s/^gnu//; t
+ s/^g//; t'`
+
+ printf '%s\n' "'$1' is $msg."
+
+ configure_deps="'configure.ac' or m4 files included by 'configure.ac'"
+ case $normalized_program in
+ autoconf*)
+ echo "You should only need it if you modified 'configure.ac',"
+ echo "or m4 files included by it."
+ program_details 'autoconf'
+ ;;
+ autoheader*)
+ echo "You should only need it if you modified 'acconfig.h' or"
+ echo "$configure_deps."
+ program_details 'autoheader'
+ ;;
+ automake*)
+ echo "You should only need it if you modified 'Makefile.am' or"
+ echo "$configure_deps."
+ program_details 'automake'
+ ;;
+ aclocal*)
+ echo "You should only need it if you modified 'acinclude.m4' or"
+ echo "$configure_deps."
+ program_details 'aclocal'
+ ;;
+ autom4te*)
+ echo "You might have modified some maintainer files that require"
+ echo "the 'autom4te' program to be rebuilt."
+ program_details 'autom4te'
+ ;;
+ bison*|yacc*)
+ echo "You should only need it if you modified a '.y' file."
+ echo "You may want to install the GNU Bison package:"
+ echo "<$gnu_software_URL/bison/>"
+ ;;
+ lex*|flex*)
+ echo "You should only need it if you modified a '.l' file."
+ echo "You may want to install the Fast Lexical Analyzer package:"
+ echo "<$flex_URL>"
+ ;;
+ help2man*)
+ echo "You should only need it if you modified a dependency" \
+ "of a man page."
+ echo "You may want to install the GNU Help2man package:"
+ echo "<$gnu_software_URL/help2man/>"
+ ;;
+ makeinfo*)
+ echo "You should only need it if you modified a '.texi' file, or"
+ echo "any other file indirectly affecting the aspect of the manual."
+ echo "You might want to install the Texinfo package:"
+ echo "<$gnu_software_URL/texinfo/>"
+ echo "The spurious makeinfo call might also be the consequence of"
+ echo "using a buggy 'make' (AIX, DU, IRIX), in which case you might"
+ echo "want to install GNU make:"
+ echo "<$gnu_software_URL/make/>"
+ ;;
+ *)
+ echo "You might have modified some files without having the proper"
+ echo "tools for further handling them. Check the 'README' file, it"
+ echo "often tells you about the needed prerequisites for installing"
+ echo "this package. You may also peek at any GNU archive site, in"
+ echo "case some other package contains this missing '$1' program."
+ ;;
+ esac
+}
+
+give_advice "$1" | sed -e '1s/^/WARNING: /' \
+ -e '2,$s/^/ /' >&2
+
+# Propagate the correct exit status (expected to be 127 for a program
+# not found, 63 for a program that failed due to version mismatch).
+exit $st
# Local variables:
# eval: (add-hook 'write-file-hooks 'time-stamp)
diff --git a/config.h.in b/config.h.in
old mode 100755
new mode 100644
diff --git a/configure b/configure
index 7f513a1..825ef5a 100755
--- a/configure
+++ b/configure
@@ -1,6 +1,6 @@
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for mmdb2 2.0.1.
+# Generated by GNU Autoconf 2.69 for mmdb2 2.0.5.
#
#
# Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.
@@ -587,8 +587,8 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='mmdb2'
PACKAGE_TARNAME='mmdb2'
-PACKAGE_VERSION='2.0.1'
-PACKAGE_STRING='mmdb2 2.0.1'
+PACKAGE_VERSION='2.0.5'
+PACKAGE_STRING='mmdb2 2.0.5'
PACKAGE_BUGREPORT=''
PACKAGE_URL=''
@@ -1323,7 +1323,7 @@ if test "$ac_init_help" = "long"; then
# Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF
-\`configure' configures mmdb2 2.0.1 to adapt to many kinds of systems.
+\`configure' configures mmdb2 2.0.5 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1393,7 +1393,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of mmdb2 2.0.1:";;
+ short | recursive ) echo "Configuration of mmdb2 2.0.5:";;
esac
cat <<\_ACEOF
@@ -1419,7 +1419,7 @@ Optional Features:
Optional Packages:
--with-PACKAGE[=ARG] use PACKAGE [ARG=yes]
--without-PACKAGE do not use PACKAGE (same as --with-PACKAGE=no)
- --with-pic try to use only PIC/non-PIC objects [default=use
+ --with-pic[=PKGS] try to use only PIC/non-PIC objects [default=use
both]
--with-gnu-ld assume the C compiler uses GNU ld [default=no]
--with-sysroot=DIR Search for dependent libraries within DIR
@@ -1504,7 +1504,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-mmdb2 configure 2.0.1
+mmdb2 configure 2.0.5
generated by GNU Autoconf 2.69
Copyright (C) 2012 Free Software Foundation, Inc.
@@ -1903,7 +1903,7 @@ cat >config.log <<_ACEOF
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
-It was created by mmdb2 $as_me 2.0.1, which was
+It was created by mmdb2 $as_me 2.0.5, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@
@@ -2285,7 +2285,7 @@ ac_configure="$SHELL $ac_aux_dir/configure" # Please don't use this var.
ac_config_headers="$ac_config_headers config.h"
-am__api_version='1.13'
+am__api_version='1.15'
# Find a good install program. We prefer a C program (faster),
# so one script is as good as another. But avoid the broken or
@@ -2457,8 +2457,8 @@ test "$program_suffix" != NONE &&
ac_script='s/[\\$]/&&/g;s/;s,x,x,$//'
program_transform_name=`$as_echo "$program_transform_name" | sed "$ac_script"`
-# expand $ac_aux_dir to an absolute path
-am_aux_dir=`cd $ac_aux_dir && pwd`
+# Expand $ac_aux_dir to an absolute path.
+am_aux_dir=`cd "$ac_aux_dir" && pwd`
if test x"${MISSING+set}" != xset; then
case $am_aux_dir in
@@ -2477,7 +2477,7 @@ else
$as_echo "$as_me: WARNING: 'missing' script is too old or missing" >&2;}
fi
-if test x"${install_sh}" != xset; then
+if test x"${install_sh+set}" != xset; then
case $am_aux_dir in
*\ * | *\ *)
install_sh="\${SHELL} '$am_aux_dir/install-sh'" ;;
@@ -2771,7 +2771,7 @@ fi
# Define the identity of the package.
PACKAGE='mmdb2'
- VERSION='2.0.1'
+ VERSION='2.0.5'
cat >>confdefs.h <<_ACEOF
@@ -2805,8 +2805,8 @@ MAKEINFO=${MAKEINFO-"${am_missing_run}makeinfo"}
# <http://lists.gnu.org/archive/html/automake/2012-07/msg00014.html>
mkdir_p='$(MKDIR_P)'
-# We need awk for the "check" target. The system "awk" is bad on
-# some platforms.
+# We need awk for the "check" target (and possibly the TAP driver). The
+# system "awk" is bad on some platforms.
# Always define AMTAR for backward compatibility. Yes, it's still used
# in the wild :-( We should find a proper way to deprecate it ...
AMTAR='$${TAR-tar}'
@@ -2822,6 +2822,48 @@ am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -'
+# POSIX will say in a future version that running "rm -f" with no argument
+# is OK; and we want to be able to make that assumption in our Makefile
+# recipes. So use an aggressive probe to check that the usage we want is
+# actually supported "in the wild" to an acceptable degree.
+# See automake bug#10828.
+# To make any issue more visible, cause the running configure to be aborted
+# by default if the 'rm' program in use doesn't match our expectations; the
+# user can still override this though.
+if rm -f && rm -fr && rm -rf; then : OK; else
+ cat >&2 <<'END'
+Oops!
+
+Your 'rm' program seems unable to run without file operands specified
+on the command line, even when the '-f' option is present. This is contrary
+to the behaviour of most rm programs out there, and not conforming with
+the upcoming POSIX standard: <http://austingroupbugs.net/view.php?id=542>
+
+Please tell bug-automake at gnu.org about your system, including the value
+of your $PATH and any error possibly output before this message. This
+can help us improve future automake versions.
+
+END
+ if test x"$ACCEPT_INFERIOR_RM_PROGRAM" = x"yes"; then
+ echo 'Configuration will proceed anyway, since you have set the' >&2
+ echo 'ACCEPT_INFERIOR_RM_PROGRAM variable to "yes"' >&2
+ echo >&2
+ else
+ cat >&2 <<'END'
+Aborting the configuration process, to ensure you take notice of the issue.
+
+You can download and install GNU coreutils to get an 'rm' implementation
+that behaves properly: <http://www.gnu.org/software/coreutils/>.
+
+If you want to complete the configuration process using your problematic
+'rm' anyway, export the environment variable ACCEPT_INFERIOR_RM_PROGRAM
+to "yes", and re-run configure.
+
+END
+ as_fn_error $? "Your 'rm' program is bad, sorry." "$LINENO" 5
+ fi
+fi
+
DEPDIR="${am__leading_dot}deps"
ac_config_commands="$ac_config_commands depfiles"
@@ -3674,6 +3716,65 @@ ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
ac_compiler_gnu=$ac_cv_c_compiler_gnu
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC understands -c and -o together" >&5
+$as_echo_n "checking whether $CC understands -c and -o together... " >&6; }
+if ${am_cv_prog_cc_c_o+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+ # Make sure it works both with $CC and with simple cc.
+ # Following AC_PROG_CC_C_O, we do the test twice because some
+ # compilers refuse to overwrite an existing .o file with -o,
+ # though they will create one.
+ am_cv_prog_cc_c_o=yes
+ for am_i in 1 2; do
+ if { echo "$as_me:$LINENO: $CC -c conftest.$ac_ext -o conftest2.$ac_objext" >&5
+ ($CC -c conftest.$ac_ext -o conftest2.$ac_objext) >&5 2>&5
+ ac_status=$?
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } \
+ && test -f conftest2.$ac_objext; then
+ : OK
+ else
+ am_cv_prog_cc_c_o=no
+ break
+ fi
+ done
+ rm -f core conftest*
+ unset am_i
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_prog_cc_c_o" >&5
+$as_echo "$am_cv_prog_cc_c_o" >&6; }
+if test "$am_cv_prog_cc_c_o" != yes; then
+ # Losing compiler, so override with the script.
+ # FIXME: It is wrong to rewrite CC.
+ # But if we don't then we get into trouble of one sort or another.
+ # A longer-term fix would be to have automake use am__CC in this case,
+ # and then we could set am__CC="\$(top_srcdir)/compile \$(CC)"
+ CC="$am_aux_dir/compile $CC"
+fi
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
depcc="$CC" am_compiler_list=
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5
@@ -3910,7 +4011,13 @@ $as_echo_n "checking the archiver ($AR) interface... " >&6; }
if ${am_cv_ar_interface+:} false; then :
$as_echo_n "(cached) " >&6
else
- am_cv_ar_interface=ar
+ ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+ am_cv_ar_interface=ar
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
int some_variable = 0;
@@ -3941,6 +4048,11 @@ if ac_fn_c_try_compile "$LINENO"; then :
fi
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
fi
{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_ar_interface" >&5
@@ -4817,6 +4929,11 @@ else
lt_cv_sys_max_cmd_len=196608
;;
+ os2*)
+ # The test takes a long time on OS/2.
+ lt_cv_sys_max_cmd_len=8192
+ ;;
+
osf*)
# Dr. Hans Ekkehard Plesser reports seeing a kernel panic running configure
# due to this test when exec_disable_arg_limit is 1 on Tru64. It is not
@@ -4856,7 +4973,7 @@ else
# If test is not a shell built-in, we'll probably end up computing a
# maximum length that is only half of the actual maximum length, but
# we can't tell.
- while { test "X"`func_fallback_echo "$teststring$teststring" 2>/dev/null` \
+ while { test "X"`env echo "$teststring$teststring" 2>/dev/null` \
= "X$teststring$teststring"; } >/dev/null 2>&1 &&
test $i != 17 # 1/2 MB should be enough
do
@@ -5282,7 +5399,7 @@ irix5* | irix6* | nonstopux*)
lt_cv_deplibs_check_method=pass_all
;;
-# This must be Linux ELF.
+# This must be glibc/ELF.
linux* | k*bsd*-gnu | kopensolaris*-gnu)
lt_cv_deplibs_check_method=pass_all
;;
@@ -5919,13 +6036,13 @@ old_postuninstall_cmds=
if test -n "$RANLIB"; then
case $host_os in
openbsd*)
- old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB -t \$oldlib"
+ old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB -t \$tool_oldlib"
;;
*)
- old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB \$oldlib"
+ old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB \$tool_oldlib"
;;
esac
- old_archive_cmds="$old_archive_cmds~\$RANLIB \$oldlib"
+ old_archive_cmds="$old_archive_cmds~\$RANLIB \$tool_oldlib"
fi
case $host_os in
@@ -6072,6 +6189,7 @@ for ac_symprfx in "" "_"; do
# which start with @ or ?.
lt_cv_sys_global_symbol_pipe="$AWK '"\
" {last_section=section; section=\$ 3};"\
+" /^COFF SYMBOL TABLE/{for(i in hide) delete hide[i]};"\
" /Section length .*#relocs.*(pick any)/{hide[last_section]=1};"\
" \$ 0!~/External *\|/{next};"\
" / 0+ UNDEF /{next}; / UNDEF \([^|]\)*()/{next};"\
@@ -6360,7 +6478,7 @@ ia64-*-hpux*)
rm -rf conftest*
;;
-x86_64-*kfreebsd*-gnu|x86_64-*linux*|ppc*-*linux*|powerpc*-*linux*| \
+x86_64-*kfreebsd*-gnu|x86_64-*linux*|powerpc*-*linux*| \
s390*-*linux*|s390*-*tpf*|sparc*-*linux*)
# Find out which ABI we are using.
echo 'int i;' > conftest.$ac_ext
@@ -6378,7 +6496,10 @@ s390*-*linux*|s390*-*tpf*|sparc*-*linux*)
x86_64-*linux*)
LD="${LD-ld} -m elf_i386"
;;
- ppc64-*linux*|powerpc64-*linux*)
+ powerpc64le-*linux*)
+ LD="${LD-ld} -m elf32lppclinux"
+ ;;
+ powerpc64-*linux*)
LD="${LD-ld} -m elf32ppclinux"
;;
s390x-*linux*)
@@ -6397,7 +6518,10 @@ s390*-*linux*|s390*-*tpf*|sparc*-*linux*)
x86_64-*linux*)
LD="${LD-ld} -m elf_x86_64"
;;
- ppc*-*linux*|powerpc*-*linux*)
+ powerpcle-*linux*)
+ LD="${LD-ld} -m elf64lppc"
+ ;;
+ powerpc-*linux*)
LD="${LD-ld} -m elf64ppc"
;;
s390*-*linux*|s390*-*tpf*)
@@ -6460,7 +6584,7 @@ $as_echo "$lt_cv_cc_needs_belf" >&6; }
CFLAGS="$SAVE_CFLAGS"
fi
;;
-sparc*-*solaris*)
+*-*solaris*)
# Find out which ABI we are using.
echo 'int i;' > conftest.$ac_ext
if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5
@@ -6471,7 +6595,20 @@ sparc*-*solaris*)
case `/usr/bin/file conftest.o` in
*64-bit*)
case $lt_cv_prog_gnu_ld in
- yes*) LD="${LD-ld} -m elf64_sparc" ;;
+ yes*)
+ case $host in
+ i?86-*-solaris*)
+ LD="${LD-ld} -m elf_x86_64"
+ ;;
+ sparc*-*-solaris*)
+ LD="${LD-ld} -m elf64_sparc"
+ ;;
+ esac
+ # GNU ld 2.21 introduced _sol2 emulations. Use them if available.
+ if ${LD-ld} -V | grep _sol2 >/dev/null 2>&1; then
+ LD="${LD-ld}_sol2"
+ fi
+ ;;
*)
if ${LD-ld} -64 -r -o conftest2.o conftest.o >/dev/null 2>&1; then
LD="${LD-ld} -64"
@@ -7111,7 +7248,13 @@ else
$LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \
-dynamiclib -Wl,-single_module conftest.c 2>conftest.err
_lt_result=$?
- if test -f libconftest.dylib && test ! -s conftest.err && test $_lt_result = 0; then
+ # If there is a non-empty error log, and "single_module"
+ # appears in it, assume the flag caused a linker warning
+ if test -s conftest.err && $GREP single_module conftest.err; then
+ cat conftest.err >&5
+ # Otherwise, if the output was created with a 0 exit code from
+ # the compiler, it worked.
+ elif test -f libconftest.dylib && test $_lt_result -eq 0; then
lt_cv_apple_cc_single_mod=yes
else
cat conftest.err >&5
@@ -7122,6 +7265,7 @@ else
fi
{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_apple_cc_single_mod" >&5
$as_echo "$lt_cv_apple_cc_single_mod" >&6; }
+
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for -exported_symbols_list linker flag" >&5
$as_echo_n "checking for -exported_symbols_list linker flag... " >&6; }
if ${lt_cv_ld_exported_symbols_list+:} false; then :
@@ -7154,6 +7298,7 @@ rm -f core conftest.err conftest.$ac_objext \
fi
{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_ld_exported_symbols_list" >&5
$as_echo "$lt_cv_ld_exported_symbols_list" >&6; }
+
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for -force_load linker flag" >&5
$as_echo_n "checking for -force_load linker flag... " >&6; }
if ${lt_cv_ld_force_load+:} false; then :
@@ -7175,7 +7320,9 @@ _LT_EOF
echo "$LTCC $LTCFLAGS $LDFLAGS -o conftest conftest.c -Wl,-force_load,./libconftest.a" >&5
$LTCC $LTCFLAGS $LDFLAGS -o conftest conftest.c -Wl,-force_load,./libconftest.a 2>conftest.err
_lt_result=$?
- if test -f conftest && test ! -s conftest.err && test $_lt_result = 0 && $GREP forced_load conftest 2>&1 >/dev/null; then
+ if test -s conftest.err && $GREP force_load conftest.err; then
+ cat conftest.err >&5
+ elif test -f conftest && test $_lt_result -eq 0 && $GREP forced_load conftest >/dev/null 2>&1 ; then
lt_cv_ld_force_load=yes
else
cat conftest.err >&5
@@ -7877,7 +8024,22 @@ fi
# Check whether --with-pic was given.
if test "${with_pic+set}" = set; then :
- withval=$with_pic; pic_mode="$withval"
+ withval=$with_pic; lt_p=${PACKAGE-default}
+ case $withval in
+ yes|no) pic_mode=$withval ;;
+ *)
+ pic_mode=default
+ # Look at the argument we got. We use all the common list separators.
+ lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+ for lt_pkg in $withval; do
+ IFS="$lt_save_ifs"
+ if test "X$lt_pkg" = "X$lt_p"; then
+ pic_mode=yes
+ fi
+ done
+ IFS="$lt_save_ifs"
+ ;;
+ esac
else
pic_mode=default
fi
@@ -7955,6 +8117,10 @@ LIBTOOL='$(SHELL) $(top_builddir)/libtool'
+
+
+
+
test -z "$LN_S" && LN_S="ln -s"
@@ -8414,7 +8580,9 @@ lt_prog_compiler_static=
case $cc_basename in
nvcc*) # Cuda Compiler Driver 2.2
lt_prog_compiler_wl='-Xlinker '
- lt_prog_compiler_pic='-Xcompiler -fPIC'
+ if test -n "$lt_prog_compiler_pic"; then
+ lt_prog_compiler_pic="-Xcompiler $lt_prog_compiler_pic"
+ fi
;;
esac
else
@@ -8505,18 +8673,33 @@ lt_prog_compiler_static=
;;
*)
case `$CC -V 2>&1 | sed 5q` in
- *Sun\ F* | *Sun*Fortran*)
+ *Sun\ Ceres\ Fortran* | *Sun*Fortran*\ [1-7].* | *Sun*Fortran*\ 8.[0-3]*)
# Sun Fortran 8.3 passes all unrecognized flags to the linker
lt_prog_compiler_pic='-KPIC'
lt_prog_compiler_static='-Bstatic'
lt_prog_compiler_wl=''
;;
+ *Sun\ F* | *Sun*Fortran*)
+ lt_prog_compiler_pic='-KPIC'
+ lt_prog_compiler_static='-Bstatic'
+ lt_prog_compiler_wl='-Qoption ld '
+ ;;
*Sun\ C*)
# Sun C 5.9
lt_prog_compiler_pic='-KPIC'
lt_prog_compiler_static='-Bstatic'
lt_prog_compiler_wl='-Wl,'
;;
+ *Intel*\ [CF]*Compiler*)
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_pic='-fPIC'
+ lt_prog_compiler_static='-static'
+ ;;
+ *Portland\ Group*)
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_pic='-fpic'
+ lt_prog_compiler_static='-Bstatic'
+ ;;
esac
;;
esac
@@ -8878,7 +9061,6 @@ $as_echo_n "checking whether the $compiler linker ($LD) supports shared librarie
hardcode_direct=no
hardcode_direct_absolute=no
hardcode_libdir_flag_spec=
- hardcode_libdir_flag_spec_ld=
hardcode_libdir_separator=
hardcode_minus_L=no
hardcode_shlibpath_var=unsupported
@@ -9128,8 +9310,7 @@ _LT_EOF
xlf* | bgf* | bgxlf* | mpixlf*)
# IBM XL Fortran 10.1 on PPC cannot create shared libs itself
whole_archive_flag_spec='--whole-archive$convenience --no-whole-archive'
- hardcode_libdir_flag_spec=
- hardcode_libdir_flag_spec_ld='-rpath $libdir'
+ hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir'
archive_cmds='$LD -shared $libobjs $deplibs $linker_flags -soname $soname -o $lib'
if test "x$supports_anon_versioning" = xyes; then
archive_expsym_cmds='echo "{ global:" > $output_objdir/$libname.ver~
@@ -9508,6 +9689,7 @@ fi
# The linker will not automatically build a static lib if we build a DLL.
# _LT_TAGVAR(old_archive_from_new_cmds, )='true'
enable_shared_with_static_runtimes=yes
+ exclude_expsyms='_NULL_IMPORT_DESCRIPTOR|_IMPORT_DESCRIPTOR_.*'
export_symbols_cmds='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[BCDGRS][ ]/s/.*[ ]\([^ ]*\)/\1,DATA/'\'' | $SED -e '\''/^[AITW][ ]/s/.*[ ]//'\'' | sort | uniq > $export_symbols'
# Don't use ranlib
old_postinstall_cmds='chmod 644 $oldlib'
@@ -9553,6 +9735,7 @@ fi
hardcode_shlibpath_var=unsupported
if test "$lt_cv_ld_force_load" = "yes"; then
whole_archive_flag_spec='`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience ${wl}-force_load,$conv\"; done; func_echo_all \"$new_convenience\"`'
+
else
whole_archive_flag_spec=''
fi
@@ -9581,10 +9764,6 @@ fi
hardcode_shlibpath_var=no
;;
- freebsd1*)
- ld_shlibs=no
- ;;
-
# FreeBSD 2.2.[012] allows us to include c++rt0.o to get C++ constructor
# support. Future versions do this automatically, but an explicit c++rt0.o
# does not break anything, and helps significantly (at the cost of a little
@@ -9597,7 +9776,7 @@ fi
;;
# Unfortunately, older versions of FreeBSD 2 do not have this feature.
- freebsd2*)
+ freebsd2.*)
archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'
hardcode_direct=yes
hardcode_minus_L=yes
@@ -9636,7 +9815,6 @@ fi
fi
if test "$with_gnu_ld" = no; then
hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir'
- hardcode_libdir_flag_spec_ld='+b $libdir'
hardcode_libdir_separator=:
hardcode_direct=yes
hardcode_direct_absolute=yes
@@ -10260,11 +10438,6 @@ esac
-
-
-
-
-
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dynamic linker characteristics" >&5
$as_echo_n "checking dynamic linker characteristics... " >&6; }
@@ -10354,7 +10527,7 @@ need_version=unknown
case $host_os in
aix3*)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
library_names_spec='${libname}${release}${shared_ext}$versuffix $libname.a'
shlibpath_var=LIBPATH
@@ -10363,7 +10536,7 @@ aix3*)
;;
aix[4-9]*)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
need_lib_prefix=no
need_version=no
hardcode_into_libs=yes
@@ -10428,7 +10601,7 @@ beos*)
;;
bsdi[45]*)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
need_version=no
library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
soname_spec='${libname}${release}${shared_ext}$major'
@@ -10567,7 +10740,7 @@ darwin* | rhapsody*)
;;
dgux*)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
need_lib_prefix=no
need_version=no
library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname$shared_ext'
@@ -10575,10 +10748,6 @@ dgux*)
shlibpath_var=LD_LIBRARY_PATH
;;
-freebsd1*)
- dynamic_linker=no
- ;;
-
freebsd* | dragonfly*)
# DragonFly does not have aout. When/if they implement a new
# versioning mechanism, adjust this.
@@ -10586,7 +10755,7 @@ freebsd* | dragonfly*)
objformat=`/usr/bin/objformat`
else
case $host_os in
- freebsd[123]*) objformat=aout ;;
+ freebsd[23].*) objformat=aout ;;
*) objformat=elf ;;
esac
fi
@@ -10604,7 +10773,7 @@ freebsd* | dragonfly*)
esac
shlibpath_var=LD_LIBRARY_PATH
case $host_os in
- freebsd2*)
+ freebsd2.*)
shlibpath_overrides_runpath=yes
;;
freebsd3.[01]* | freebsdelf3.[01]*)
@@ -10624,17 +10793,18 @@ freebsd* | dragonfly*)
;;
gnu*)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
need_lib_prefix=no
need_version=no
library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}'
soname_spec='${libname}${release}${shared_ext}$major'
shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
hardcode_into_libs=yes
;;
haiku*)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
need_lib_prefix=no
need_version=no
dynamic_linker="$host_os runtime_loader"
@@ -10695,7 +10865,7 @@ hpux9* | hpux10* | hpux11*)
;;
interix[3-9]*)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
need_lib_prefix=no
need_version=no
library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
@@ -10711,7 +10881,7 @@ irix5* | irix6* | nonstopux*)
nonstopux*) version_type=nonstopux ;;
*)
if test "$lt_cv_prog_gnu_ld" = yes; then
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
else
version_type=irix
fi ;;
@@ -10748,9 +10918,9 @@ linux*oldld* | linux*aout* | linux*coff*)
dynamic_linker=no
;;
-# This must be Linux ELF.
+# This must be glibc/ELF.
linux* | k*bsd*-gnu | kopensolaris*-gnu)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
need_lib_prefix=no
need_version=no
library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
@@ -10836,7 +11006,7 @@ netbsd*)
;;
newsos6)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
shlibpath_var=LD_LIBRARY_PATH
shlibpath_overrides_runpath=yes
@@ -10905,7 +11075,7 @@ rdos*)
;;
solaris*)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
need_lib_prefix=no
need_version=no
library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
@@ -10930,7 +11100,7 @@ sunos4*)
;;
sysv4 | sysv4.3*)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
soname_spec='${libname}${release}${shared_ext}$major'
shlibpath_var=LD_LIBRARY_PATH
@@ -10954,7 +11124,7 @@ sysv4 | sysv4.3*)
sysv4*MP*)
if test -d /usr/nec ;then
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
library_names_spec='$libname${shared_ext}.$versuffix $libname${shared_ext}.$major $libname${shared_ext}'
soname_spec='$libname${shared_ext}.$major'
shlibpath_var=LD_LIBRARY_PATH
@@ -10985,7 +11155,7 @@ sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*)
tpf*)
# TPF is a cross-target only. Preferred cross-host = GNU/Linux.
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
need_lib_prefix=no
need_version=no
library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
@@ -10995,7 +11165,7 @@ tpf*)
;;
uts4*)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
soname_spec='${libname}${release}${shared_ext}$major'
shlibpath_var=LD_LIBRARY_PATH
@@ -11777,6 +11947,8 @@ CC="$lt_save_CC"
+
+
ac_config_commands="$ac_config_commands libtool"
@@ -12335,7 +12507,6 @@ export_dynamic_flag_spec_CXX=
hardcode_direct_CXX=no
hardcode_direct_absolute_CXX=no
hardcode_libdir_flag_spec_CXX=
-hardcode_libdir_flag_spec_ld_CXX=
hardcode_libdir_separator_CXX=
hardcode_minus_L_CXX=no
hardcode_shlibpath_var_CXX=unsupported
@@ -12919,6 +13090,7 @@ fi
hardcode_shlibpath_var_CXX=unsupported
if test "$lt_cv_ld_force_load" = "yes"; then
whole_archive_flag_spec_CXX='`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience ${wl}-force_load,$conv\"; done; func_echo_all \"$new_convenience\"`'
+
else
whole_archive_flag_spec_CXX=''
fi
@@ -12963,7 +13135,7 @@ fi
esac
;;
- freebsd[12]*)
+ freebsd2.*)
# C++ shared libraries reported to be fairly broken before
# switch to ELF
ld_shlibs_CXX=no
@@ -13639,6 +13811,7 @@ _lt_libdeps_save_CFLAGS=$CFLAGS
case "$CC $CFLAGS " in #(
*\ -flto*\ *) CFLAGS="$CFLAGS -fno-lto" ;;
*\ -fwhopr*\ *) CFLAGS="$CFLAGS -fno-whopr" ;;
+*\ -fuse-linker-plugin*\ *) CFLAGS="$CFLAGS -fno-use-linker-plugin" ;;
esac
if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5
@@ -14428,7 +14601,9 @@ $as_echo_n "checking whether the $compiler linker ($LD) supports shared librarie
;;
cygwin* | mingw* | cegcc*)
case $cc_basename in
- cl*) ;;
+ cl*)
+ exclude_expsyms_CXX='_NULL_IMPORT_DESCRIPTOR|_IMPORT_DESCRIPTOR_.*'
+ ;;
*)
export_symbols_cmds_CXX='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[BCDGRS][ ]/s/.*[ ]\([^ ]*\)/\1 DATA/;s/^.*[ ]__nm__\([^ ]*\)[ ][^ ]*/\1 DATA/;/^I[ ]/d;/^[AITW][ ]/s/.* //'\'' | sort | uniq > $export_symbols'
exclude_expsyms_CXX='[_]+GLOBAL_OFFSET_TABLE_|[_]+GLOBAL__[FID]_.*|[_]+head_[A-Za-z0-9_]+_dll|[A-Za-z0-9_]+_dll_iname'
@@ -14581,8 +14756,6 @@ esac
-
-
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dynamic linker characteristics" >&5
$as_echo_n "checking dynamic linker characteristics... " >&6; }
@@ -14608,7 +14781,7 @@ need_version=unknown
case $host_os in
aix3*)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
library_names_spec='${libname}${release}${shared_ext}$versuffix $libname.a'
shlibpath_var=LIBPATH
@@ -14617,7 +14790,7 @@ aix3*)
;;
aix[4-9]*)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
need_lib_prefix=no
need_version=no
hardcode_into_libs=yes
@@ -14682,7 +14855,7 @@ beos*)
;;
bsdi[45]*)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
need_version=no
library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
soname_spec='${libname}${release}${shared_ext}$major'
@@ -14819,7 +14992,7 @@ darwin* | rhapsody*)
;;
dgux*)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
need_lib_prefix=no
need_version=no
library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname$shared_ext'
@@ -14827,10 +15000,6 @@ dgux*)
shlibpath_var=LD_LIBRARY_PATH
;;
-freebsd1*)
- dynamic_linker=no
- ;;
-
freebsd* | dragonfly*)
# DragonFly does not have aout. When/if they implement a new
# versioning mechanism, adjust this.
@@ -14838,7 +15007,7 @@ freebsd* | dragonfly*)
objformat=`/usr/bin/objformat`
else
case $host_os in
- freebsd[123]*) objformat=aout ;;
+ freebsd[23].*) objformat=aout ;;
*) objformat=elf ;;
esac
fi
@@ -14856,7 +15025,7 @@ freebsd* | dragonfly*)
esac
shlibpath_var=LD_LIBRARY_PATH
case $host_os in
- freebsd2*)
+ freebsd2.*)
shlibpath_overrides_runpath=yes
;;
freebsd3.[01]* | freebsdelf3.[01]*)
@@ -14876,17 +15045,18 @@ freebsd* | dragonfly*)
;;
gnu*)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
need_lib_prefix=no
need_version=no
library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}'
soname_spec='${libname}${release}${shared_ext}$major'
shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
hardcode_into_libs=yes
;;
haiku*)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
need_lib_prefix=no
need_version=no
dynamic_linker="$host_os runtime_loader"
@@ -14947,7 +15117,7 @@ hpux9* | hpux10* | hpux11*)
;;
interix[3-9]*)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
need_lib_prefix=no
need_version=no
library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
@@ -14963,7 +15133,7 @@ irix5* | irix6* | nonstopux*)
nonstopux*) version_type=nonstopux ;;
*)
if test "$lt_cv_prog_gnu_ld" = yes; then
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
else
version_type=irix
fi ;;
@@ -15000,9 +15170,9 @@ linux*oldld* | linux*aout* | linux*coff*)
dynamic_linker=no
;;
-# This must be Linux ELF.
+# This must be glibc/ELF.
linux* | k*bsd*-gnu | kopensolaris*-gnu)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
need_lib_prefix=no
need_version=no
library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
@@ -15088,7 +15258,7 @@ netbsd*)
;;
newsos6)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
shlibpath_var=LD_LIBRARY_PATH
shlibpath_overrides_runpath=yes
@@ -15157,7 +15327,7 @@ rdos*)
;;
solaris*)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
need_lib_prefix=no
need_version=no
library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
@@ -15182,7 +15352,7 @@ sunos4*)
;;
sysv4 | sysv4.3*)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
soname_spec='${libname}${release}${shared_ext}$major'
shlibpath_var=LD_LIBRARY_PATH
@@ -15206,7 +15376,7 @@ sysv4 | sysv4.3*)
sysv4*MP*)
if test -d /usr/nec ;then
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
library_names_spec='$libname${shared_ext}.$versuffix $libname${shared_ext}.$major $libname${shared_ext}'
soname_spec='$libname${shared_ext}.$major'
shlibpath_var=LD_LIBRARY_PATH
@@ -15237,7 +15407,7 @@ sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*)
tpf*)
# TPF is a cross-target only. Preferred cross-host = GNU/Linux.
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
need_lib_prefix=no
need_version=no
library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
@@ -15247,7 +15417,7 @@ tpf*)
;;
uts4*)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
soname_spec='${libname}${release}${shared_ext}$major'
shlibpath_var=LD_LIBRARY_PATH
@@ -16028,7 +16198,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
-This file was extended by mmdb2 $as_me 2.0.1, which was
+This file was extended by mmdb2 $as_me 2.0.5, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
@@ -16094,7 +16264,7 @@ _ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
-mmdb2 config.status 2.0.1
+mmdb2 config.status 2.0.5
configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
@@ -16234,6 +16404,7 @@ pic_mode='`$ECHO "$pic_mode" | $SED "$delay_single_quote_subst"`'
enable_fast_install='`$ECHO "$enable_fast_install" | $SED "$delay_single_quote_subst"`'
SHELL='`$ECHO "$SHELL" | $SED "$delay_single_quote_subst"`'
ECHO='`$ECHO "$ECHO" | $SED "$delay_single_quote_subst"`'
+PATH_SEPARATOR='`$ECHO "$PATH_SEPARATOR" | $SED "$delay_single_quote_subst"`'
host_alias='`$ECHO "$host_alias" | $SED "$delay_single_quote_subst"`'
host='`$ECHO "$host" | $SED "$delay_single_quote_subst"`'
host_os='`$ECHO "$host_os" | $SED "$delay_single_quote_subst"`'
@@ -16314,7 +16485,6 @@ with_gnu_ld='`$ECHO "$with_gnu_ld" | $SED "$delay_single_quote_subst"`'
allow_undefined_flag='`$ECHO "$allow_undefined_flag" | $SED "$delay_single_quote_subst"`'
no_undefined_flag='`$ECHO "$no_undefined_flag" | $SED "$delay_single_quote_subst"`'
hardcode_libdir_flag_spec='`$ECHO "$hardcode_libdir_flag_spec" | $SED "$delay_single_quote_subst"`'
-hardcode_libdir_flag_spec_ld='`$ECHO "$hardcode_libdir_flag_spec_ld" | $SED "$delay_single_quote_subst"`'
hardcode_libdir_separator='`$ECHO "$hardcode_libdir_separator" | $SED "$delay_single_quote_subst"`'
hardcode_direct='`$ECHO "$hardcode_direct" | $SED "$delay_single_quote_subst"`'
hardcode_direct_absolute='`$ECHO "$hardcode_direct_absolute" | $SED "$delay_single_quote_subst"`'
@@ -16386,7 +16556,6 @@ with_gnu_ld_CXX='`$ECHO "$with_gnu_ld_CXX" | $SED "$delay_single_quote_subst"`'
allow_undefined_flag_CXX='`$ECHO "$allow_undefined_flag_CXX" | $SED "$delay_single_quote_subst"`'
no_undefined_flag_CXX='`$ECHO "$no_undefined_flag_CXX" | $SED "$delay_single_quote_subst"`'
hardcode_libdir_flag_spec_CXX='`$ECHO "$hardcode_libdir_flag_spec_CXX" | $SED "$delay_single_quote_subst"`'
-hardcode_libdir_flag_spec_ld_CXX='`$ECHO "$hardcode_libdir_flag_spec_ld_CXX" | $SED "$delay_single_quote_subst"`'
hardcode_libdir_separator_CXX='`$ECHO "$hardcode_libdir_separator_CXX" | $SED "$delay_single_quote_subst"`'
hardcode_direct_CXX='`$ECHO "$hardcode_direct_CXX" | $SED "$delay_single_quote_subst"`'
hardcode_direct_absolute_CXX='`$ECHO "$hardcode_direct_absolute_CXX" | $SED "$delay_single_quote_subst"`'
@@ -16428,6 +16597,7 @@ DLLTOOL \
OBJDUMP \
SHELL \
ECHO \
+PATH_SEPARATOR \
SED \
GREP \
EGREP \
@@ -16476,7 +16646,6 @@ with_gnu_ld \
allow_undefined_flag \
no_undefined_flag \
hardcode_libdir_flag_spec \
-hardcode_libdir_flag_spec_ld \
hardcode_libdir_separator \
exclude_expsyms \
include_expsyms \
@@ -16510,7 +16679,6 @@ with_gnu_ld_CXX \
allow_undefined_flag_CXX \
no_undefined_flag_CXX \
hardcode_libdir_flag_spec_CXX \
-hardcode_libdir_flag_spec_ld_CXX \
hardcode_libdir_separator_CXX \
exclude_expsyms_CXX \
include_expsyms_CXX \
@@ -17316,8 +17484,8 @@ $as_echo X"$file" |
# NOTE: Changes made to this file will be lost: look at ltmain.sh.
#
# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005,
-# 2006, 2007, 2008, 2009, 2010 Free Software Foundation,
-# Inc.
+# 2006, 2007, 2008, 2009, 2010, 2011 Free Software
+# Foundation, Inc.
# Written by Gordon Matzigkeit, 1996
#
# This file is part of GNU Libtool.
@@ -17380,6 +17548,9 @@ SHELL=$lt_SHELL
# An echo program that protects backslashes.
ECHO=$lt_ECHO
+# The PATH separator for the build system.
+PATH_SEPARATOR=$lt_PATH_SEPARATOR
+
# The host system.
host_alias=$host_alias
host=$host
@@ -17675,10 +17846,6 @@ no_undefined_flag=$lt_no_undefined_flag
# This must work even if \$libdir does not exist
hardcode_libdir_flag_spec=$lt_hardcode_libdir_flag_spec
-# If ld is used when linking, flag to hardcode \$libdir into a binary
-# during linking. This must work even if \$libdir does not exist.
-hardcode_libdir_flag_spec_ld=$lt_hardcode_libdir_flag_spec_ld
-
# Whether we need a single "-rpath" flag with a separated argument.
hardcode_libdir_separator=$lt_hardcode_libdir_separator
@@ -18021,10 +18188,6 @@ no_undefined_flag=$lt_no_undefined_flag_CXX
# This must work even if \$libdir does not exist
hardcode_libdir_flag_spec=$lt_hardcode_libdir_flag_spec_CXX
-# If ld is used when linking, flag to hardcode \$libdir into a binary
-# during linking. This must work even if \$libdir does not exist.
-hardcode_libdir_flag_spec_ld=$lt_hardcode_libdir_flag_spec_ld_CXX
-
# Whether we need a single "-rpath" flag with a separated argument.
hardcode_libdir_separator=$lt_hardcode_libdir_separator_CXX
diff --git a/configure.ac b/configure.ac
index f685b56..7fde3f3 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,5 +1,5 @@
-AC_INIT(mmdb2, 2.0.1) # keep in sync with mmdb2/mmdb_defs.h
+AC_INIT(mmdb2, 2.0.5) # keep in sync with mmdb2/mmdb_defs.h
AC_CONFIG_AUX_DIR(build-aux)
AC_CONFIG_MACRO_DIR(m4)
diff --git a/m4/libtool.m4 b/m4/libtool.m4
old mode 100755
new mode 100644
index 88de383..f12cfdf
--- a/m4/libtool.m4
+++ b/m4/libtool.m4
@@ -1,8 +1,8 @@
# libtool.m4 - Configure libtool for the host system. -*-Autoconf-*-
#
# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005,
-# 2006, 2007, 2008, 2009, 2010 Free Software Foundation,
-# Inc.
+# 2006, 2007, 2008, 2009, 2010, 2011 Free Software
+# Foundation, Inc.
# Written by Gordon Matzigkeit, 1996
#
# This file is free software; the Free Software Foundation gives
@@ -11,8 +11,8 @@
m4_define([_LT_COPYING], [dnl
# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005,
-# 2006, 2007, 2008, 2009, 2010 Free Software Foundation,
-# Inc.
+# 2006, 2007, 2008, 2009, 2010, 2011 Free Software
+# Foundation, Inc.
# Written by Gordon Matzigkeit, 1996
#
# This file is part of GNU Libtool.
@@ -146,6 +146,8 @@ AC_REQUIRE([AC_CANONICAL_BUILD])dnl
AC_REQUIRE([_LT_PREPARE_SED_QUOTE_VARS])dnl
AC_REQUIRE([_LT_PROG_ECHO_BACKSLASH])dnl
+_LT_DECL([], [PATH_SEPARATOR], [1], [The PATH separator for the build system])dnl
+dnl
_LT_DECL([], [host_alias], [0], [The host system])dnl
_LT_DECL([], [host], [0])dnl
_LT_DECL([], [host_os], [0])dnl
@@ -637,7 +639,7 @@ m4_ifset([AC_PACKAGE_NAME], [AC_PACKAGE_NAME ])config.lt[]dnl
m4_ifset([AC_PACKAGE_VERSION], [ AC_PACKAGE_VERSION])
configured by $[0], generated by m4_PACKAGE_STRING.
-Copyright (C) 2010 Free Software Foundation, Inc.
+Copyright (C) 2011 Free Software Foundation, Inc.
This config.lt script is free software; the Free Software Foundation
gives unlimited permision to copy, distribute and modify it."
@@ -801,6 +803,7 @@ AC_DEFUN([LT_LANG],
m4_case([$1],
[C], [_LT_LANG(C)],
[C++], [_LT_LANG(CXX)],
+ [Go], [_LT_LANG(GO)],
[Java], [_LT_LANG(GCJ)],
[Fortran 77], [_LT_LANG(F77)],
[Fortran], [_LT_LANG(FC)],
@@ -822,6 +825,31 @@ m4_defun([_LT_LANG],
])# _LT_LANG
+m4_ifndef([AC_PROG_GO], [
+############################################################
+# NOTE: This macro has been submitted for inclusion into #
+# GNU Autoconf as AC_PROG_GO. When it is available in #
+# a released version of Autoconf we should remove this #
+# macro and use it instead. #
+############################################################
+m4_defun([AC_PROG_GO],
+[AC_LANG_PUSH(Go)dnl
+AC_ARG_VAR([GOC], [Go compiler command])dnl
+AC_ARG_VAR([GOFLAGS], [Go compiler flags])dnl
+_AC_ARG_VAR_LDFLAGS()dnl
+AC_CHECK_TOOL(GOC, gccgo)
+if test -z "$GOC"; then
+ if test -n "$ac_tool_prefix"; then
+ AC_CHECK_PROG(GOC, [${ac_tool_prefix}gccgo], [${ac_tool_prefix}gccgo])
+ fi
+fi
+if test -z "$GOC"; then
+ AC_CHECK_PROG(GOC, gccgo, gccgo, false)
+fi
+])#m4_defun
+])#m4_ifndef
+
+
# _LT_LANG_DEFAULT_CONFIG
# -----------------------
m4_defun([_LT_LANG_DEFAULT_CONFIG],
@@ -852,6 +880,10 @@ AC_PROVIDE_IFELSE([AC_PROG_GCJ],
m4_ifdef([LT_PROG_GCJ],
[m4_define([LT_PROG_GCJ], defn([LT_PROG_GCJ])[LT_LANG(GCJ)])])])])])
+AC_PROVIDE_IFELSE([AC_PROG_GO],
+ [LT_LANG(GO)],
+ [m4_define([AC_PROG_GO], defn([AC_PROG_GO])[LT_LANG(GO)])])
+
AC_PROVIDE_IFELSE([LT_PROG_RC],
[LT_LANG(RC)],
[m4_define([LT_PROG_RC], defn([LT_PROG_RC])[LT_LANG(RC)])])
@@ -954,7 +986,13 @@ m4_defun_once([_LT_REQUIRED_DARWIN_CHECKS],[
$LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \
-dynamiclib -Wl,-single_module conftest.c 2>conftest.err
_lt_result=$?
- if test -f libconftest.dylib && test ! -s conftest.err && test $_lt_result = 0; then
+ # If there is a non-empty error log, and "single_module"
+ # appears in it, assume the flag caused a linker warning
+ if test -s conftest.err && $GREP single_module conftest.err; then
+ cat conftest.err >&AS_MESSAGE_LOG_FD
+ # Otherwise, if the output was created with a 0 exit code from
+ # the compiler, it worked.
+ elif test -f libconftest.dylib && test $_lt_result -eq 0; then
lt_cv_apple_cc_single_mod=yes
else
cat conftest.err >&AS_MESSAGE_LOG_FD
@@ -962,6 +1000,7 @@ m4_defun_once([_LT_REQUIRED_DARWIN_CHECKS],[
rm -rf libconftest.dylib*
rm -f conftest.*
fi])
+
AC_CACHE_CHECK([for -exported_symbols_list linker flag],
[lt_cv_ld_exported_symbols_list],
[lt_cv_ld_exported_symbols_list=no
@@ -973,6 +1012,7 @@ m4_defun_once([_LT_REQUIRED_DARWIN_CHECKS],[
[lt_cv_ld_exported_symbols_list=no])
LDFLAGS="$save_LDFLAGS"
])
+
AC_CACHE_CHECK([for -force_load linker flag],[lt_cv_ld_force_load],
[lt_cv_ld_force_load=no
cat > conftest.c << _LT_EOF
@@ -990,7 +1030,9 @@ _LT_EOF
echo "$LTCC $LTCFLAGS $LDFLAGS -o conftest conftest.c -Wl,-force_load,./libconftest.a" >&AS_MESSAGE_LOG_FD
$LTCC $LTCFLAGS $LDFLAGS -o conftest conftest.c -Wl,-force_load,./libconftest.a 2>conftest.err
_lt_result=$?
- if test -f conftest && test ! -s conftest.err && test $_lt_result = 0 && $GREP forced_load conftest 2>&1 >/dev/null; then
+ if test -s conftest.err && $GREP force_load conftest.err; then
+ cat conftest.err >&AS_MESSAGE_LOG_FD
+ elif test -f conftest && test $_lt_result -eq 0 && $GREP forced_load conftest >/dev/null 2>&1 ; then
lt_cv_ld_force_load=yes
else
cat conftest.err >&AS_MESSAGE_LOG_FD
@@ -1035,8 +1077,8 @@ _LT_EOF
])
-# _LT_DARWIN_LINKER_FEATURES
-# --------------------------
+# _LT_DARWIN_LINKER_FEATURES([TAG])
+# ---------------------------------
# Checks for linker and compiler features on darwin
m4_defun([_LT_DARWIN_LINKER_FEATURES],
[
@@ -1047,6 +1089,8 @@ m4_defun([_LT_DARWIN_LINKER_FEATURES],
_LT_TAGVAR(hardcode_shlibpath_var, $1)=unsupported
if test "$lt_cv_ld_force_load" = "yes"; then
_LT_TAGVAR(whole_archive_flag_spec, $1)='`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience ${wl}-force_load,$conv\"; done; func_echo_all \"$new_convenience\"`'
+ m4_case([$1], [F77], [_LT_TAGVAR(compiler_needs_object, $1)=yes],
+ [FC], [_LT_TAGVAR(compiler_needs_object, $1)=yes])
else
_LT_TAGVAR(whole_archive_flag_spec, $1)=''
fi
@@ -1268,7 +1312,7 @@ ia64-*-hpux*)
rm -rf conftest*
;;
-x86_64-*kfreebsd*-gnu|x86_64-*linux*|ppc*-*linux*|powerpc*-*linux*| \
+x86_64-*kfreebsd*-gnu|x86_64-*linux*|powerpc*-*linux*| \
s390*-*linux*|s390*-*tpf*|sparc*-*linux*)
# Find out which ABI we are using.
echo 'int i;' > conftest.$ac_ext
@@ -1282,7 +1326,10 @@ s390*-*linux*|s390*-*tpf*|sparc*-*linux*)
x86_64-*linux*)
LD="${LD-ld} -m elf_i386"
;;
- ppc64-*linux*|powerpc64-*linux*)
+ powerpc64le-*linux*)
+ LD="${LD-ld} -m elf32lppclinux"
+ ;;
+ powerpc64-*linux*)
LD="${LD-ld} -m elf32ppclinux"
;;
s390x-*linux*)
@@ -1301,7 +1348,10 @@ s390*-*linux*|s390*-*tpf*|sparc*-*linux*)
x86_64-*linux*)
LD="${LD-ld} -m elf_x86_64"
;;
- ppc*-*linux*|powerpc*-*linux*)
+ powerpcle-*linux*)
+ LD="${LD-ld} -m elf64lppc"
+ ;;
+ powerpc-*linux*)
LD="${LD-ld} -m elf64ppc"
;;
s390*-*linux*|s390*-*tpf*)
@@ -1330,14 +1380,27 @@ s390*-*linux*|s390*-*tpf*|sparc*-*linux*)
CFLAGS="$SAVE_CFLAGS"
fi
;;
-sparc*-*solaris*)
+*-*solaris*)
# Find out which ABI we are using.
echo 'int i;' > conftest.$ac_ext
if AC_TRY_EVAL(ac_compile); then
case `/usr/bin/file conftest.o` in
*64-bit*)
case $lt_cv_prog_gnu_ld in
- yes*) LD="${LD-ld} -m elf64_sparc" ;;
+ yes*)
+ case $host in
+ i?86-*-solaris*)
+ LD="${LD-ld} -m elf_x86_64"
+ ;;
+ sparc*-*-solaris*)
+ LD="${LD-ld} -m elf64_sparc"
+ ;;
+ esac
+ # GNU ld 2.21 introduced _sol2 emulations. Use them if available.
+ if ${LD-ld} -V | grep _sol2 >/dev/null 2>&1; then
+ LD="${LD-ld}_sol2"
+ fi
+ ;;
*)
if ${LD-ld} -64 -r -o conftest2.o conftest.o >/dev/null 2>&1; then
LD="${LD-ld} -64"
@@ -1414,13 +1477,13 @@ old_postuninstall_cmds=
if test -n "$RANLIB"; then
case $host_os in
openbsd*)
- old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB -t \$oldlib"
+ old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB -t \$tool_oldlib"
;;
*)
- old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB \$oldlib"
+ old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB \$tool_oldlib"
;;
esac
- old_archive_cmds="$old_archive_cmds~\$RANLIB \$oldlib"
+ old_archive_cmds="$old_archive_cmds~\$RANLIB \$tool_oldlib"
fi
case $host_os in
@@ -1600,6 +1663,11 @@ AC_CACHE_VAL([lt_cv_sys_max_cmd_len], [dnl
lt_cv_sys_max_cmd_len=196608
;;
+ os2*)
+ # The test takes a long time on OS/2.
+ lt_cv_sys_max_cmd_len=8192
+ ;;
+
osf*)
# Dr. Hans Ekkehard Plesser reports seeing a kernel panic running configure
# due to this test when exec_disable_arg_limit is 1 on Tru64. It is not
@@ -1639,7 +1707,7 @@ AC_CACHE_VAL([lt_cv_sys_max_cmd_len], [dnl
# If test is not a shell built-in, we'll probably end up computing a
# maximum length that is only half of the actual maximum length, but
# we can't tell.
- while { test "X"`func_fallback_echo "$teststring$teststring" 2>/dev/null` \
+ while { test "X"`env echo "$teststring$teststring" 2>/dev/null` \
= "X$teststring$teststring"; } >/dev/null 2>&1 &&
test $i != 17 # 1/2 MB should be enough
do
@@ -2185,7 +2253,7 @@ need_version=unknown
case $host_os in
aix3*)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
library_names_spec='${libname}${release}${shared_ext}$versuffix $libname.a'
shlibpath_var=LIBPATH
@@ -2194,7 +2262,7 @@ aix3*)
;;
aix[[4-9]]*)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
need_lib_prefix=no
need_version=no
hardcode_into_libs=yes
@@ -2259,7 +2327,7 @@ beos*)
;;
bsdi[[45]]*)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
need_version=no
library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
soname_spec='${libname}${release}${shared_ext}$major'
@@ -2398,7 +2466,7 @@ m4_if([$1], [],[
;;
dgux*)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
need_lib_prefix=no
need_version=no
library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname$shared_ext'
@@ -2406,10 +2474,6 @@ dgux*)
shlibpath_var=LD_LIBRARY_PATH
;;
-freebsd1*)
- dynamic_linker=no
- ;;
-
freebsd* | dragonfly*)
# DragonFly does not have aout. When/if they implement a new
# versioning mechanism, adjust this.
@@ -2417,7 +2481,7 @@ freebsd* | dragonfly*)
objformat=`/usr/bin/objformat`
else
case $host_os in
- freebsd[[123]]*) objformat=aout ;;
+ freebsd[[23]].*) objformat=aout ;;
*) objformat=elf ;;
esac
fi
@@ -2435,7 +2499,7 @@ freebsd* | dragonfly*)
esac
shlibpath_var=LD_LIBRARY_PATH
case $host_os in
- freebsd2*)
+ freebsd2.*)
shlibpath_overrides_runpath=yes
;;
freebsd3.[[01]]* | freebsdelf3.[[01]]*)
@@ -2455,17 +2519,18 @@ freebsd* | dragonfly*)
;;
gnu*)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
need_lib_prefix=no
need_version=no
library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}'
soname_spec='${libname}${release}${shared_ext}$major'
shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
hardcode_into_libs=yes
;;
haiku*)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
need_lib_prefix=no
need_version=no
dynamic_linker="$host_os runtime_loader"
@@ -2526,7 +2591,7 @@ hpux9* | hpux10* | hpux11*)
;;
interix[[3-9]]*)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
need_lib_prefix=no
need_version=no
library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
@@ -2542,7 +2607,7 @@ irix5* | irix6* | nonstopux*)
nonstopux*) version_type=nonstopux ;;
*)
if test "$lt_cv_prog_gnu_ld" = yes; then
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
else
version_type=irix
fi ;;
@@ -2579,9 +2644,9 @@ linux*oldld* | linux*aout* | linux*coff*)
dynamic_linker=no
;;
-# This must be Linux ELF.
+# This must be glibc/ELF.
linux* | k*bsd*-gnu | kopensolaris*-gnu)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
need_lib_prefix=no
need_version=no
library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
@@ -2648,7 +2713,7 @@ netbsd*)
;;
newsos6)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
shlibpath_var=LD_LIBRARY_PATH
shlibpath_overrides_runpath=yes
@@ -2717,7 +2782,7 @@ rdos*)
;;
solaris*)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
need_lib_prefix=no
need_version=no
library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
@@ -2742,7 +2807,7 @@ sunos4*)
;;
sysv4 | sysv4.3*)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
soname_spec='${libname}${release}${shared_ext}$major'
shlibpath_var=LD_LIBRARY_PATH
@@ -2766,7 +2831,7 @@ sysv4 | sysv4.3*)
sysv4*MP*)
if test -d /usr/nec ;then
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
library_names_spec='$libname${shared_ext}.$versuffix $libname${shared_ext}.$major $libname${shared_ext}'
soname_spec='$libname${shared_ext}.$major'
shlibpath_var=LD_LIBRARY_PATH
@@ -2797,7 +2862,7 @@ sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*)
tpf*)
# TPF is a cross-target only. Preferred cross-host = GNU/Linux.
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
need_lib_prefix=no
need_version=no
library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
@@ -2807,7 +2872,7 @@ tpf*)
;;
uts4*)
- version_type=linux
+ version_type=linux # correct to gnu/linux during the next big refactor
library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
soname_spec='${libname}${release}${shared_ext}$major'
shlibpath_var=LD_LIBRARY_PATH
@@ -3229,7 +3294,7 @@ irix5* | irix6* | nonstopux*)
lt_cv_deplibs_check_method=pass_all
;;
-# This must be Linux ELF.
+# This must be glibc/ELF.
linux* | k*bsd*-gnu | kopensolaris*-gnu)
lt_cv_deplibs_check_method=pass_all
;;
@@ -3649,6 +3714,7 @@ for ac_symprfx in "" "_"; do
# which start with @ or ?.
lt_cv_sys_global_symbol_pipe="$AWK ['"\
" {last_section=section; section=\$ 3};"\
+" /^COFF SYMBOL TABLE/{for(i in hide) delete hide[i]};"\
" /Section length .*#relocs.*(pick any)/{hide[last_section]=1};"\
" \$ 0!~/External *\|/{next};"\
" / 0+ UNDEF /{next}; / UNDEF \([^|]\)*()/{next};"\
@@ -4233,7 +4299,9 @@ m4_if([$1], [CXX], [
case $cc_basename in
nvcc*) # Cuda Compiler Driver 2.2
_LT_TAGVAR(lt_prog_compiler_wl, $1)='-Xlinker '
- _LT_TAGVAR(lt_prog_compiler_pic, $1)='-Xcompiler -fPIC'
+ if test -n "$_LT_TAGVAR(lt_prog_compiler_pic, $1)"; then
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)="-Xcompiler $_LT_TAGVAR(lt_prog_compiler_pic, $1)"
+ fi
;;
esac
else
@@ -4325,18 +4393,33 @@ m4_if([$1], [CXX], [
;;
*)
case `$CC -V 2>&1 | sed 5q` in
- *Sun\ F* | *Sun*Fortran*)
+ *Sun\ Ceres\ Fortran* | *Sun*Fortran*\ [[1-7]].* | *Sun*Fortran*\ 8.[[0-3]]*)
# Sun Fortran 8.3 passes all unrecognized flags to the linker
_LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
_LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
_LT_TAGVAR(lt_prog_compiler_wl, $1)=''
;;
+ *Sun\ F* | *Sun*Fortran*)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld '
+ ;;
*Sun\ C*)
# Sun C 5.9
_LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
_LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
_LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
;;
+ *Intel*\ [[CF]]*Compiler*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-static'
+ ;;
+ *Portland\ Group*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fpic'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
esac
;;
esac
@@ -4496,7 +4579,9 @@ m4_if([$1], [CXX], [
;;
cygwin* | mingw* | cegcc*)
case $cc_basename in
- cl*) ;;
+ cl*)
+ _LT_TAGVAR(exclude_expsyms, $1)='_NULL_IMPORT_DESCRIPTOR|_IMPORT_DESCRIPTOR_.*'
+ ;;
*)
_LT_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[[BCDGRS]][[ ]]/s/.*[[ ]]\([[^ ]]*\)/\1 DATA/;s/^.*[[ ]]__nm__\([[^ ]]*\)[[ ]][[^ ]]*/\1 DATA/;/^I[[ ]]/d;/^[[AITW]][[ ]]/s/.* //'\'' | sort | uniq > $export_symbols'
_LT_TAGVAR(exclude_expsyms, $1)=['[_]+GLOBAL_OFFSET_TABLE_|[_]+GLOBAL__[FID]_.*|[_]+head_[A-Za-z0-9_]+_dll|[A-Za-z0-9_]+_dll_iname']
@@ -4521,7 +4606,6 @@ m4_if([$1], [CXX], [
_LT_TAGVAR(hardcode_direct, $1)=no
_LT_TAGVAR(hardcode_direct_absolute, $1)=no
_LT_TAGVAR(hardcode_libdir_flag_spec, $1)=
- _LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)=
_LT_TAGVAR(hardcode_libdir_separator, $1)=
_LT_TAGVAR(hardcode_minus_L, $1)=no
_LT_TAGVAR(hardcode_shlibpath_var, $1)=unsupported
@@ -4772,8 +4856,7 @@ _LT_EOF
xlf* | bgf* | bgxlf* | mpixlf*)
# IBM XL Fortran 10.1 on PPC cannot create shared libs itself
_LT_TAGVAR(whole_archive_flag_spec, $1)='--whole-archive$convenience --no-whole-archive'
- _LT_TAGVAR(hardcode_libdir_flag_spec, $1)=
- _LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)='-rpath $libdir'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
_LT_TAGVAR(archive_cmds, $1)='$LD -shared $libobjs $deplibs $linker_flags -soname $soname -o $lib'
if test "x$supports_anon_versioning" = xyes; then
_LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $output_objdir/$libname.ver~
@@ -5068,6 +5151,7 @@ _LT_EOF
# The linker will not automatically build a static lib if we build a DLL.
# _LT_TAGVAR(old_archive_from_new_cmds, $1)='true'
_LT_TAGVAR(enable_shared_with_static_runtimes, $1)=yes
+ _LT_TAGVAR(exclude_expsyms, $1)='_NULL_IMPORT_DESCRIPTOR|_IMPORT_DESCRIPTOR_.*'
_LT_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[[BCDGRS]][[ ]]/s/.*[[ ]]\([[^ ]]*\)/\1,DATA/'\'' | $SED -e '\''/^[[AITW]][[ ]]/s/.*[[ ]]//'\'' | sort | uniq > $export_symbols'
# Don't use ranlib
_LT_TAGVAR(old_postinstall_cmds, $1)='chmod 644 $oldlib'
@@ -5114,10 +5198,6 @@ _LT_EOF
_LT_TAGVAR(hardcode_shlibpath_var, $1)=no
;;
- freebsd1*)
- _LT_TAGVAR(ld_shlibs, $1)=no
- ;;
-
# FreeBSD 2.2.[012] allows us to include c++rt0.o to get C++ constructor
# support. Future versions do this automatically, but an explicit c++rt0.o
# does not break anything, and helps significantly (at the cost of a little
@@ -5130,7 +5210,7 @@ _LT_EOF
;;
# Unfortunately, older versions of FreeBSD 2 do not have this feature.
- freebsd2*)
+ freebsd2.*)
_LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'
_LT_TAGVAR(hardcode_direct, $1)=yes
_LT_TAGVAR(hardcode_minus_L, $1)=yes
@@ -5169,7 +5249,6 @@ _LT_EOF
fi
if test "$with_gnu_ld" = no; then
_LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir'
- _LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)='+b $libdir'
_LT_TAGVAR(hardcode_libdir_separator, $1)=:
_LT_TAGVAR(hardcode_direct, $1)=yes
_LT_TAGVAR(hardcode_direct_absolute, $1)=yes
@@ -5611,9 +5690,6 @@ _LT_TAGDECL([], [no_undefined_flag], [1],
_LT_TAGDECL([], [hardcode_libdir_flag_spec], [1],
[Flag to hardcode $libdir into a binary during linking.
This must work even if $libdir does not exist])
-_LT_TAGDECL([], [hardcode_libdir_flag_spec_ld], [1],
- [[If ld is used when linking, flag to hardcode $libdir into a binary
- during linking. This must work even if $libdir does not exist]])
_LT_TAGDECL([], [hardcode_libdir_separator], [1],
[Whether we need a single "-rpath" flag with a separated argument])
_LT_TAGDECL([], [hardcode_direct], [0],
@@ -5771,7 +5847,6 @@ _LT_TAGVAR(export_dynamic_flag_spec, $1)=
_LT_TAGVAR(hardcode_direct, $1)=no
_LT_TAGVAR(hardcode_direct_absolute, $1)=no
_LT_TAGVAR(hardcode_libdir_flag_spec, $1)=
-_LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)=
_LT_TAGVAR(hardcode_libdir_separator, $1)=
_LT_TAGVAR(hardcode_minus_L, $1)=no
_LT_TAGVAR(hardcode_shlibpath_var, $1)=unsupported
@@ -6141,7 +6216,7 @@ if test "$_lt_caught_CXX_error" != yes; then
esac
;;
- freebsd[[12]]*)
+ freebsd2.*)
# C++ shared libraries reported to be fairly broken before
# switch to ELF
_LT_TAGVAR(ld_shlibs, $1)=no
@@ -6902,12 +6977,18 @@ public class foo {
}
};
_LT_EOF
+], [$1], [GO], [cat > conftest.$ac_ext <<_LT_EOF
+package foo
+func foo() {
+}
+_LT_EOF
])
_lt_libdeps_save_CFLAGS=$CFLAGS
case "$CC $CFLAGS " in #(
*\ -flto*\ *) CFLAGS="$CFLAGS -fno-lto" ;;
*\ -fwhopr*\ *) CFLAGS="$CFLAGS -fno-whopr" ;;
+*\ -fuse-linker-plugin*\ *) CFLAGS="$CFLAGS -fno-use-linker-plugin" ;;
esac
dnl Parse the compiler output and extract the necessary
@@ -7104,7 +7185,6 @@ _LT_TAGVAR(export_dynamic_flag_spec, $1)=
_LT_TAGVAR(hardcode_direct, $1)=no
_LT_TAGVAR(hardcode_direct_absolute, $1)=no
_LT_TAGVAR(hardcode_libdir_flag_spec, $1)=
-_LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)=
_LT_TAGVAR(hardcode_libdir_separator, $1)=
_LT_TAGVAR(hardcode_minus_L, $1)=no
_LT_TAGVAR(hardcode_automatic, $1)=no
@@ -7237,7 +7317,6 @@ _LT_TAGVAR(export_dynamic_flag_spec, $1)=
_LT_TAGVAR(hardcode_direct, $1)=no
_LT_TAGVAR(hardcode_direct_absolute, $1)=no
_LT_TAGVAR(hardcode_libdir_flag_spec, $1)=
-_LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)=
_LT_TAGVAR(hardcode_libdir_separator, $1)=
_LT_TAGVAR(hardcode_minus_L, $1)=no
_LT_TAGVAR(hardcode_automatic, $1)=no
@@ -7424,6 +7503,77 @@ CFLAGS=$lt_save_CFLAGS
])# _LT_LANG_GCJ_CONFIG
+# _LT_LANG_GO_CONFIG([TAG])
+# --------------------------
+# Ensure that the configuration variables for the GNU Go compiler
+# are suitably defined. These variables are subsequently used by _LT_CONFIG
+# to write the compiler configuration to `libtool'.
+m4_defun([_LT_LANG_GO_CONFIG],
+[AC_REQUIRE([LT_PROG_GO])dnl
+AC_LANG_SAVE
+
+# Source file extension for Go test sources.
+ac_ext=go
+
+# Object file extension for compiled Go test sources.
+objext=o
+_LT_TAGVAR(objext, $1)=$objext
+
+# Code to be used in simple compile tests
+lt_simple_compile_test_code="package main; func main() { }"
+
+# Code to be used in simple link tests
+lt_simple_link_test_code='package main; func main() { }'
+
+# ltmain only uses $CC for tagged configurations so make sure $CC is set.
+_LT_TAG_COMPILER
+
+# save warnings/boilerplate of simple test code
+_LT_COMPILER_BOILERPLATE
+_LT_LINKER_BOILERPLATE
+
+# Allow CC to be a program name with arguments.
+lt_save_CC=$CC
+lt_save_CFLAGS=$CFLAGS
+lt_save_GCC=$GCC
+GCC=yes
+CC=${GOC-"gccgo"}
+CFLAGS=$GOFLAGS
+compiler=$CC
+_LT_TAGVAR(compiler, $1)=$CC
+_LT_TAGVAR(LD, $1)="$LD"
+_LT_CC_BASENAME([$compiler])
+
+# Go did not exist at the time GCC didn't implicitly link libc in.
+_LT_TAGVAR(archive_cmds_need_lc, $1)=no
+
+_LT_TAGVAR(old_archive_cmds, $1)=$old_archive_cmds
+_LT_TAGVAR(reload_flag, $1)=$reload_flag
+_LT_TAGVAR(reload_cmds, $1)=$reload_cmds
+
+## CAVEAT EMPTOR:
+## There is no encapsulation within the following macros, do not change
+## the running order or otherwise move them around unless you know exactly
+## what you are doing...
+if test -n "$compiler"; then
+ _LT_COMPILER_NO_RTTI($1)
+ _LT_COMPILER_PIC($1)
+ _LT_COMPILER_C_O($1)
+ _LT_COMPILER_FILE_LOCKS($1)
+ _LT_LINKER_SHLIBS($1)
+ _LT_LINKER_HARDCODE_LIBPATH($1)
+
+ _LT_CONFIG($1)
+fi
+
+AC_LANG_RESTORE
+
+GCC=$lt_save_GCC
+CC=$lt_save_CC
+CFLAGS=$lt_save_CFLAGS
+])# _LT_LANG_GO_CONFIG
+
+
# _LT_LANG_RC_CONFIG([TAG])
# -------------------------
# Ensure that the configuration variables for the Windows resource compiler
@@ -7493,6 +7643,13 @@ dnl aclocal-1.4 backwards compatibility:
dnl AC_DEFUN([LT_AC_PROG_GCJ], [])
+# LT_PROG_GO
+# ----------
+AC_DEFUN([LT_PROG_GO],
+[AC_CHECK_TOOL(GOC, gccgo,)
+])
+
+
# LT_PROG_RC
# ----------
AC_DEFUN([LT_PROG_RC],
diff --git a/m4/ltoptions.m4 b/m4/ltoptions.m4
old mode 100755
new mode 100644
index 17cfd51..5d9acd8
--- a/m4/ltoptions.m4
+++ b/m4/ltoptions.m4
@@ -326,9 +326,24 @@ dnl AC_DEFUN([AM_DISABLE_FAST_INSTALL], [])
# MODE is either `yes' or `no'. If omitted, it defaults to `both'.
m4_define([_LT_WITH_PIC],
[AC_ARG_WITH([pic],
- [AS_HELP_STRING([--with-pic],
+ [AS_HELP_STRING([--with-pic@<:@=PKGS@:>@],
[try to use only PIC/non-PIC objects @<:@default=use both@:>@])],
- [pic_mode="$withval"],
+ [lt_p=${PACKAGE-default}
+ case $withval in
+ yes|no) pic_mode=$withval ;;
+ *)
+ pic_mode=default
+ # Look at the argument we got. We use all the common list separators.
+ lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+ for lt_pkg in $withval; do
+ IFS="$lt_save_ifs"
+ if test "X$lt_pkg" = "X$lt_p"; then
+ pic_mode=yes
+ fi
+ done
+ IFS="$lt_save_ifs"
+ ;;
+ esac],
[pic_mode=default])
test -z "$pic_mode" && pic_mode=m4_default([$1], [default])
diff --git a/m4/ltsugar.m4 b/m4/ltsugar.m4
old mode 100755
new mode 100644
diff --git a/m4/ltversion.m4 b/m4/ltversion.m4
old mode 100755
new mode 100644
diff --git a/m4/lt~obsolete.m4 b/m4/lt~obsolete.m4
old mode 100755
new mode 100644
diff --git a/mmdb2/hybrid_36.cpp b/mmdb2/hybrid_36.cpp
index 243f660..b2b03a0 100644
--- a/mmdb2/hybrid_36.cpp
+++ b/mmdb2/hybrid_36.cpp
@@ -1,12 +1,16 @@
-
+// $Id: hybrid_36.cpp $
+// =================================================================
+//
+// CCP4 Coordinate Library: support of coordinate-related
+// functionality in protein crystallography applications.
//
-// This is free software: you can redistribute it and/or
-// modify it under the terms of the GNU Lesser General Public
-// License version 3, modified in accordance with the provisions
+// This library is free software: you can redistribute it and/or
+// modify it under the terms of the GNU Lesser General Public
+// License version 3, modified in accordance with the provisions
// of the license to address the requirements of UK law.
//
-// You should have received a copy of the modified GNU Lesser
-// General Public License along with this library. If not, copies
+// You should have received a copy of the modified GNU Lesser
+// General Public License along with this library. If not, copies
// may be downloaded from http://www.ccp4.ac.uk/ccp4license.php
//
// This program is distributed in the hope that it will be useful,
@@ -14,6 +18,8 @@
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU Lesser General Public License for more details.
//
+// =================================================================
+//
/*! C port of the hy36encode() and hy36decode() functions in the
hybrid_36.py Python prototype/reference implementation.
diff --git a/mmdb2/hybrid_36.h b/mmdb2/hybrid_36.h
index 4811b00..cd65d96 100644
--- a/mmdb2/hybrid_36.h
+++ b/mmdb2/hybrid_36.h
@@ -1,3 +1,26 @@
+// $Id: hybrid_36.h $
+// =================================================================
+//
+// CCP4 Coordinate Library: support of coordinate-related
+// functionality in protein crystallography applications.
+//
+// This library is free software: you can redistribute it and/or
+// modify it under the terms of the GNU Lesser General Public
+// License version 3, modified in accordance with the provisions
+// of the license to address the requirements of UK law.
+//
+// You should have received a copy of the modified GNU Lesser
+// General Public License along with this library. If not, copies
+// may be downloaded from http://www.ccp4.ac.uk/ccp4license.php
+//
+// This program 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 Lesser General Public License for more details.
+//
+// =================================================================
+//
+
/* If you change the include guards, please be sure to also rename the
functions below. Otherwise your project will clash with the original
iotbx declarations and definitions.
diff --git a/mmdb2/mmdb_atom.cpp b/mmdb2/mmdb_atom.cpp
index 0dcc986..1beddd9 100644
--- a/mmdb2/mmdb_atom.cpp
+++ b/mmdb2/mmdb_atom.cpp
@@ -4,7 +4,7 @@
// CCP4 Coordinate Library: support of coordinate-related
// functionality in protein crystallography applications.
//
-// Copyright (C) Eugene Krissinel 2000-2013.
+// Copyright (C) Eugene Krissinel 2000-2015.
//
// This library is free software: you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
@@ -22,7 +22,7 @@
//
// =================================================================
//
-// 18.10.13 <-- Date of Last Modification.
+// 07.09.15 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
@@ -35,7 +35,7 @@
// **** Functions: mmdb::BondAngle
// ~~~~~~~~~~
//
-// Copyright (C) E. Krissinel 2000-2013
+// Copyright (C) E. Krissinel 2000-2015
//
// =================================================================
//
@@ -56,9 +56,9 @@ namespace mmdb {
// ================================================================
- #define ASET_ShortBinary 0x10000000
- #define ASET_ShortTer 0x20000000
- #define ASET_ShortHet 0x40000000
+ #define ASET_CompactBinary 0x10000000
+ #define ASET_ShortTer 0x20000000
+ #define ASET_ShortHet 0x40000000
bool ignoreSegID = false;
bool ignoreElement = false;
@@ -1218,7 +1218,7 @@ namespace mmdb {
dz = r[2][0]*a->x + r[2][1]*a->y + r[2][2]*a->z + t[2] - z;
return dx*dx + dy*dy + dz*dz;
}
-
+
realtype Atom::GetDist2 ( realtype ax, realtype ay, realtype az ) {
realtype dx,dy,dz;
dx = ax - x;
@@ -1226,6 +1226,14 @@ namespace mmdb {
dz = az - z;
return dx*dx + dy*dy + dz*dz;
}
+
+ realtype Atom::GetDist2 ( vect3 & xyz ) {
+ realtype dx,dy,dz;
+ dx = xyz[0] - x;
+ dy = xyz[1] - y;
+ dz = xyz[2] - z;
+ return dx*dx + dy*dy + dz*dz;
+ }
realtype Atom::GetCosine ( PAtom a1, PAtom a2 ) {
// Calculates cosing of angle a1-this-a2, i.e. that between
@@ -1784,15 +1792,21 @@ namespace mmdb {
y = y1;
z = z1;
}
-
+
void Atom::TransformCopy ( mat44 & tm,
- realtype & xx,
- realtype & yy,
- realtype & zz ) {
+ realtype & xx,
+ realtype & yy,
+ realtype & zz ) {
xx = tm[0][0]*x + tm[0][1]*y + tm[0][2]*z + tm[0][3];
yy = tm[1][0]*x + tm[1][1]*y + tm[1][2]*z + tm[1][3];
zz = tm[2][0]*x + tm[2][1]*y + tm[2][2]*z + tm[2][3];
}
+
+ void Atom::TransformCopy ( mat44 & tm, vect3 & xyz ) {
+ xyz[0] = tm[0][0]*x + tm[0][1]*y + tm[0][2]*z + tm[0][3];
+ xyz[1] = tm[1][0]*x + tm[1][1]*y + tm[1][2]*z + tm[1][3];
+ xyz[2] = tm[2][0]*x + tm[2][1]*y + tm[2][2]*z + tm[2][3];
+ }
void Atom::TransformSet ( mat44 & tm,
realtype xx,
@@ -1942,8 +1956,8 @@ namespace mmdb {
return CheckID ( aname,elname,aloc );
}
- void Atom::SetShortBinary() {
- WhatIsSet |= ASET_ShortBinary;
+ void Atom::SetCompactBinary() {
+ WhatIsSet |= ASET_CompactBinary;
}
void Atom::write ( io::RFile f ) {
@@ -1952,7 +1966,7 @@ namespace mmdb {
byte nb;
f.WriteWord ( &WhatIsSet );
- if (WhatIsSet & ASET_ShortBinary) {
+ if (WhatIsSet & ASET_CompactBinary) {
if (Ter) WhatIsSet |= ASET_ShortTer;
if (Het) WhatIsSet |= ASET_ShortHet;
f.WriteInt ( &index );
@@ -1960,9 +1974,30 @@ namespace mmdb {
f.WriteTerLine ( altLoc ,false );
f.WriteTerLine ( element,false );
if (WhatIsSet & ASET_Coordinates) {
+ /*
+ char S[100];
+ sprintf ( S,"%8.3f%8.3f%8.3f",x,y,z );
+ f.WriteFile ( S,24 );
+ */
+ /*
+ f.WriteReal ( &x );
+ f.WriteReal ( &y );
+ f.WriteReal ( &z );
+ */
+
+ // Make integer conversion in order to eliminate round-offs
+ // from PDB format %8.3f for coordinates and save space
+ // comparing to real*8 numbers. Writing floats causes
+ // precision loss
+ k = mround(x*10000.0); f.WriteInt ( &k );
+ k = mround(y*10000.0); f.WriteInt ( &k );
+ k = mround(z*10000.0); f.WriteInt ( &k );
+
+ /*
f.WriteFloat ( &x );
f.WriteFloat ( &y );
f.WriteFloat ( &z );
+ */
}
return;
}
@@ -2042,15 +2077,38 @@ namespace mmdb {
FreeMemory();
f.ReadWord ( &WhatIsSet );
- if (WhatIsSet & ASET_ShortBinary) {
+ if (WhatIsSet & ASET_CompactBinary) {
f.ReadInt ( &index );
f.ReadTerLine ( name ,false );
f.ReadTerLine ( altLoc ,false );
f.ReadTerLine ( element,false );
if (WhatIsSet & ASET_Coordinates) {
+ /*
+ char S[100];
+ f.ReadFile ( S,24 );
+ GetReal(x,&(S[0]),8);
+ GetReal(y,&(S[8]),8);
+ GetReal(z,&(S[16]),8);
+ */
+ /*
+ f.ReadReal ( &x );
+ f.ReadReal( &y );
+ f.ReadReal ( &z );
+ */
+
+ // Make integer conversion in order to eliminate round-offs
+ // from PDB format %8.3f for coordinates and save space
+ // comparing to real*8 numbers. Writing floats causes
+ // precision loss
+ f.ReadInt ( &k ); x = realtype(k)/10000.0;
+ f.ReadInt ( &k ); y = realtype(k)/10000.0;
+ f.ReadInt ( &k ); z = realtype(k)/10000.0;
+
+ /*
f.ReadFloat ( &x );
f.ReadFloat ( &y );
f.ReadFloat ( &z );
+ */
}
serNum = index;
Ter = WhatIsSet & ASET_ShortTer;
@@ -3410,34 +3468,97 @@ namespace mmdb {
}
- void Residue::write ( io::RFile f ) {
+ void Residue::write ( io::RFile f ) {
int i;
- byte Version=2;
+ bool shortBinary = false;
+ byte Version=3;
- UDData::write ( f );
+ f.WriteByte ( &Version );
+
+ if (nAtoms>0) {
+ if (atom[0]->WhatIsSet & ASET_CompactBinary)
+ shortBinary = true;
+ }
- f.WriteByte ( &Version );
- f.WriteInt ( &seqNum );
- f.WriteInt ( &label_seq_id );
- f.WriteInt ( &label_entity_id );
- f.WriteInt ( &index );
- f.WriteInt ( &nAtoms );
- f.WriteByte ( &SSE );
- f.WriteTerLine ( name ,false );
- f.WriteTerLine ( label_comp_id,false );
- f.WriteTerLine ( label_asym_id,false );
- f.WriteTerLine ( insCode ,false );
+ f.WriteBool ( &shortBinary );
+
+ if (!shortBinary) {
+ UDData::write ( f );
+ f.WriteInt ( &label_seq_id );
+ f.WriteInt ( &label_entity_id );
+ f.WriteTerLine ( label_comp_id,false );
+ f.WriteTerLine ( label_asym_id,false );
+ }
+
+ f.WriteInt ( &seqNum );
+ f.WriteInt ( &index );
+ f.WriteInt ( &nAtoms );
+ f.WriteByte ( &SSE );
+ f.WriteTerLine ( name ,false );
+ f.WriteTerLine ( insCode,false );
for (i=0;i<nAtoms;i++)
f.WriteInt ( &(atom[i]->index) );
}
+
+ void Residue::read ( io::RFile f ) {
+ // IMPORTANT: array Atom in Root class should be
+ // read prior calling this function!
+ PPAtom A;
+ int i,k;
+ byte Version;
+ bool shortBinary;
+ FreeMemory();
+
+ f.ReadByte ( &Version );
+ f.ReadBool ( &shortBinary );
+
+ if (!shortBinary) {
+ UDData::read ( f );
+ f.ReadInt ( &label_seq_id );
+ f.ReadInt ( &label_entity_id );
+ f.ReadTerLine ( label_comp_id,false );
+ f.ReadTerLine ( label_asym_id,false );
+ }
+
+ f.ReadInt ( &seqNum );
+ f.ReadInt ( &index );
+ f.ReadInt ( &nAtoms );
+ f.ReadByte ( &SSE );
+ f.ReadTerLine ( name ,false );
+ f.ReadTerLine ( insCode,false );
+ AtmLen = nAtoms;
+ A = NULL;
+ if (chain) {
+ if (chain->model)
+ A = chain->model->GetAllAtoms();
+ }
+ if ((nAtoms>0) && (A)) {
+ atom = new PAtom[nAtoms];
+ for (i=0;i<nAtoms;i++) {
+ f.ReadInt ( &k );
+ atom[i] = A[k-1];
+ atom[i]->SetResidue ( this );
+ atom[i]->_setBonds ( A );
+ }
+ } else {
+ for (i=0;i<nAtoms;i++)
+ f.ReadInt ( &k );
+ nAtoms = 0;
+ AtmLen = 0;
+ }
+
+ }
+
+
+ /* === old function, keep for a while
void Residue::read ( io::RFile f ) {
// IMPORTANT: array Atom in Root class should be
// read prior calling this function!
PPAtom A;
- int i,k;
- byte Version;
+ int i,k;
+ byte Version;
FreeMemory ();
@@ -3479,7 +3600,7 @@ namespace mmdb {
AtmLen = 0;
}
}
-
+*/
MakeFactoryFunctions(Residue)
diff --git a/mmdb2/mmdb_atom.h b/mmdb2/mmdb_atom.h
index 63d5cb3..626af12 100644
--- a/mmdb2/mmdb_atom.h
+++ b/mmdb2/mmdb_atom.h
@@ -4,7 +4,7 @@
// CCP4 Coordinate Library: support of coordinate-related
// functionality in protein crystallography applications.
//
-// Copyright (C) Eugene Krissinel 2000-2013.
+// Copyright (C) Eugene Krissinel 2000-2015.
//
// This library is free software: you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
@@ -22,7 +22,7 @@
//
// =================================================================
//
-// 12.09.13 <-- Date of Last Modification.
+// 07.09.15 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
@@ -35,7 +35,7 @@
// **** Functions: mmdb::BondAngle
// ~~~~~~~~~~
//
-// Copyright (C) E. Krissinel 2000-2013
+// Copyright (C) E. Krissinel 2000-2015
//
// =================================================================
//
@@ -308,6 +308,7 @@ namespace mmdb {
realtype GetDist2 ( PAtom a, mat44 & tm ); // tm applies to A
realtype GetDist2 ( PAtom a, mat33 & r, vect3 & t );// tm applies to A
realtype GetDist2 ( realtype ax, realtype ay, realtype az );
+ realtype GetDist2 ( vect3 & xyz );
// GetCosine(a1,a2) calculates cosine of angle a1-this-a2,
// i.e. that between vectors [a1,this] and [this,a2].
@@ -316,8 +317,8 @@ namespace mmdb {
PResidue GetResidue ();
PChain GetChain ();
PModel GetModel ();
- int GetResidueNo();
- void * GetCoordHierarchy(); // PRoot
+ int GetResidueNo();
+ void * GetCoordHierarchy(); // PRoot
// GetAtomID(..) generates atom ID in the form
// /m/c/r(rn).i/n[e]:a
@@ -396,6 +397,7 @@ namespace mmdb {
void Transform ( mat44 & tm );
void TransformCopy ( mat44 & tm,
realtype & xx, realtype & yy, realtype & zz );
+ void TransformCopy ( mat44 & tm, vect3 & xyz );
void TransformSet ( mat44 & tm,
realtype xx, realtype yy, realtype zz );
@@ -416,7 +418,7 @@ namespace mmdb {
virtual void Copy ( PAtom atom ); // without references in
// residues
- void SetShortBinary(); // leaves only coordinates in binary files
+ void SetCompactBinary(); // leaves only coordinates in binary files
void write ( io::RFile f );
void read ( io::RFile f );
diff --git a/mmdb2/mmdb_chain.cpp b/mmdb2/mmdb_chain.cpp
index 1c3ab8e..98fc664 100644
--- a/mmdb2/mmdb_chain.cpp
+++ b/mmdb2/mmdb_chain.cpp
@@ -50,7 +50,7 @@
#include "mmdb_chain.h"
#include "mmdb_model.h"
-#include "mmdb_root.h"
+#include "mmdb_manager.h"
#include "mmdb_cifdefs.h"
namespace mmdb {
@@ -2440,25 +2440,35 @@ namespace mmdb {
void Chain::write ( io::RFile f ) {
int i;
- byte Version=1;
-
- f.WriteByte ( &Version );
-
- UDData::write ( f );
-
- f.WriteTerLine ( chainID ,false );
- f.WriteTerLine ( prevChainID,false );
-
- DBRef .write ( f ); // Database reference
- seqAdv.write ( f ); // SEQADV records
- seqRes.write ( f ); // SEQRES data
- modRes.write ( f ); // MODRES records
- Het .write ( f ); // HET records
-
+ byte Version=2;
+ bool compactBinary = false;
+
+ PManager M = GetCoordHierarchy();
+ if (M)
+ compactBinary = M->isCompactBinary();
+
+ f.WriteByte ( &Version );
+ f.WriteBool ( &compactBinary );
+ f.WriteTerLine ( chainID,false );
+
f.WriteInt ( &nResidues );
for (i=0;i<nResidues;i++)
residue[i]->write ( f );
+ if (!compactBinary) {
+
+ UDData::write ( f );
+
+ f.WriteTerLine ( prevChainID,false );
+
+ DBRef .write ( f ); // Database reference
+ seqAdv.write ( f ); // SEQADV records
+ seqRes.write ( f ); // SEQRES data
+ modRes.write ( f ); // MODRES records
+ Het .write ( f ); // HET records
+
+ }
+
}
void Chain::read ( io::RFile f ) {
@@ -2466,24 +2476,16 @@ namespace mmdb {
// prior to calling this function!
int i;
byte Version;
+ bool compactBinary;
FreeMemory();
- f.ReadByte ( &Version );
-
- UDData::read ( f );
-
- f.ReadTerLine ( chainID ,false );
- f.ReadTerLine ( prevChainID,false );
-
- DBRef .read ( f ); // Database reference
- seqAdv.read ( f ); // SEQADV records
- seqRes.read ( f ); // SEQRES data
- modRes.read ( f ); // MODRES records
- Het .read ( f ); // HET records
-
+ f.ReadByte ( &Version );
+ f.ReadBool ( &compactBinary );
+ f.ReadTerLine ( chainID,false );
+
SetChain ( chainID );
-
+
f.ReadInt ( &nResidues );
resLen = nResidues;
if (nResidues>0) {
@@ -2495,6 +2497,20 @@ namespace mmdb {
}
}
+ if (!compactBinary) {
+
+ UDData::read ( f );
+
+ f.ReadTerLine ( prevChainID,false );
+
+ DBRef .read ( f ); // Database reference
+ seqAdv.read ( f ); // SEQADV records
+ seqRes.read ( f ); // SEQRES data
+ modRes.read ( f ); // MODRES records
+ Het .read ( f ); // HET records
+
+ }
+
}
diff --git a/mmdb2/mmdb_coormngr.cpp b/mmdb2/mmdb_coormngr.cpp
index 0ab4fbf..455227d 100644
--- a/mmdb2/mmdb_coormngr.cpp
+++ b/mmdb2/mmdb_coormngr.cpp
@@ -22,7 +22,7 @@
//
// =================================================================
//
-// 14.07.13 <-- Date of Last Modification.
+// 07.09.15 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
@@ -33,7 +33,7 @@
// **** Classes : mmdb::Brick ( space brick )
// ~~~~~~~~~ mmdb::CoorManager ( MMDB atom coordinate manager )
//
-// (C) E. Krissinel 2000-2013
+// (C) E. Krissinel 2000-2015
//
// =================================================================
//
@@ -2463,23 +2463,32 @@ namespace mmdb {
}
void CoorManager::GetBrickCoor ( PAtom A,
- int & nx, int & ny, int & nz ) {
+ int & nx, int & ny, int & nz ) {
nx = (int)floor((A->x-xbrick_0)/brick_size);
ny = (int)floor((A->y-ybrick_0)/brick_size);
nz = (int)floor((A->z-zbrick_0)/brick_size);
if ((ny<0) || (nz<0) || (nx>=nbrick_x) ||
(ny>=nbrick_y) || (nz>=nbrick_z)) nx = -1;
}
-
+
void CoorManager::GetBrickCoor ( realtype x, realtype y,
realtype z, int & nx,
- int & ny, int & nz ) {
+ int & ny, int & nz ) {
nx = (int)floor((x-xbrick_0)/brick_size);
ny = (int)floor((y-ybrick_0)/brick_size);
nz = (int)floor((z-zbrick_0)/brick_size);
if ((ny<0) || (nz<0) || (nx>=nbrick_x) ||
(ny>=nbrick_y) || (nz>=nbrick_z)) nx = -1;
}
+
+ void CoorManager::GetBrickCoor ( vect3 & xyz,
+ int & nx, int & ny, int & nz ) {
+ nx = (int)floor((xyz[0]-xbrick_0)/brick_size);
+ ny = (int)floor((xyz[1]-ybrick_0)/brick_size);
+ nz = (int)floor((xyz[2]-zbrick_0)/brick_size);
+ if ((ny<0) || (nz<0) || (nx>=nbrick_x) ||
+ (ny>=nbrick_y) || (nz>=nbrick_z)) nx = -1;
+ }
void CoorManager::GetBrickDimension (
int & nxmax, int & nymax, int & nzmax ) {
@@ -2504,16 +2513,17 @@ namespace mmdb {
return NULL;
}
- void CoorManager::MakeBricks ( PPAtom atmvec, int avlen,
- realtype Margin,
- realtype BrickSize ) {
+ void CoorManager::MakeBricks ( PPAtom atmvec,
+ int avlen,
+ realtype Margin,
+ realtype BrickSize ) {
// Makes bricking for atoms contained in vector atmvec of length
// avlen, with brick size BrickSize (in angstroms). The previous
// bricking, if there was any, is removed.
int i,j, nx,ny,nz, alen;
realtype x1,x2, y1,y2, z1,z2, dx,dy,dz;
- PPAtom A;
-
+ PPAtom A;
+
RemoveBricks();
brick_size = BrickSize;
@@ -3895,20 +3905,84 @@ namespace mmdb {
}
+
+ void CoorManager::SeekContacts ( vect3 * xyz,
+ int nxyz,
+ realtype contDist,
+ PContact contact,
+ int & ncontacts
+ ) {
+ // Simplified optimized for speed and convenience version:
+ // - bricking is pre-done
+ // - contacting set of atoms is given as a bare vect3 (xyz)
+ // coordinate vector
+ // - no checks for identity atoms
+ // - contact must be pre-allocated with at least ilen1*ilen2
+ // elements
+ // - contact returns square distances
+ // - ncontacts is always reset
+ realtype contDist2, dx,dy,dz, d2;
+ int i,j, nx,ny,nz, dn;
+ int ix1,ix2, iy1,iy2, iz1,iz2, ix,iy,iz;
+ PBrick B;
- void CoorManager::SeekContacts ( PPAtom AIndex1,
- int ilen1,
- PPAtom * AIndex2,
- ivector ilen2,
- int nStructures,
- realtype dist1,
- realtype dist2,
- PPMContact & contact,
- int bricking
- ) {
+ contDist2 = contDist*contDist;
+
+ ncontacts = 0;
+
+ if (!brick) return;
+
+ dn = (int)floor(contDist/brick_size)+1;
+
+ for (i=0;i<nxyz;i++) {
+ // Find brick location
+ GetBrickCoor ( xyz[i],nx,ny,nz );
+ if (nx>=0) {
+ ix1 = IMax ( 0,nx-dn );
+ iy1 = IMax ( 0,ny-dn );
+ iz1 = IMax ( 0,nz-dn );
+ ix2 = IMin ( nbrick_x,nx+dn+1 );
+ iy2 = IMin ( nbrick_y,ny+dn+1 );
+ iz2 = IMin ( nbrick_z,nz+dn+1 );
+ for (ix=ix1;ix<ix2;ix++)
+ if (brick[ix])
+ for (iy=iy1;iy<iy2;iy++)
+ if (brick[ix][iy])
+ for (iz=iz1;iz<iz2;iz++) {
+ B = brick[ix][iy][iz];
+ if (B)
+ for (j=0;j<B->nAtoms;j++) {
+ dx = xyz[i][0] - B->atom[j]->x;
+ dy = xyz[i][1] - B->atom[j]->y;
+ dz = xyz[i][2] - B->atom[j]->z;
+ d2 = dx*dx + dy*dy + dz*dz;
+ if (d2<=contDist2) {
+ contact[ncontacts].id1 = B->id[j];
+ contact[ncontacts].id2 = i;
+ contact[ncontacts].dist = d2;
+ ncontacts++;
+ }
+ }
+ }
+ }
+ }
+
+ }
+
+
+ void CoorManager::SeekContacts ( PPAtom AIndex1,
+ int ilen1,
+ PPAtom * AIndex2,
+ ivector ilen2,
+ int nStructures,
+ realtype dist1,
+ realtype dist2,
+ PPMContact & contact,
+ int bricking
+ ) {
// It is Ok to have NULL pointers in AIndex1 and AIndex2
- PMBrick B;
- PAtom A;
+ PMBrick B;
+ PAtom A;
realtype d12,d22,d2;
int dn, i,j,k, nx,ny,nz, ix1,iy1,iz1, ix2,iy2,iz2;
int ix,iy,iz;
@@ -4051,28 +4125,32 @@ namespace mmdb {
byte Version=1;
f.WriteByte ( &Version );
Root::write ( f );
- f.WriteInt ( &CoorIDCode );
- f.WriteReal ( &brick_size );
- f.WriteReal ( &xbrick_0 );
- f.WriteReal ( &ybrick_0 );
- f.WriteReal ( &zbrick_0 );
- f.WriteInt ( &nbrick_x );
- f.WriteInt ( &nbrick_y );
- f.WriteInt ( &nbrick_z );
+ if (!isCompactBinary()) {
+ f.WriteInt ( &CoorIDCode );
+ f.WriteReal ( &brick_size );
+ f.WriteReal ( &xbrick_0 );
+ f.WriteReal ( &ybrick_0 );
+ f.WriteReal ( &zbrick_0 );
+ f.WriteInt ( &nbrick_x );
+ f.WriteInt ( &nbrick_y );
+ f.WriteInt ( &nbrick_z );
+ }
}
void CoorManager::read ( io::RFile f ) {
byte Version;
f.ReadByte ( &Version );
Root::read ( f );
- f.ReadInt ( &CoorIDCode );
- f.ReadReal ( &brick_size );
- f.ReadReal ( &xbrick_0 );
- f.ReadReal ( &ybrick_0 );
- f.ReadReal ( &zbrick_0 );
- f.ReadInt ( &nbrick_x );
- f.ReadInt ( &nbrick_y );
- f.ReadInt ( &nbrick_z );
+ if (!isCompactBinary()) {
+ f.ReadInt ( &CoorIDCode );
+ f.ReadReal ( &brick_size );
+ f.ReadReal ( &xbrick_0 );
+ f.ReadReal ( &ybrick_0 );
+ f.ReadReal ( &zbrick_0 );
+ f.ReadInt ( &nbrick_x );
+ f.ReadInt ( &nbrick_y );
+ f.ReadInt ( &nbrick_z );
+ }
}
@@ -4080,7 +4158,6 @@ namespace mmdb {
-
// ===================================================================
int SuperposeAtoms ( mat44 & T, PPAtom A1, int nA, PPAtom A2,
diff --git a/mmdb2/mmdb_coormngr.h b/mmdb2/mmdb_coormngr.h
index c493169..9343544 100644
--- a/mmdb2/mmdb_coormngr.h
+++ b/mmdb2/mmdb_coormngr.h
@@ -22,7 +22,7 @@
//
// =================================================================
//
-// 14.07.13 <-- Date of Last Modification.
+// 07.09.15 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
@@ -33,7 +33,7 @@
// **** Classes : mmdb::Brick ( space brick )
// ~~~~~~~~~ mmdb::CoorManager ( MMDB atom coordinate manager )
//
-// (C) E. Krissinel 2000-2013
+// (C) E. Krissinel 2000-2015
//
// =================================================================
//
@@ -230,7 +230,7 @@ namespace mmdb {
// ---------------- Bricking ------------------------------
void RemoveBricks ();
- bool areBricks () { return (brick!=NULL); }
+ bool areBricks () { return (brick!=NULL); }
void MakeBricks ( PPAtom atmvec, int avlen,
realtype Margin, realtype BrickSize=6.0 );
void GetBrickDimension (
@@ -238,10 +238,11 @@ namespace mmdb {
void GetBrickCoor ( PAtom A, int & nx, int & ny, int & nz );
void GetBrickCoor ( realtype x, realtype y, realtype z,
int & nx, int & ny, int & nz );
- PBrick GetBrick ( int nx, int ny, int nz );
+ void GetBrickCoor ( vect3 & xyz, int & nx, int & ny, int & nz );
+ PBrick GetBrick ( int nx, int ny, int nz );
void RemoveMBricks ();
- bool areMBricks () { return (mbrick!=NULL); }
+ bool areMBricks () { return (mbrick!=NULL); }
void MakeMBricks ( PPAtom * atmvec, ivector avlen,
int nStructures, realtype Margin,
realtype BrickSize=6.0 );
@@ -593,7 +594,7 @@ namespace mmdb {
// ==================== Seeking contacts ======================
void SeekContacts (
- PPAtom AIndex, // index of atoms [0..ilen-1]
+ PPAtom AIndex, // index of atoms [0..ilen-1]
int ilen, // length of index
int atomNum, // number of 1st contact atom
// in the index. All other atoms
@@ -616,7 +617,7 @@ namespace mmdb {
// [-(seqDist-1)..seqDist-1], the
// section of neglection is
// shortened to that gap.
- RPContact contact, // indices of contacting atoms
+ RPContact contact, // indices of contacting atoms
// [0..ncontacts-1]. contact[i].id1
// is set to atomNum and
// contact[i].id2 is set to the
@@ -648,8 +649,8 @@ namespace mmdb {
);
void SeekContacts (
- PAtom A, // 1st atom in contact
- PPAtom AIndex, // index of atoms [0..ilen-1] to
+ PAtom A, // 1st atom in contact
+ PPAtom AIndex, // index of atoms [0..ilen-1] to
// check for contact with 1st atom
int ilen, // length of index
realtype dist1, // minimal contact distance
@@ -668,7 +669,7 @@ namespace mmdb {
// [-(seqDist-1)..seqDist-1], the
// section of neglection is
// shortened to that gap.
- RPContact contact, // indices of contacting atoms
+ RPContact contact, // indices of contacting atoms
// [0..ncontacts-1]. contact[i].id1
// is set to -1, and contact[i].id2
// is set to the index of 2nd
@@ -698,9 +699,9 @@ namespace mmdb {
);
void SeekContacts (
- PPAtom AIndex1, // 1st atom index [0..ilen1-1]
+ PPAtom AIndex1, // 1st atom index [0..ilen1-1]
int ilen1, // length of 1st index
- PPAtom AIndex2, // 2nd atom index [0..ilen2-1] to
+ PPAtom AIndex2, // 2nd atom index [0..ilen2-1] to
// check for contact with 1st index
int ilen2, // length of 2nd index
realtype dist1, // minimal contact distance
@@ -720,7 +721,7 @@ namespace mmdb {
// [-(seqDist-1)..seqDist-1], the
// section of neglection is
// shortened to that gap.
- RPContact contact, // indices of contacting atoms
+ RPContact contact, // indices of contacting atoms
// [0..ncontacts-1]. contact[i].id1
// contains number of atom from 1st
// index, and contact[i].id2
@@ -766,13 +767,13 @@ namespace mmdb {
// - contact returns square distances
// - ncontacts is always reset
void SeekContacts (
- PPAtom AIndex1, // 1st atom index [0..ilen1-1]
+ PPAtom AIndex1, // 1st atom index [0..ilen1-1]
int ilen1, // length of 1st index
- PPAtom AIndex2, // 2nd atom index [0..ilen2-1] to
+ PPAtom AIndex2, // 2nd atom index [0..ilen2-1] to
// check for contact with 1st index
int ilen2, // length of 2nd index
realtype contDist, // maximal contact distance
- PContact contact, // indices of contacting atoms
+ PContact contact, // indices of contacting atoms
// [0..ncontacts-1]. contact[i].id1
// contains number of atom from 1st
// index, and contact[i].id2
@@ -780,15 +781,40 @@ namespace mmdb {
// index, contacting with the former
// one. Must be pre-allocated
int & ncontacts, // number of contacts found
- int bricking=0 // bricking control; may be a
+ int bricking=0 // bricking control; may be a
// combination of BRICK_ON_1 or
// BRICK_ON_2 with BRICK_READY
);
-
+
+ // Simplified optimized for speed and convenience version:
+ // - bricking is pre-done
+ // - contacting set of atoms is given as a bare vect3 (xyz)
+ // coordinate vector
+ // - no checks for identity atoms
+ // - contact must be pre-allocated with at least ilen1*ilen2
+ // elements
+ // - contact returns square distances
+ // - ncontacts is always reset
+ void SeekContacts (
+ vect3 * xyz, // 2nd atom index [0..ilen2-1] to
+ // check for contact with 1st index
+ // which was used for bricking
+ int nxyz, // length of 2nd index
+ realtype contDist, // maximal contact distance
+ PContact contact, // indices of contacting atoms
+ // [0..ncontacts-1]. contact[i].id1
+ // contains number of atom from 1st
+ // index, and contact[i].id2
+ // contains number of atom from 2nd
+ // index, contacting with the former
+ // one. Must be pre-allocated
+ int & ncontacts // number of contacts found
+ );
+
void SeekContacts (
- PPAtom AIndex1, // 1st atom index [0..ilen1-1]
+ PPAtom AIndex1, // 1st atom index [0..ilen1-1]
int ilen1, // length of 1st index
- PPAtom * AIndex2, // indexes of atoms to be checked
+ PPAtom * AIndex2, // indexes of atoms to be checked
// for contact with each atom from
// Aindex1; dimension
// [0..nStructures-1][0..ilen2[i]-1]
@@ -796,7 +822,7 @@ namespace mmdb {
int nStructures, // number of indexes AIndex2
realtype dist1, // minimal contact distance
realtype dist2, // maximal contact distance
- PPMContact & contact, // resulting contacts, one structure
+ PPMContact & contact, // resulting contacts, one structure
// per each position in AIndex1. If
// AIndex1[i] is NULL, contact[i] is
// also NULL. "contact" is always
@@ -804,7 +830,7 @@ namespace mmdb {
// re-allocation is attempted.
int bricking=0 // bricking control; may be
// BRICK_READY if AIndex2 does not
- // change
+ // change
);
protected :
diff --git a/mmdb2/mmdb_defs.h b/mmdb2/mmdb_defs.h
index da06dac..dc5d1f6 100644
--- a/mmdb2/mmdb_defs.h
+++ b/mmdb2/mmdb_defs.h
@@ -4,7 +4,7 @@
// CCP4 Coordinate Library: support of coordinate-related
// functionality in protein crystallography applications.
//
-// Copyright (C) Eugene Krissinel 2000-2008.
+// Copyright (C) Eugene Krissinel 2000-2015.
//
// This library is free software: you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
@@ -22,7 +22,7 @@
//
// =================================================================
//
-// 10.09.13 <-- Date of Last Modification.
+// 07.09.15 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
@@ -33,7 +33,7 @@
//
// Definition of types, constants and important classes.
//
-// (C) E. Krissinel 2000-2013
+// (C) E. Krissinel 2000-2015
//
// =================================================================
//
@@ -48,7 +48,7 @@ namespace mmdb {
enum MMDB_VERSION {
MAJOR_VERSION = 2, //!< MMDB major version
MINOR_VERSION = 0, //!< MMDB minor version
- MICRO_VERSION = 1 //!< MMDB micro version
+ MICRO_VERSION = 5 //!< MMDB micro version
};
// ======================= types =================================
diff --git a/mmdb2/mmdb_io_file.cpp b/mmdb2/mmdb_io_file.cpp
index 606bdf2..04ea814 100644
--- a/mmdb2/mmdb_io_file.cpp
+++ b/mmdb2/mmdb_io_file.cpp
@@ -976,7 +976,7 @@ namespace mmdb {
else ll = 0;
if (!longLine) {
sl = byte(ll);
- B = WriteFile ( &sl,sizeof(sl) );
+ B = WriteFile ( &sl,sizeof(sl) );
} else if (UniBin) {
word2UniBin ( ll,wUB );
B = WriteFile ( wUB,sizeof(wordUniBin) );
diff --git a/mmdb2/mmdb_io_file.h b/mmdb2/mmdb_io_file.h
index 726666e..26ec48d 100644
--- a/mmdb2/mmdb_io_file.h
+++ b/mmdb2/mmdb_io_file.h
@@ -133,6 +133,7 @@ namespace mmdb {
word ReadFile ( void * Buffer, word Count );
word CreateRead ( pstr & Line );
word ReadTerLine ( pstr Line, bool longLine=false );
+ word ReadShortLine ( pstr Line, bool longLine=false );
bool WriteFile ( const void * Buffer, word Count );
bool CreateWrite ( cpstr Line );
bool WriteTerLine ( cpstr Line, bool longLine=false );
diff --git a/mmdb2/mmdb_math_bfgsmin.cpp b/mmdb2/mmdb_math_bfgsmin.cpp
index 989608a..bd7bd48 100644
--- a/mmdb2/mmdb_math_bfgsmin.cpp
+++ b/mmdb2/mmdb_math_bfgsmin.cpp
@@ -478,7 +478,7 @@ namespace mmdb {
(StepSize[i]*StepSize[i]);
X[i] = TempI+StepSize[i];
if (i<N)
- for (j=i+1;j<=N;j++)
+ for (j=i+1;j<=N;j++) {
if (!Freese[j]) {
TempJ = X[j];
X[j] += StepSize[j];
@@ -490,6 +490,7 @@ namespace mmdb {
X[j] = TempJ;
} else
Hsn[i][j] = 0.0;
+ }
X[i] = TempI;
} else
for (j=i;j<=N;j++)
diff --git a/mmdb2/mmdb_mattype.h b/mmdb2/mmdb_mattype.h
index 08cf55c..9a51336 100644
--- a/mmdb2/mmdb_mattype.h
+++ b/mmdb2/mmdb_mattype.h
@@ -189,9 +189,9 @@ namespace mmdb {
// ------------------------------------------------------------
- inline int mround ( realtype X ) { return (int)floor(X+0.5); }
- inline int ifloor ( realtype X ) { return (int)floor(X); }
- inline int Abs ( int x ) { return ( x >= 0 ? x : -x ); }
+ inline int mround ( realtype X ) { return (int)floor(X+0.5); }
+ inline int ifloor ( realtype X ) { return (int)floor(X); }
+ inline int Abs ( int x ) { return ( x >= 0 ? x : -x ); }
inline void ISwap ( int & x, int & y )
{ int b = x; x = y; y = b; }
diff --git a/mmdb2/mmdb_mmcif_.cpp b/mmdb2/mmdb_mmcif_.cpp
index e5b962e..f77d147 100644
--- a/mmdb2/mmdb_mmcif_.cpp
+++ b/mmdb2/mmdb_mmcif_.cpp
@@ -22,7 +22,7 @@
//
// =================================================================
//
-// 12.09.13 <-- Date of Last Modification.
+// 10.05.15 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
@@ -36,7 +36,7 @@
// mmdb::mmcif::Data ( mmCIF data block )
// mmdb::mmcif::File ( mmCIF file )
//
-// (C) E. Krissinel 2000-2013
+// (C) E. Krissinel 2000-2015
//
// =================================================================
//
@@ -1548,8 +1548,8 @@ namespace mmdb {
int i,j;
Category::write ( f );
f.WriteInt ( &nRows );
- if ((nTags>0) && (nRows>0))
- for (i=0;i<nRows;i++)
+ if ((nTags>0) && (nRows>0)) {
+ for (i=0;i<nRows;i++) {
if (field[i]) {
j = 1;
f.WriteInt ( &j );
@@ -1559,6 +1559,8 @@ namespace mmdb {
j = 0;
f.WriteInt ( &j );
}
+ }
+ }
f.WriteInt ( &iColumn );
}
diff --git a/mmdb2/mmdb_model.cpp b/mmdb2/mmdb_model.cpp
index ca1d537..23e63ae 100644
--- a/mmdb2/mmdb_model.cpp
+++ b/mmdb2/mmdb_model.cpp
@@ -22,7 +22,7 @@
//
// =================================================================
//
-// 12.09.13 <-- Date of Last Modification.
+// 11.09.15 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
@@ -46,7 +46,7 @@
// mmdb::CisPep ( CisPep data )
// mmdb::Model ( PDB model )
//
-// Copyright (C) E. Krissinel 2000-2013
+// Copyright (C) E. Krissinel 2000-2015
//
// =================================================================
//
@@ -2116,14 +2116,15 @@ namespace mmdb {
strcpy ( chainID2," " ); // chain ID of 2nd linked atom
seqNum2 = 0; // sequence number of 2nd linked atom
strcpy ( insCode2," " ); // insertion code of 2nd linked atom
- s1 = 1; // sym id of 1st atom
- i1 = 5;
- j1 = 5;
- k1 = 5;
- s2 = 1; // sym id of 2nd atom
- i2 = 5;
- j2 = 5;
- k2 = 5;
+ s1 = 1; // sym id of 1st atom
+ i1 = 5;
+ j1 = 5;
+ k1 = 5;
+ s2 = 1; // sym id of 2nd atom
+ i2 = 5;
+ j2 = 5;
+ k2 = 5;
+ dist = -1.0; // no distance
}
@@ -2157,6 +2158,9 @@ namespace mmdb {
PutInteger ( &(S[70]),j2,1 );
PutInteger ( &(S[71]),k2,1 );
+ if (dist>0.0)
+ PutRealF ( &(S[73]),dist,5,3 );
+
}
@@ -2184,6 +2188,8 @@ namespace mmdb {
Loop->AddLoopTag ( CIFTAG_CONN_PTNR1_SYMMETRY );
Loop->AddLoopTag ( CIFTAG_CONN_PTNR2_SYMMETRY );
+ Loop->AddLoopTag ( CIFTAG_CONN_DIST );
+
}
@@ -2219,6 +2225,8 @@ namespace mmdb {
sprintf ( S,"%i%i%i%i",s2,i2,j2,k2 );
Loop->AddString ( S );
+ Loop->AddReal ( dist );
+
}
ERROR_CODE Link::ConvertPDBASCII ( cpstr S ) {
@@ -2245,6 +2253,8 @@ namespace mmdb {
GetInteger ( j2,&(S[70]),1 );
GetInteger ( k2,&(S[71]),1 );
+ if (!GetReal(dist,&(S[73]),5)) dist = -1.0;
+
return Error_NoError;
}
@@ -2336,6 +2346,10 @@ namespace mmdb {
s2 = atoi(S);
}
+ rc = CIFGetReal ( dist,Loop,CIFTAG_CONN_DIST,n );
+ if (rc==Error_NoData) return Error_EmptyCIF;
+ if (rc!=Error_NoError) return rc;
+
n++;
return Error_NoError;
@@ -2368,10 +2382,12 @@ namespace mmdb {
j2 = PLink(Link)->j2;
k2 = PLink(Link)->k2;
+ dist = PLink(Link)->dist;
+
}
void Link::write ( io::RFile f ) {
- byte Version=1;
+ byte Version=2;
f.WriteByte ( &Version );
@@ -2399,6 +2415,8 @@ namespace mmdb {
f.WriteInt ( &j2 );
f.WriteInt ( &k2 );
+ f.WriteReal ( &dist );
+
}
void Link::read ( io::RFile f ) {
@@ -2430,6 +2448,9 @@ namespace mmdb {
f.ReadInt ( &j2 );
f.ReadInt ( &k2 );
+ if (Version>1)
+ f.ReadReal ( &dist );
+
}
MakeStreamFunctions(Link)
@@ -2553,7 +2574,7 @@ namespace mmdb {
void LinkR::MakeCIF ( mmcif::PData CIF, int N ) {
UNUSED_ARGUMENT(N);
mmcif::PLoop Loop;
- int RC;
+ int RC;
RC = CIF->AddLoop ( CIFCAT_STRUCT_LINKR,Loop );
if (RC!=mmcif::CIFRC_Ok) // the category was (re)created, provide tags
@@ -5048,6 +5069,7 @@ namespace mmdb {
ncontacts = 0;
manager->SeekContacts ( Ca,nres, Ca,nres, 2.0,10.0, 2,
contact,ncontacts,0 );
+ manager->RemoveBricks();
if (ncontacts<=0) {
delete[] Res;
delete[] Ca;
@@ -5268,12 +5290,16 @@ namespace mmdb {
void Model::write ( io::RFile f ) {
int i,k;
- byte Version=3;
-
- f.WriteByte ( &Version );
-
- ProModel::write ( f );
-
+ byte Version=4;
+ bool compactBinary = false;
+
+ PManager M = GetCoordHierarchy();
+ if (M)
+ compactBinary = M->isCompactBinary();
+
+ f.WriteByte ( &Version );
+ f.WriteBool ( &compactBinary );
+
f.WriteInt ( &serNum );
f.WriteInt ( &nChains );
@@ -5284,25 +5310,31 @@ namespace mmdb {
if (chain[i]) chain[i]->write ( f );
}
- hetCompounds.write ( f );
- helices .write ( f );
- sheets .write ( f );
- turns .write ( f );
- links .write ( f );
- linkRs .write ( f );
+ if (!compactBinary) {
+
+ ProModel::write ( f );
+
+ hetCompounds.write ( f );
+ helices .write ( f );
+ sheets .write ( f );
+ turns .write ( f );
+ links .write ( f );
+ linkRs .write ( f );
+
+ }
}
void Model::read ( io::RFile f ) {
int i,k;
byte Version;
+ bool compactBinary;
FreeMemory();
- f.ReadByte ( &Version );
-
- ProModel::read ( f );
-
+ f.ReadByte ( &Version );
+ f.ReadBool ( &compactBinary );
+
f.ReadInt ( &serNum );
f.ReadInt ( &nChains );
nChainsAlloc = nChains;
@@ -5318,12 +5350,18 @@ namespace mmdb {
}
}
- hetCompounds.read ( f );
- helices .read ( f );
- sheets .read ( f );
- turns .read ( f );
- if (Version>1) links .read ( f );
- if (Version>2) linkRs.read ( f );
+ if (!compactBinary) {
+
+ ProModel::read ( f );
+
+ hetCompounds.read ( f );
+ helices .read ( f );
+ sheets .read ( f );
+ turns .read ( f );
+ links .read ( f );
+ linkRs .read ( f );
+
+ }
}
diff --git a/mmdb2/mmdb_model.h b/mmdb2/mmdb_model.h
index 3e184a9..587ae8b 100644
--- a/mmdb2/mmdb_model.h
+++ b/mmdb2/mmdb_model.h
@@ -22,7 +22,7 @@
//
// =================================================================
//
-// 12.09.13 <-- Date of Last Modification.
+// 10.05.15 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
@@ -46,7 +46,7 @@
// mmdb::CisPep ( CisPep data )
// mmdb::Model ( PDB model )
//
-// Copyright (C) E. Krissinel 2000-2013
+// Copyright (C) E. Krissinel 2000-2015
//
// =================================================================
//
@@ -423,6 +423,7 @@ namespace mmdb {
InsCode insCode2; // insertion code of 2nd linked atom
int s1,i1,j1,k1; // sym id of 1st atom
int s2,i2,j2,k2; // sym id of 2nd atom
+ realtype dist; // link distance
Link ();
Link ( cpstr S );
@@ -968,7 +969,7 @@ namespace mmdb {
// ---- Working Links
- int GetNumberOfLinks ();
+ int GetNumberOfLinks ();
PLink GetLink ( int serialNum ); // 1<=serNum<=NofLinks
PLinkContainer GetLinks() { return &links; }
diff --git a/mmdb2/mmdb_root.cpp b/mmdb2/mmdb_root.cpp
index 3a98edb..bef2da1 100644
--- a/mmdb2/mmdb_root.cpp
+++ b/mmdb2/mmdb_root.cpp
@@ -22,7 +22,7 @@
//
// =================================================================
//
-// 14.09.13 <-- Date of Last Modification.
+// 10.05.15 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
@@ -33,7 +33,7 @@
// **** Classes : mmdb::Root
// ~~~~~~~~~
//
-// (C) E. Krissinel 2000-2013
+// (C) E. Krissinel 2000-2015
//
// =================================================================
//
@@ -986,20 +986,21 @@ namespace mmdb {
crModel0->nChains = k;
}
}
- if (CleanKey & PDBCLEAN_CHAIN_ORDER)
+ if (CleanKey & PDBCLEAN_CHAIN_ORDER) {
for (i=0;i<nAtoms;i++)
if (atom[i]) {
crChain0 = atom[i]->GetChain();
crChain0->nWeights++;
crChain0->Weight += atom[i]->serNum;
}
- else
+ } else {
for (i=0;i<nAtoms;i++)
if (atom[i]) {
crChain0 = atom[i]->GetChain();
crChain0->nWeights++;
crChain0->Weight += atom[i]->GetIndex();
}
+ }
for (i=0;i<nModels;i++) {
crModel0 = model[i];
if (crModel0) {
@@ -1488,7 +1489,12 @@ namespace mmdb {
}
}
+ bool Root::isCompactBinary() {
+ if (Flags & MMDBF_MakeCompactBinary) return true;
+ return false;
+ }
+
int Root::CrystReady() {
// Returns flags:
// CRRDY_Complete if crystallographic information is complete
@@ -1681,15 +1687,15 @@ namespace mmdb {
}
int Root::PutAtom ( int index,
- int serNum,
- const AtomName atomName,
- const ResName resName,
- const ChainID chainID,
- int seqNum,
- const InsCode insCode,
- const AltLoc altLoc,
- const SegID segID,
- const Element element ) {
+ int serNum,
+ const AtomName atomName,
+ const ResName resName,
+ const ChainID chainID,
+ int seqNum,
+ const InsCode insCode,
+ const AltLoc altLoc,
+ const SegID segID,
+ const Element element ) {
// An atom with the specified properties is put into the
// structure. The current model is used; if no model is
@@ -1766,15 +1772,14 @@ namespace mmdb {
}
- int Root::PutAtom ( int index, // same meaning as above
- PAtom A, // pointer to completed atom
- // class
- int serNum // 0 means that the serial
- // number will be set equal
- // to "index". Otherwise,
- // the serial number is set
- // to the specified value
- ) {
+ int Root::PutAtom ( int index, // same meaning as above
+ PAtom A, // pointer to completed atom class
+ int serNum // 0 means that the serial
+ // number will be set equal
+ // to "index". Otherwise,
+ // the serial number is set
+ // to the specified value
+ ) {
int i,kndex,RC,sn;
if (!A) return -1;
@@ -2125,7 +2130,7 @@ namespace mmdb {
int label_seq_id,
int label_entity_id,
const InsCode insCode,
- bool Replace ) {
+ bool Replace ) {
if ((!resName[0]) && (insCode[0]!=char(1)))
return Error_EmptyResidueName;
@@ -2413,6 +2418,7 @@ namespace mmdb {
else return Error_NoLogicalName;
}
+ /*
ERROR_CODE Root::WriteMMDBF ( cpstr MMDBRootName, io::GZ_MODE gzipMode ) {
io::File f;
char Label[100];
@@ -2432,7 +2438,30 @@ namespace mmdb {
return Error_NoError;
}
+*/
+ ERROR_CODE Root::WriteMMDBF ( cpstr MMDBRootName,
+ io::GZ_MODE gzipMode ) {
+ io::File f;
+ f.assign ( MMDBRootName,false,true,gzipMode );
+ if (f.rewrite()) {
+ WriteMMDBF ( f );
+ f.shut();
+ } else
+ return Error_CantOpenFile;
+ return Error_NoError;
+ }
+
+ void Root::WriteMMDBF ( io::RFile f ) {
+ char Label[100];
+ byte Version=Edition;
+ FType = MMDB_FILE_Binary;
+ strcpy ( Label,MMDBFLabel );
+ f.WriteFile ( Label,sizeof(MMDBFLabel) );
+ f.WriteByte ( &Version );
+ write ( f );
+ }
+
pstr Root::GetEntryID() {
return title.idCode;
@@ -2554,8 +2583,8 @@ namespace mmdb {
}
int Root::GetTMatrix ( mat44 & TMatrix, int Nop,
- int cellshift_a, int cellshift_b,
- int cellshift_c ) {
+ int cellshift_a, int cellshift_b,
+ int cellshift_c ) {
// GetTMatrix(..) calculates and returns the coordinate transformation
// matrix, which converts orthogonal coordinates according to
// the symmetry operation number Nop and places them into unit cell
@@ -2572,9 +2601,9 @@ namespace mmdb {
int Root::GetUCTMatrix ( mat44 & TMatrix, int Nop,
- realtype x, realtype y, realtype z,
- int cellshift_a, int cellshift_b,
- int cellshift_c ) {
+ realtype x, realtype y, realtype z,
+ int cellshift_a, int cellshift_b,
+ int cellshift_c ) {
// GetUCTMatrix(..) calculates and returns the coordinate
// transformation matrix, which converts orthogonal coordinates
// according to the symmetry operation number Nop. Translation
@@ -2595,8 +2624,8 @@ namespace mmdb {
int Root::GetFractMatrix ( mat44 & TMatrix, int Nop,
- int cellshift_a, int cellshift_b,
- int cellshift_c ) {
+ int cellshift_a, int cellshift_b,
+ int cellshift_c ) {
// GetFractMatrix(..) calculates and returns the coordinate
// transformation matrix, which converts fractional coordinates
// according to the symmetry operation number Nop and places them
@@ -2811,28 +2840,22 @@ namespace mmdb {
return title.GetStructureTitle ( L );
}
- void Root::SetShortBinary() {
+ void Root::SetCompactBinary() {
// leaves only coordinates in binary files
int i;
+ SetFlag ( MMDBF_MakeCompactBinary );
for (i=0;i<nAtoms;i++)
- if (atom[i]) atom[i]->SetShortBinary();
+ if (atom[i]) atom[i]->SetCompactBinary();
}
void Root::write ( io::RFile f ) {
int i,k;
- byte Version=1;
+ byte Version=2;
f.WriteByte ( &Version );
-
- UDData::write ( f );
-
- title .write ( f );
- cryst .write ( f );
- udRegister.write ( f );
- DefPath .write ( f );
-
- f.WriteWord ( &Flags );
+ f.WriteWord ( &Flags );
+
f.WriteInt ( &nAtoms );
for (i=0;i<nAtoms;i++) {
if (atom[i]) k = 1;
@@ -2848,13 +2871,31 @@ namespace mmdb {
f.WriteInt ( &k );
if (model[i]) model[i]->write ( f );
}
+
+ if (Flags & MMDBF_MakeCompactBinary) {
+
+ f.WriteTerLine ( title.idCode,false );
+ f.WriteReal ( &title.resolution );
+ title.title.write ( f );
+ cryst .write ( f );
+
+ } else {
- SA .write ( f );
- Footnote.write ( f );
- SB .write ( f );
- SC .write ( f );
-
- StreamWrite ( f,CIF );
+ UDData::write ( f );
+
+ title .write ( f );
+ cryst .write ( f );
+ udRegister.write ( f );
+ DefPath .write ( f );
+
+ SA .write ( f );
+ Footnote.write ( f );
+ SB .write ( f );
+ SC .write ( f );
+
+ StreamWrite ( f,CIF );
+
+ }
}
@@ -2866,17 +2907,10 @@ namespace mmdb {
FreeFileMemory();
f.ReadByte ( &Version );
-
- UDData::read ( f );
-
- title .read ( f );
- cryst .read ( f );
- udRegister.read ( f );
- DefPath .read ( f );
-
+ f.ReadWord ( &Flags );
+
// It is important to read atoms before models,
// residues and chains!
- f.ReadWord ( &Flags );
f.ReadInt ( &nAtoms );
atmLen = nAtoms;
if (nAtoms>0) {
@@ -2907,13 +2941,30 @@ namespace mmdb {
model[i] = NULL;
}
}
-
- SA .read ( f );
- Footnote.read ( f );
- SB .read ( f );
- SC .read ( f );
-
- StreamRead ( f,CIF );
+ if (Flags & MMDBF_MakeCompactBinary) {
+
+ f.ReadTerLine ( title.idCode,false );
+ f.ReadReal ( &title.resolution );
+ title.title.read ( f );
+ cryst .read ( f );
+
+ } else {
+
+ UDData::read ( f );
+
+ title .read ( f );
+ cryst .read ( f );
+ udRegister.read ( f );
+ DefPath .read ( f );
+
+ SA .read ( f );
+ Footnote.read ( f );
+ SB .read ( f );
+ SC .read ( f );
+
+ StreamRead ( f,CIF );
+
+ }
}
diff --git a/mmdb2/mmdb_root.h b/mmdb2/mmdb_root.h
index df5c0e1..bec8b78 100644
--- a/mmdb2/mmdb_root.h
+++ b/mmdb2/mmdb_root.h
@@ -22,7 +22,7 @@
//
// =================================================================
//
-// 14.09.13 <-- Date of Last Modification.
+// 24.07.15 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
@@ -33,7 +33,7 @@
// **** Classes : mmdb::Root
// ~~~~~~~~~
//
-// (C) E. Krissinel 2000-2013
+// (C) E. Krissinel 2000-2015
//
// =================================================================
//
@@ -73,7 +73,8 @@ namespace mmdb {
MMDBF_FixSpaceGroup = 0x00008000,
MMDBF_EnforceAtomNames = 0x00010000,
MMDBF_EnforceUniqueChainID = 0x00020000,
- MMDBF_DoNotProcessSpaceGroup = 0x00040000
+ MMDBF_DoNotProcessSpaceGroup = 0x00040000,
+ MMDBF_MakeCompactBinary = 0x00080000
};
// MMDBF_EnforceUniqueChainID will make MMDB to rename chains on
@@ -199,6 +200,7 @@ namespace mmdb {
io::GZ_MODE gzipMode=io::GZM_CHECK );
ERROR_CODE WriteMMDBF1 ( cpstr MMDBLFName,
io::GZ_MODE gzipMode=io::GZM_CHECK );
+ void WriteMMDBF ( io::RFile f );
void GetInputBuffer ( pstr Line, int & count );
@@ -330,6 +332,8 @@ namespace mmdb {
bool GetNewChainID ( int modelNo, ChainID chID, int length=1 );
// --------------- Enquiring -------------------------------
+
+ bool isCompactBinary();
int CrystReady();
// Returns flags:
@@ -498,7 +502,7 @@ namespace mmdb {
void Copy ( PRoot MMDBRoot );
- void SetShortBinary(); // leaves only coordinates in binary files
+ void SetCompactBinary(); // leaves only coordinates in binary files
// ------- user-defined data handlers
int PutUDData ( int UDDhandle, int iudd );
diff --git a/mmdb2/mmdb_rwbrook.cpp b/mmdb2/mmdb_rwbrook.cpp
index 5bc056c..f5c7b77 100644
--- a/mmdb2/mmdb_rwbrook.cpp
+++ b/mmdb2/mmdb_rwbrook.cpp
@@ -61,6 +61,7 @@
// mmdb_f_wremark_ ( writes a remark statement )
// mmdb_f_setter
// mmdb_f_sethet
+// mmdb_f_getnofncsmates_
// rberrstop_ ( error messenger )
// rbcheckerr_ ( a simple error messenger )
//
@@ -154,6 +155,11 @@ class Channel {
mmdb::realtype & cell_gammas,
mmdb::realtype & cell_vs );
+ int GetNumberOfNCSMates(); // Returns the number of
+ // NCS mates not given in
+ // the file (iGiven==0)
+
+
void MakeCoordStructure();
void Read ();
void Write();
@@ -249,6 +255,12 @@ void Channel::MakeCoordStructure() {
}
}
+int Channel::GetNumberOfNCSMates() {
+// Returns the number of NCS mates not given in the file (iGiven==0)
+ if (!MMDBManager) return RWBERR_NoData;
+ return MMDBManager->GetNumberOfNCSMates();
+}
+
void Channel::Read() {
int RC;
@@ -1704,6 +1716,39 @@ mmdb::PAtom atom;
}
+
+// ------------------------------------------------------------------
+
+// mmdb_f_getnofncsmates_(..) returns the number of NCS mates not
+// given in the file (iGiven=0).
+//
+// Negative returns N<0 mean an error.
+//
+// FORTRAN equivalent: subroutine MMDB_F_GetNofNCSMates ( iUnit,N )
+// ~~~~~~~~~~~~~~~~~~~ integer iUnit,N
+
+FORTRAN_SUBR ( MMDB_F_GETNOFNCSMATES, mmdb_f_getnofncsmates,
+ ( int * iUnit, int * N ),
+ ( int * iUnit, int * N ),
+ ( int * iUnit, int * N ) ) {
+int k;
+
+ strcpy ( LastFunc,"mmdb_f_getnofncsmates" );
+ LastUnit = *iUnit;
+
+ k = GetChannel ( *iUnit );
+ if (k<0) {
+ *N = RWBERR_NoChannel;
+ LastRC = *N;
+ return;
+ }
+
+ *N = channel[k]->GetNumberOfNCSMates();
+ return;
+
+}
+
+
FORTRAN_SUBR ( MMDB_F_COPYATOM, mmdb_f_copyatom,
( int * iUnit1, int * iUnit2, int * iRet ),
( int * iUnit1, int * iUnit2, int * iRet ),
diff --git a/mmdb2/mmdb_rwbrook.h b/mmdb2/mmdb_rwbrook.h
index 2f59f5f..eba2a6f 100644
--- a/mmdb2/mmdb_rwbrook.h
+++ b/mmdb2/mmdb_rwbrook.h
@@ -61,6 +61,7 @@
// mmdb_f_wremark_ ( writes a remark statement )
// mmdb_f_setter
// mmdb_f_sethet
+// mmdb_f_getnofncsmates_
// rberrstop_ ( error messenger )
// rbcheckerr_ ( a simple error messenger )
//
@@ -907,6 +908,21 @@ FORTRAN_SUBR ( MMDB_F_SETHET, mmdb_f_sethet,
( int * iUnit, int * iRet ) );
+// ------------------------------------------------------------------
+
+// mmdb_f_getnofncsmates_(..) returns the number of NCS mates not
+// given in the file (iGiven=0).
+//
+// Negative returns N<0 mean an error.
+//
+// FORTRAN equivalent: subroutine MMDB_F_GetNofNCSMates ( iUnit,N )
+// ~~~~~~~~~~~~~~~~~~~ integer iUnit,N
+
+FORTRAN_SUBR ( MMDB_F_GETNOFNCSMATES, mmdb_f_getnofncsmates,
+ ( int * iUnit, int * N ),
+ ( int * iUnit, int * N ),
+ ( int * iUnit, int * N ) );
+
// ------------------------------------------------------------------
diff --git a/mmdb2/mmdb_selmngr.cpp b/mmdb2/mmdb_selmngr.cpp
index 3aeec25..88a249e 100644
--- a/mmdb2/mmdb_selmngr.cpp
+++ b/mmdb2/mmdb_selmngr.cpp
@@ -3372,13 +3372,15 @@ namespace mmdb {
f.WriteByte ( &Version );
CoorManager::write ( f );
-
- f.WriteInt ( &nSelections );
- for (i=0;i<nSelections;i++) {
- StreamWrite ( f,mask[i] );
- f.WriteInt ( &(nSelItems[i]) );
- sType = selType[i];
- f.WriteInt ( &(sType) );
+
+ if (!isCompactBinary()) {
+ f.WriteInt ( &nSelections );
+ for (i=0;i<nSelections;i++) {
+ StreamWrite ( f,mask[i] );
+ f.WriteInt ( &(nSelItems[i]) );
+ sType = selType[i];
+ f.WriteInt ( &(sType) );
+ }
}
}
@@ -3393,22 +3395,24 @@ namespace mmdb {
CoorManager::read ( f );
- f.ReadInt ( &nSelections );
- if (nSelections>0) {
- mask = new PMask [nSelections];
- selection = new PPMask[nSelections];
- nSelItems = new int [nSelections];
- selType = new SELECTION_TYPE[nSelections];
- for (i=0;i<nSelections;i++) {
- mask[i] = NULL;
- StreamRead ( f,mask[i] );
- f.ReadInt ( &(nSelItems[i]) );
- f.ReadInt ( &(sType) );
- selType [i] = (SELECTION_TYPE)sType;
- selection[i] = NULL;
- if (mask[i])
- MakeSelIndex ( i+1,selType[i],-1 );
- else nSelItems[i] = 0;
+ if (!isCompactBinary()) {
+ f.ReadInt ( &nSelections );
+ if (nSelections>0) {
+ mask = new PMask [nSelections];
+ selection = new PPMask[nSelections];
+ nSelItems = new int [nSelections];
+ selType = new SELECTION_TYPE[nSelections];
+ for (i=0;i<nSelections;i++) {
+ mask[i] = NULL;
+ StreamRead ( f,mask[i] );
+ f.ReadInt ( &(nSelItems[i]) );
+ f.ReadInt ( &(sType) );
+ selType [i] = (SELECTION_TYPE)sType;
+ selection[i] = NULL;
+ if (mask[i])
+ MakeSelIndex ( i+1,selType[i],-1 );
+ else nSelItems[i] = 0;
+ }
}
}
diff --git a/mmdb2/mmdb_selmngr.h b/mmdb2/mmdb_selmngr.h
index fab8499..20e6d11 100644
--- a/mmdb2/mmdb_selmngr.h
+++ b/mmdb2/mmdb_selmngr.h
@@ -134,7 +134,7 @@ namespace mmdb {
SelManager ();
SelManager ( io::RPStream Object );
- ~ SelManager();
+ ~SelManager();
// ==================== Selecting atoms =======================
diff --git a/mmdb2/mmdb_tables.cpp b/mmdb2/mmdb_tables.cpp
index d1e7c61..3eaddae 100644
--- a/mmdb2/mmdb_tables.cpp
+++ b/mmdb2/mmdb_tables.cpp
@@ -22,7 +22,7 @@
//
// =================================================================
//
-// 12.09.13 <-- Date of Last Modification.
+// 24.07.15 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
@@ -42,7 +42,7 @@
// RName1 ( 1-characters amino acid names )
//
//
-// (C) E. Krissinel 2000-2013
+// (C) E. Krissinel 2000-2015
//
// =================================================================
//
@@ -727,6 +727,34 @@ namespace mmdb {
}
+ void Get1LetterCode ( cpstr res3name, char & res1code ) {
+ char r[4];
+ int i;
+
+ strncpy ( r,res3name,3 );
+ r[3] = char(0);
+ UpperCase ( r );
+ i = 0;
+ res1code = char(1);
+ while (Res1Code[i][0]) {
+ if (Res1Code[i][0]==r[0]) {
+ if (Res1Code[i][1]==r[1]) {
+ if (Res1Code[i][2]==r[2]) {
+ res1code = Res1Code[i][4];
+ break;
+ }
+ }
+ }
+ i++;
+ }
+
+ if (res1code==char(1)) {
+ if (isNucleotide(r)) res1code = r[0];
+ else res1code = 'X';
+ }
+
+ }
+
void Get3LetterCode ( cpstr res1name, pstr res3code ) {
int i;
diff --git a/mmdb2/mmdb_tables.h b/mmdb2/mmdb_tables.h
index f2d4d9d..2f50e38 100644
--- a/mmdb2/mmdb_tables.h
+++ b/mmdb2/mmdb_tables.h
@@ -22,7 +22,7 @@
//
// =================================================================
//
-// 12.09.13 <-- Date of Last Modification.
+// 24.07.15 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
@@ -42,7 +42,7 @@
// RName1 ( 1-characters amino acid names )
//
//
-// (C) E. Krissinel 2000-2013
+// (C) E. Krissinel 2000-2015
//
// =================================================================
//
@@ -118,8 +118,9 @@ namespace mmdb {
extern int isDNARNA ( cpstr resName ); // 0,1(DNA),2(RNA)
extern bool isSugar ( cpstr resName );
- extern void Get1LetterCode ( cpstr res3name, pstr res1code );
- extern void Get3LetterCode ( cpstr res1name, pstr res3code );
+ extern void Get1LetterCode ( cpstr res3name, pstr res1code );
+ extern void Get1LetterCode ( cpstr res3name, char & res1code );
+ extern void Get3LetterCode ( cpstr res1name, pstr res3code );
} // namespace mmdb
diff --git a/mmdb2/mmdb_title.h b/mmdb2/mmdb_title.h
index 1e00d38..19b60d3 100644
--- a/mmdb2/mmdb_title.h
+++ b/mmdb2/mmdb_title.h
@@ -667,7 +667,7 @@ namespace mmdb {
TitleContainer source; // source
KeyWords keyWords; // key words
TitleContainer expData; // experimental data
- TitleContainer mdlType; // model desctiptions
+ TitleContainer mdlType; // model descriptions
TitleContainer author; // author data
TitleContainer revData; // revision data
TitleContainer supersede; // supersede records
diff --git a/mmdb2/mmdb_utils.cpp b/mmdb2/mmdb_utils.cpp
index a39f79b..669bf15 100644
--- a/mmdb2/mmdb_utils.cpp
+++ b/mmdb2/mmdb_utils.cpp
@@ -744,10 +744,9 @@ namespace mmdb {
ACopy[i][j] = A[i][j];
}
- bool isMat4Eq ( mat44 & A, mat44 & B, realtype eps,
- bool rotOnly ) {
+ bool isMat4Eq ( mat44 & A, mat44 & B, realtype eps, bool rotOnly ) {
// returns true if A is equal to B within precision eps
- int i,j,k;
+ int i,j,k;
bool Eq;
if (rotOnly) k = 3;
diff --git a/mmdb2/mmdb_utils.h b/mmdb2/mmdb_utils.h
index e17ed74..981cf52 100644
--- a/mmdb2/mmdb_utils.h
+++ b/mmdb2/mmdb_utils.h
@@ -198,7 +198,7 @@ namespace mmdb {
extern void Mat4Copy ( mat44 & A, mat44 & ACopy );
extern void Mat3Copy ( mat33 & A, mat33 & ACopy );
extern bool isMat4Eq ( mat44 & A, mat44 & B, realtype eps,
- bool rotOnly );
+ bool rotOnly );
extern void TransformXYZ ( mat44 & T,
realtype & X, realtype & Y, realtype & Z );
--
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