New upstream version 2018-07-04 (67e6e979) · Commits · Debian Med / gmap

ChangeLog

+1290 −83

File changed.

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Makefile.in

+2 −1

Original line number	Diff line number	Diff line
		@@ -184,7 +184,7 @@ am__DIST_COMMON = $(srcdir)/Makefile.in $(top_srcdir)/config/compile \
		$(top_srcdir)/config/config.sub \
		$(top_srcdir)/config/install-sh $(top_srcdir)/config/ltmain.sh \
		$(top_srcdir)/config/missing AUTHORS COPYING ChangeLog INSTALL \
		NEWS README config/compile config/config.guess \
		NEWS README TODO config/compile config/config.guess \
		config/config.sub config/install-sh config/ltmain.sh \
		config/missing
		DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
		@@ -259,6 +259,7 @@ EXEEXT = @EXEEXT@
		FGREP = @FGREP@
		GMAPDB = @GMAPDB@
		GREP = @GREP@
		HAVE_INLINE = @HAVE_INLINE@
		INSTALL = @INSTALL@
		INSTALL_DATA = @INSTALL_DATA@
		INSTALL_PROGRAM = @INSTALL_PROGRAM@

TODO

0 → 100644

+3 −0

Original line number	Diff line number	Diff line

		Add flag that allows for splitting afterwards.

VERSION

+1 −1

Original line number	Diff line number	Diff line
		2017-11-15
		No newline at end of file
		2018-07-04
		No newline at end of file

configure

+96 −202

Original line number	Diff line number	Diff line
		#! /bin/sh
		# Guess values for system-dependent variables and create Makefiles.
		# Generated by GNU Autoconf 2.69 for gmap 2017-11-15.
		# Generated by GNU Autoconf 2.69 for gmap 2018-07-04.
		#
		# Report bugs to <Thomas Wu <twu@gene.com>>.
		#
		@@ -590,8 +590,8 @@ MAKEFLAGS=
		# Identity of this package.
		PACKAGE_NAME='gmap'
		PACKAGE_TARNAME='gmap'
		PACKAGE_VERSION='2017-11-15'
		PACKAGE_STRING='gmap 2017-11-15'
		PACKAGE_VERSION='2018-07-04'
		PACKAGE_STRING='gmap 2018-07-04'
		PACKAGE_BUGREPORT='Thomas Wu <twu@gene.com>'
		PACKAGE_URL=''

		@@ -660,6 +660,7 @@ SIMD_SSSE3_CFLAGS
		SIMD_SSE2_CFLAGS
		POPCNT_CFLAGS
		ALLOCA
		HAVE_INLINE
		PTHREAD_CFLAGS
		PTHREAD_LIBS
		PTHREAD_CC
		@@ -689,6 +690,8 @@ SED
		LIBTOOL
		PERL
		BINDIR
		MAKE_LIB_FALSE
		MAKE_LIB_TRUE
		MAINTAINER_FALSE
		MAINTAINER_TRUE
		FULLDIST_FALSE
		@@ -800,6 +803,7 @@ enable_silent_rules
		enable_maintainer_mode
		enable_fulldist
		enable_maintainer
		enable_lib
		enable_shared
		enable_static
		with_pic
		@@ -1369,7 +1373,7 @@ 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 gmap 2017-11-15 to adapt to many kinds of systems.
		\`configure' configures gmap 2018-07-04 to adapt to many kinds of systems.

		Usage: $0 [OPTION]... [VAR=VALUE]...

		@@ -1440,7 +1444,7 @@ fi

		if test -n "$ac_init_help"; then
		case $ac_init_help in
		short \| recursive ) echo "Configuration of gmap 2017-11-15:";;
		short \| recursive ) echo "Configuration of gmap 2018-07-04:";;
		esac
		cat <<\_ACEOF

		@@ -1460,6 +1464,9 @@ Optional Features:
		sometimes confusing) to the casual installer
		--enable-fulldist For use by program maintainer
		--enable-maintainer For use by program maintainer
		--enable-lib Build and install a GMAP library (Warning: will put
		headers into include subdirectory)
		(default=disable-lib)
		--enable-shared[=PKGS] build shared libraries [default=yes]
		--enable-static[=PKGS] build static libraries [default=yes]
		--enable-fast-install[=PKGS]
		@@ -1469,8 +1476,9 @@ Optional Features:
		(default=yes). Note: Use only if you have a parallel
		I/O file system, like Lustre
		--enable-pthreads Enable pthreads (default=yes)
		--enable-alloca Enable alloca (default=yes) for stack-based memory
		allocation.
		--enable-alloca Enable alloca (default=no) for stack-based memory
		allocation. Warning: Can cause GMAP to crash on long
		sequences.
		--enable-mmap Enable mmap (default=yes). Recommend that you do not
		disable this unless absolutely necessary.
		--enable-simd Enable simd commands in general if they compile and
		@@ -1577,7 +1585,7 @@ fi
		test -n "$ac_init_help" && exit $ac_status
		if $ac_init_version; then
		cat <<\_ACEOF
		gmap configure 2017-11-15
		gmap configure 2018-07-04
		generated by GNU Autoconf 2.69

		Copyright (C) 2012 Free Software Foundation, Inc.
		@@ -2183,7 +2191,7 @@ 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 gmap $as_me 2017-11-15, which was
		It was created by gmap $as_me 2018-07-04, which was
		generated by GNU Autoconf 2.69. Invocation command line was

		$ $0 $@
		@@ -2533,8 +2541,8 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu

		{ $as_echo "$as_me:${as_lineno-$LINENO}: checking package version" >&5
		$as_echo_n "checking package version... " >&6; }
		{ $as_echo "$as_me:${as_lineno-$LINENO}: result: 2017-11-15" >&5
		$as_echo "2017-11-15" >&6; }
		{ $as_echo "$as_me:${as_lineno-$LINENO}: result: 2018-07-04" >&5
		$as_echo "2018-07-04" >&6; }


		### Read defaults
		@@ -4401,7 +4409,7 @@ fi

		# Define the identity of the package.
		PACKAGE='gmap'
		VERSION='2017-11-15'
		VERSION='2018-07-04'


		cat >>confdefs.h <<_ACEOF
		@@ -4679,6 +4687,22 @@ else
		fi


		if test "x$enable_library" = xyes; then
		MAKE_LIB_TRUE=
		MAKE_LIB_FALSE='#'
		else
		MAKE_LIB_TRUE='#'
		MAKE_LIB_FALSE=
		fi

		# Check whether --enable-lib was given.
		if test "${enable_lib+set}" = set; then :
		enableval=$enable_lib; enable_library="yes"
		else
		enable_library="no"
		fi


		# For Perl scripts, because otherwise configure inserts
		# @bindir@ => "${exec_prefix}/bin";
		{ $as_echo "$as_me:${as_lineno-$LINENO}: checking bindir" >&5
		@@ -14502,6 +14526,55 @@ done


		# Checks for typedefs, structures, and compiler characteristics.
		{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for inline" >&5
		$as_echo_n "checking for inline... " >&6; }
		if ${ac_cv_c_inline+:} false; then :
		$as_echo_n "(cached) " >&6
		else
		ac_cv_c_inline=no
		for ac_kw in inline __inline__ __inline; do
		cat confdefs.h - <<_ACEOF >conftest.$ac_ext
		/* end confdefs.h. */
		#ifndef __cplusplus
		typedef int foo_t;
		static $ac_kw foo_t static_foo () {return 0; }
		$ac_kw foo_t foo () {return 0; }
		#endif

		_ACEOF
		if ac_fn_c_try_compile "$LINENO"; then :
		ac_cv_c_inline=$ac_kw
		fi
		rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
		test "$ac_cv_c_inline" != no && break
		done

		fi
		{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_inline" >&5
		$as_echo "$ac_cv_c_inline" >&6; }

		case $ac_cv_c_inline in
		inline \| yes) ;;
		*)
		case $ac_cv_c_inline in
		no) ac_val=;;
		*) ac_val=$ac_cv_c_inline;;
		esac
		cat >>confdefs.h <<_ACEOF
		#ifndef __cplusplus
		#define inline $ac_val
		#endif
		_ACEOF
		;;
		esac

		if test "$ac_cv_c_line" != no; then

		$as_echo "#define HAVE_INLINE 1" >>confdefs.h


		fi

		{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether byte ordering is bigendian" >&5
		$as_echo_n "checking whether byte ordering is bigendian... " >&6; }
		if ${ac_cv_c_bigendian+:} false; then :
		@@ -15258,194 +15331,8 @@ $as_echo "disabled" >&6; }
		;;

		x)
		{ $as_echo "$as_me:${as_lineno-$LINENO}: result: not specified so enabled by default" >&5
		$as_echo "not specified so enabled by default" >&6; }
		# The Ultrix 4.2 mips builtin alloca declared by alloca.h only works
		# for constant arguments. Useless!
		{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for working alloca.h" >&5
		$as_echo_n "checking for working alloca.h... " >&6; }
		if ${ac_cv_working_alloca_h+:} false; then :
		$as_echo_n "(cached) " >&6
		else
		cat confdefs.h - <<_ACEOF >conftest.$ac_ext
		/* end confdefs.h. */
		#include <alloca.h>
		int
		main ()
		{
		char p = (char ) alloca (2 * sizeof (int));
		if (p) return 0;
		;
		return 0;
		}
		_ACEOF
		if ac_fn_c_try_link "$LINENO"; then :
		ac_cv_working_alloca_h=yes
		else
		ac_cv_working_alloca_h=no
		fi
		rm -f core conftest.err conftest.$ac_objext \
		conftest$ac_exeext conftest.$ac_ext
		fi
		{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_working_alloca_h" >&5
		$as_echo "$ac_cv_working_alloca_h" >&6; }
		if test $ac_cv_working_alloca_h = yes; then

		$as_echo "#define HAVE_ALLOCA_H 1" >>confdefs.h

		fi

		{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for alloca" >&5
		$as_echo_n "checking for alloca... " >&6; }
		if ${ac_cv_func_alloca_works+:} false; then :
		$as_echo_n "(cached) " >&6
		else
		cat confdefs.h - <<_ACEOF >conftest.$ac_ext
		/* end confdefs.h. */
		#ifdef __GNUC__
		# define alloca __builtin_alloca
		#else
		# ifdef _MSC_VER
		# include <malloc.h>
		# define alloca _alloca
		# else
		# ifdef HAVE_ALLOCA_H
		# include <alloca.h>
		# else
		# ifdef _AIX
		#pragma alloca
		# else
		# ifndef alloca /* predefined by HP cc +Olibcalls */
		void *alloca (size_t);
		# endif
		# endif
		# endif
		# endif
		#endif

		int
		main ()
		{
		char p = (char ) alloca (1);
		if (p) return 0;
		;
		return 0;
		}
		_ACEOF
		if ac_fn_c_try_link "$LINENO"; then :
		ac_cv_func_alloca_works=yes
		else
		ac_cv_func_alloca_works=no
		fi
		rm -f core conftest.err conftest.$ac_objext \
		conftest$ac_exeext conftest.$ac_ext
		fi
		{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_func_alloca_works" >&5
		$as_echo "$ac_cv_func_alloca_works" >&6; }

		if test $ac_cv_func_alloca_works = yes; then

		$as_echo "#define HAVE_ALLOCA 1" >>confdefs.h

		else
		# The SVR3 libPW and SVR4 libucb both contain incompatible functions
		# that cause trouble. Some versions do not even contain alloca or
		# contain a buggy version. If you still want to use their alloca,
		# use ar to extract alloca.o from them instead of compiling alloca.c.

		ALLOCA=\${LIBOBJDIR}alloca.$ac_objext

		$as_echo "#define C_ALLOCA 1" >>confdefs.h


		{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether \`alloca.c' needs Cray hooks" >&5
		$as_echo_n "checking whether \`alloca.c' needs Cray hooks... " >&6; }
		if ${ac_cv_os_cray+:} false; then :
		$as_echo_n "(cached) " >&6
		else
		cat confdefs.h - <<_ACEOF >conftest.$ac_ext
		/* end confdefs.h. */
		#if defined CRAY && ! defined CRAY2
		webecray
		#else
		wenotbecray
		#endif

		_ACEOF
		if (eval "$ac_cpp conftest.$ac_ext") 2>&5 \|
		$EGREP "webecray" >/dev/null 2>&1; then :
		ac_cv_os_cray=yes
		else
		ac_cv_os_cray=no
		fi
		rm -f conftest*

		fi
		{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_os_cray" >&5
		$as_echo "$ac_cv_os_cray" >&6; }
		if test $ac_cv_os_cray = yes; then
		for ac_func in _getb67 GETB67 getb67; do
		as_ac_var=`$as_echo "ac_cv_func_$ac_func" \| $as_tr_sh`
		ac_fn_c_check_func "$LINENO" "$ac_func" "$as_ac_var"
		if eval test \"x\$"$as_ac_var"\" = x"yes"; then :

		cat >>confdefs.h <<_ACEOF
		#define CRAY_STACKSEG_END $ac_func
		_ACEOF

		break
		fi

		done
		fi

		{ $as_echo "$as_me:${as_lineno-$LINENO}: checking stack direction for C alloca" >&5
		$as_echo_n "checking stack direction for C alloca... " >&6; }
		if ${ac_cv_c_stack_direction+:} false; then :
		$as_echo_n "(cached) " >&6
		else
		if test "$cross_compiling" = yes; then :
		ac_cv_c_stack_direction=0
		else
		cat confdefs.h - <<_ACEOF >conftest.$ac_ext
		/* end confdefs.h. */
		$ac_includes_default
		int
		find_stack_direction (int *addr, int depth)
		{
		int dir, dummy = 0;
		if (! addr)
		addr = &dummy;
		*addr = addr < &dummy ? 1 : addr == &dummy ? 0 : -1;
		dir = depth ? find_stack_direction (addr, depth - 1) : 0;
		return dir + dummy;
		}

		int
		main (int argc, char **argv)
		{
		return find_stack_direction (0, argc + !argv + 20) < 0;
		}
		_ACEOF
		if ac_fn_c_try_run "$LINENO"; then :
		ac_cv_c_stack_direction=1
		else
		ac_cv_c_stack_direction=-1
		fi
		rm -f core .core core.conftest. gmon.out bb.out conftest$ac_exeext \
		conftest.$ac_objext conftest.beam conftest.$ac_ext
		fi

		fi
		{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_stack_direction" >&5
		$as_echo "$ac_cv_c_stack_direction" >&6; }
		cat >>confdefs.h <<_ACEOF
		#define STACK_DIRECTION $ac_cv_c_stack_direction
		_ACEOF


		fi

		{ $as_echo "$as_me:${as_lineno-$LINENO}: result: not specified so disabled by default" >&5
		$as_echo "not specified so disabled by default" >&6; }
		;;
		esac

		@@ -19400,6 +19287,8 @@ ac_config_files="$ac_config_files util/gvf_iit.pl"

		ac_config_files="$ac_config_files util/vcf_iit.pl"

		ac_config_files="$ac_config_files util/sam-exons.pl"

		ac_config_files="$ac_config_files tests/Makefile"

		ac_config_files="$ac_config_files tests/align.test"
		@@ -19556,6 +19445,10 @@ if test -z "${MAINTAINER_TRUE}" && test -z "${MAINTAINER_FALSE}"; then
		as_fn_error $? "conditional \"MAINTAINER\" was never defined.
		Usually this means the macro was only invoked conditionally." "$LINENO" 5
		fi
		if test -z "${MAKE_LIB_TRUE}" && test -z "${MAKE_LIB_FALSE}"; then
		as_fn_error $? "conditional \"MAKE_LIB\" was never defined.
		Usually this means the macro was only invoked conditionally." "$LINENO" 5
		fi

		if test -z "${MAKE_AVX512_TRUE}" && test -z "${MAKE_AVX512_FALSE}"; then
		as_fn_error $? "conditional \"MAKE_AVX512\" was never defined.
		@@ -19978,7 +19871,7 @@ cat >>$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 gmap $as_me 2017-11-15, which was
		This file was extended by gmap $as_me 2018-07-04, which was
		generated by GNU Autoconf 2.69. Invocation command line was

		CONFIG_FILES = $CONFIG_FILES
		@@ -20044,7 +19937,7 @@ _ACEOF
		cat >>$CONFIG_STATUS <<_ACEOF \|\| ac_write_fail=1
		ac_cs_config="`$as_echo "$ac_configure_args" \| sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
		ac_cs_version="\\
		gmap config.status 2017-11-15
		gmap config.status 2018-07-04
		configured by $0, generated by GNU Autoconf 2.69,
		with options \\"\$ac_cs_config\\"

		@@ -20483,6 +20376,7 @@ do
		"util/dbsnp_iit.pl") CONFIG_FILES="$CONFIG_FILES util/dbsnp_iit.pl" ;;
		"util/gvf_iit.pl") CONFIG_FILES="$CONFIG_FILES util/gvf_iit.pl" ;;
		"util/vcf_iit.pl") CONFIG_FILES="$CONFIG_FILES util/vcf_iit.pl" ;;
		"util/sam-exons.pl") CONFIG_FILES="$CONFIG_FILES util/sam-exons.pl" ;;
		"tests/Makefile") CONFIG_FILES="$CONFIG_FILES tests/Makefile" ;;
		"tests/align.test") CONFIG_FILES="$CONFIG_FILES tests/align.test" ;;
		"tests/coords1.test") CONFIG_FILES="$CONFIG_FILES tests/coords1.test" ;;