diff options
Diffstat (limited to 'sci-biology/samtools/files/samtools-1.3-ncurses.patch')
| -rw-r--r-- | sci-biology/samtools/files/samtools-1.3-ncurses.patch | 737 |
1 files changed, 0 insertions, 737 deletions
diff --git a/sci-biology/samtools/files/samtools-1.3-ncurses.patch b/sci-biology/samtools/files/samtools-1.3-ncurses.patch deleted file mode 100644 index baeb6701cd2f..000000000000 --- a/sci-biology/samtools/files/samtools-1.3-ncurses.patch +++ /dev/null @@ -1,737 +0,0 @@ -* Add modern AX_WITH_CURSES that prefers using pkg-config for detecting ncurses -* Change macro structure by moving AX_WITH_HTSLIB into its own file - ---- samtools-1.3/configure.ac -+++ samtools-1.3/configure.ac -@@ -28,6 +28,7 @@ - AC_PREREQ([2.63]) dnl This version introduced 4-argument AC_CHECK_HEADER - AC_CONFIG_SRCDIR([bamtk.c]) - AC_CONFIG_HEADERS([config.h]) -+AC_CONFIG_MACRO_DIR([m4]) - - dnl Copyright notice to be copied into the generated configure script - AC_COPYRIGHT([Portions copyright (C) 2015 Genome Research Ltd. ---- samtools-1.3/m4/ax_with_curses.m4 -+++ samtools-1.3/m4/ax_with_curses.m4 -@@ -0,0 +1,578 @@ -+# =========================================================================== -+# http://www.gnu.org/software/autoconf-archive/ax_with_curses.html -+# =========================================================================== -+# -+# SYNOPSIS -+# -+# AX_WITH_CURSES -+# -+# DESCRIPTION -+# -+# This macro checks whether a SysV or X/Open-compatible Curses library is -+# present, along with the associated header file. The NcursesW -+# (wide-character) library is searched for first, followed by Ncurses, -+# then the system-default plain Curses. The first library found is the -+# one returned. Finding libraries will first be attempted by using -+# pkg-config, and should the pkg-config files not be available, will -+# fallback to combinations of known flags itself. -+# -+# The following options are understood: --with-ncursesw, --with-ncurses, -+# --without-ncursesw, --without-ncurses. The "--with" options force the -+# macro to use that particular library, terminating with an error if not -+# found. The "--without" options simply skip the check for that library. -+# The effect on the search pattern is: -+# -+# (no options) - NcursesW, Ncurses, Curses -+# --with-ncurses --with-ncursesw - NcursesW only [*] -+# --without-ncurses --with-ncursesw - NcursesW only [*] -+# --with-ncursesw - NcursesW only [*] -+# --with-ncurses --without-ncursesw - Ncurses only [*] -+# --with-ncurses - NcursesW, Ncurses [**] -+# --without-ncurses --without-ncursesw - Curses only -+# --without-ncursesw - Ncurses, Curses -+# --without-ncurses - NcursesW, Curses -+# -+# [*] If the library is not found, abort the configure script. -+# -+# [**] If the second library (Ncurses) is not found, abort configure. -+# -+# The following preprocessor symbols may be defined by this macro if the -+# appropriate conditions are met: -+# -+# HAVE_CURSES - if any SysV or X/Open Curses library found -+# HAVE_CURSES_ENHANCED - if library supports X/Open Enhanced functions -+# HAVE_CURSES_COLOR - if library supports color (enhanced functions) -+# HAVE_CURSES_OBSOLETE - if library supports certain obsolete features -+# HAVE_NCURSESW - if NcursesW (wide char) library is to be used -+# HAVE_NCURSES - if the Ncurses library is to be used -+# -+# HAVE_CURSES_H - if <curses.h> is present and should be used -+# HAVE_NCURSESW_H - if <ncursesw.h> should be used -+# HAVE_NCURSES_H - if <ncurses.h> should be used -+# HAVE_NCURSESW_CURSES_H - if <ncursesw/curses.h> should be used -+# HAVE_NCURSES_CURSES_H - if <ncurses/curses.h> should be used -+# -+# (These preprocessor symbols are discussed later in this document.) -+# -+# The following output variables are defined by this macro; they are -+# precious and may be overridden on the ./configure command line: -+# -+# CURSES_LIB - library to add to xxx_LDADD -+# CURSES_CPPFLAGS - include paths to add to xxx_CPPFLAGS -+# -+# Neither the library listed in CURSES_LIB, nor the flags in -+# CURSES_CPPFLAGS are added to LIBS, respectively CPPFLAGS, by default. -+# You need to add both to the appropriate xxx_LDADD/xxx_CPPFLAGS line in -+# your Makefile.am. For example: -+# -+# prog_LDADD = @CURSES_LIB@ -+# prog_CPPFLAGS = @CURSES_CPPFLAGS@ -+# -+# If CURSES_LIB is set on the configure command line (such as by running -+# "./configure CURSES_LIB=-lmycurses"), then the only header searched for -+# is <curses.h>. If the user needs to specify an alternative path for a -+# library (such as for a non-standard NcurseW), the user should use the -+# LDFLAGS variable. -+# -+# The following shell variables may be defined by this macro: -+# -+# ax_cv_curses - set to "yes" if any Curses library found -+# ax_cv_curses_enhanced - set to "yes" if Enhanced functions present -+# ax_cv_curses_color - set to "yes" if color functions present -+# ax_cv_curses_obsolete - set to "yes" if obsolete features present -+# -+# ax_cv_ncursesw - set to "yes" if NcursesW library found -+# ax_cv_ncurses - set to "yes" if Ncurses library found -+# ax_cv_plaincurses - set to "yes" if plain Curses library found -+# ax_cv_curses_which - set to "ncursesw", "ncurses", "plaincurses" or "no" -+# -+# These variables can be used in your configure.ac to determine the level -+# of support you need from the Curses library. For example, if you must -+# have either Ncurses or NcursesW, you could include: -+# -+# AX_WITH_CURSES -+# if test "x$ax_cv_ncursesw" != xyes && test "x$ax_cv_ncurses" != xyes; then -+# AC_MSG_ERROR([requires either NcursesW or Ncurses library]) -+# fi -+# -+# If any Curses library will do (but one must be present and must support -+# color), you could use: -+# -+# AX_WITH_CURSES -+# if test "x$ax_cv_curses" != xyes || test "x$ax_cv_curses_color" != xyes; then -+# AC_MSG_ERROR([requires an X/Open-compatible Curses library with color]) -+# fi -+# -+# Certain preprocessor symbols and shell variables defined by this macro -+# can be used to determine various features of the Curses library. In -+# particular, HAVE_CURSES and ax_cv_curses are defined if the Curses -+# library found conforms to the traditional SysV and/or X/Open Base Curses -+# definition. Any working Curses library conforms to this level. -+# -+# HAVE_CURSES_ENHANCED and ax_cv_curses_enhanced are defined if the -+# library supports the X/Open Enhanced Curses definition. In particular, -+# the wide-character types attr_t, cchar_t and wint_t, the functions -+# wattr_set() and wget_wch() and the macros WA_NORMAL and _XOPEN_CURSES -+# are checked. The Ncurses library does NOT conform to this definition, -+# although NcursesW does. -+# -+# HAVE_CURSES_COLOR and ax_cv_curses_color are defined if the library -+# supports color functions and macros such as COLOR_PAIR, A_COLOR, -+# COLOR_WHITE, COLOR_RED and init_pair(). These are NOT part of the -+# X/Open Base Curses definition, but are part of the Enhanced set of -+# functions. The Ncurses library DOES support these functions, as does -+# NcursesW. -+# -+# HAVE_CURSES_OBSOLETE and ax_cv_curses_obsolete are defined if the -+# library supports certain features present in SysV and BSD Curses but not -+# defined in the X/Open definition. In particular, the functions -+# getattrs(), getcurx() and getmaxx() are checked. -+# -+# To use the HAVE_xxx_H preprocessor symbols, insert the following into -+# your system.h (or equivalent) header file: -+# -+# #if defined HAVE_NCURSESW_CURSES_H -+# # include <ncursesw/curses.h> -+# #elif defined HAVE_NCURSESW_H -+# # include <ncursesw.h> -+# #elif defined HAVE_NCURSES_CURSES_H -+# # include <ncurses/curses.h> -+# #elif defined HAVE_NCURSES_H -+# # include <ncurses.h> -+# #elif defined HAVE_CURSES_H -+# # include <curses.h> -+# #else -+# # error "SysV or X/Open-compatible Curses header file required" -+# #endif -+# -+# For previous users of this macro: you should not need to change anything -+# in your configure.ac or Makefile.am, as the previous (serial 10) -+# semantics are still valid. However, you should update your system.h (or -+# equivalent) header file to the fragment shown above. You are encouraged -+# also to make use of the extended functionality provided by this version -+# of AX_WITH_CURSES, as well as in the additional macros -+# AX_WITH_CURSES_PANEL, AX_WITH_CURSES_MENU and AX_WITH_CURSES_FORM. -+# -+# LICENSE -+# -+# Copyright (c) 2009 Mark Pulford <mark@kyne.com.au> -+# Copyright (c) 2009 Damian Pietras <daper@daper.net> -+# Copyright (c) 2012 Reuben Thomas <rrt@sc3d.org> -+# Copyright (c) 2011 John Zaitseff <J.Zaitseff@zap.org.au> -+# -+# 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 3 of the License, 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, the respective Autoconf Macro's copyright owner -+# gives unlimited permission to copy, distribute and modify the configure -+# scripts that are the output of Autoconf when processing the Macro. You -+# need not follow the terms of the GNU General Public License when using -+# or distributing such scripts, even though portions of the text of the -+# Macro appear in them. The GNU General Public License (GPL) does govern -+# all other use of the material that constitutes the Autoconf Macro. -+# -+# This special exception to the GPL applies to versions of the Autoconf -+# Macro released by the Autoconf Archive. When you make and distribute a -+# modified version of the Autoconf Macro, you may extend this special -+# exception to the GPL to apply to your modified version as well. -+ -+#serial 16 -+ -+# internal function to factorize common code that is used by both ncurses -+# and ncursesw -+AC_DEFUN([_FIND_CURSES_FLAGS], [ -+ AC_MSG_CHECKING([for $1 via pkg-config]) -+ -+ _PKG_CONFIG([_ax_cv_$1_lib], [libs], [$1]) -+ _PKG_CONFIG([_ax_cv_$1_cppflags], [cflags], [$1]) -+ -+ AS_IF([test "x$pkg_failed" = "xyes" || test "x$pkg_failed" = "xuntried"],[ -+ AC_MSG_RESULT([no]) -+ # No suitable .pc file found, have to find flags via fallback -+ AC_CACHE_CHECK([for $1 via fallback], [ax_cv_$1], [ -+ AS_ECHO() -+ pkg_cv__ax_cv_$1_lib="-l$1" -+ pkg_cv__ax_cv_$1_cppflags="$CURSES_CPPFLAGS" -+ LIBS="$ax_saved_LIBS $pkg_cv__ax_cv_$1_lib" -+ CPPFLAGS="$ax_saved_CPPFLAGS $pkg_cv__ax_cv_$1_cppflags" -+ -+ AC_MSG_CHECKING([for initscr() with $pkg_cv__ax_cv_$1_lib]) -+ AC_LINK_IFELSE([AC_LANG_CALL([], [initscr])], -+ [ -+ AC_MSG_RESULT([yes]) -+ AC_MSG_CHECKING([for nodelay() with $pkg_cv__ax_cv_$1_lib]) -+ AC_LINK_IFELSE([AC_LANG_CALL([], [nodelay])],[ -+ ax_cv_$1=yes -+ ],[ -+ AC_MSG_RESULT([no]) -+ m4_if( -+ [$1],[ncursesw],[pkg_cv__ax_cv_$1_lib="$pkg_cv__ax_cv_$1_lib -ltinfow"], -+ [$1],[ncurses],[pkg_cv__ax_cv_$1_lib="$pkg_cv__ax_cv_$1_lib -ltinfo"] -+ ) -+ LIBS="$ax_saved_LIBS $pkg_cv__ax_cv_$1_lib" -+ -+ AC_MSG_CHECKING([for nodelay() with $pkg_cv__ax_cv_$1_lib]) -+ AC_LINK_IFELSE([AC_LANG_CALL([], [nodelay])],[ -+ ax_cv_$1=yes -+ ],[ -+ ax_cv_$1=no -+ ]) -+ ]) -+ ],[ -+ ax_cv_$1=no -+ ]) -+ ]) -+ ],[ -+ AC_MSG_RESULT([yes]) -+ # Found .pc file, using its information -+ LIBS="$ax_saved_LIBS $pkg_cv__ax_cv_$1_lib" -+ CPPFLAGS="$ax_saved_CPPFLAGS $pkg_cv__ax_cv_$1_cppflags" -+ ax_cv_$1=yes -+ ]) -+]) -+ -+AU_ALIAS([MP_WITH_CURSES], [AX_WITH_CURSES]) -+AC_DEFUN([AX_WITH_CURSES], [ -+ AC_ARG_VAR([CURSES_LIB], [linker library for Curses, e.g. -lcurses]) -+ AC_ARG_VAR([CURSES_CPPFLAGS], [preprocessor flags for Curses, e.g. -I/usr/include/ncursesw]) -+ AC_ARG_WITH([ncurses], [AS_HELP_STRING([--with-ncurses], -+ [force the use of Ncurses or NcursesW])], -+ [], [with_ncurses=check]) -+ AC_ARG_WITH([ncursesw], [AS_HELP_STRING([--without-ncursesw], -+ [do not use NcursesW (wide character support)])], -+ [], [with_ncursesw=check]) -+ AC_REQUIRE([PKG_PROG_PKG_CONFIG]) -+ -+ ax_saved_LIBS=$LIBS -+ ax_saved_CPPFLAGS=$CPPFLAGS -+ -+ AS_IF([test "x$with_ncurses" = xyes || test "x$with_ncursesw" = xyes], -+ [ax_with_plaincurses=no], [ax_with_plaincurses=check]) -+ -+ ax_cv_curses_which=no -+ -+ # Test for NcursesW -+ AS_IF([test "x$CURSES_LIB" = x && test "x$with_ncursesw" != xno], [ -+ _FIND_CURSES_FLAGS([ncursesw]) -+ -+ AS_IF([test "x$ax_cv_ncursesw" = xno && test "x$with_ncursesw" = xyes], [ -+ AC_MSG_ERROR([--with-ncursesw specified but could not find NcursesW library]) -+ ]) -+ -+ AS_IF([test "x$ax_cv_ncursesw" = xyes], [ -+ ax_cv_curses=yes -+ ax_cv_curses_which=ncursesw -+ CURSES_LIB="$pkg_cv__ax_cv_ncursesw_lib" -+ CURSES_CPPFLAGS="$pkg_cv__ax_cv_ncursesw_cppflags" -+ AC_DEFINE([HAVE_NCURSESW], [1], [Define to 1 if the NcursesW library is present]) -+ AC_DEFINE([HAVE_CURSES], [1], [Define to 1 if a SysV or X/Open compatible Curses library is present]) -+ -+ AC_CACHE_CHECK([for working ncursesw/curses.h], [ax_cv_header_ncursesw_curses_h], [ -+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ -+ @%:@define _XOPEN_SOURCE_EXTENDED 1 -+ @%:@include <ncursesw/curses.h> -+ ]], [[ -+ chtype a = A_BOLD; -+ int b = KEY_LEFT; -+ chtype c = COLOR_PAIR(1) & A_COLOR; -+ attr_t d = WA_NORMAL; -+ cchar_t e; -+ wint_t f; -+ int g = getattrs(stdscr); -+ int h = getcurx(stdscr) + getmaxx(stdscr); -+ initscr(); -+ init_pair(1, COLOR_WHITE, COLOR_RED); -+ wattr_set(stdscr, d, 0, NULL); -+ wget_wch(stdscr, &f); -+ ]])], -+ [ax_cv_header_ncursesw_curses_h=yes], -+ [ax_cv_header_ncursesw_curses_h=no]) -+ ]) -+ AS_IF([test "x$ax_cv_header_ncursesw_curses_h" = xyes], [ -+ ax_cv_curses_enhanced=yes -+ ax_cv_curses_color=yes -+ ax_cv_curses_obsolete=yes -+ AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions]) -+ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) -+ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) -+ AC_DEFINE([HAVE_NCURSESW_CURSES_H], [1], [Define to 1 if <ncursesw/curses.h> is present]) -+ ]) -+ -+ AC_CACHE_CHECK([for working ncursesw.h], [ax_cv_header_ncursesw_h], [ -+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ -+ @%:@define _XOPEN_SOURCE_EXTENDED 1 -+ @%:@include <ncursesw.h> -+ ]], [[ -+ chtype a = A_BOLD; -+ int b = KEY_LEFT; -+ chtype c = COLOR_PAIR(1) & A_COLOR; -+ attr_t d = WA_NORMAL; -+ cchar_t e; -+ wint_t f; -+ int g = getattrs(stdscr); -+ int h = getcurx(stdscr) + getmaxx(stdscr); -+ initscr(); -+ init_pair(1, COLOR_WHITE, COLOR_RED); -+ wattr_set(stdscr, d, 0, NULL); -+ wget_wch(stdscr, &f); -+ ]])], -+ [ax_cv_header_ncursesw_h=yes], -+ [ax_cv_header_ncursesw_h=no]) -+ ]) -+ AS_IF([test "x$ax_cv_header_ncursesw_h" = xyes], [ -+ ax_cv_curses_enhanced=yes -+ ax_cv_curses_color=yes -+ ax_cv_curses_obsolete=yes -+ AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions]) -+ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) -+ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) -+ AC_DEFINE([HAVE_NCURSESW_H], [1], [Define to 1 if <ncursesw.h> is present]) -+ ]) -+ -+ AC_CACHE_CHECK([for working ncurses.h], [ax_cv_header_ncurses_h_with_ncursesw], [ -+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ -+ @%:@define _XOPEN_SOURCE_EXTENDED 1 -+ @%:@include <ncurses.h> -+ ]], [[ -+ chtype a = A_BOLD; -+ int b = KEY_LEFT; -+ chtype c = COLOR_PAIR(1) & A_COLOR; -+ attr_t d = WA_NORMAL; -+ cchar_t e; -+ wint_t f; -+ int g = getattrs(stdscr); -+ int h = getcurx(stdscr) + getmaxx(stdscr); -+ initscr(); -+ init_pair(1, COLOR_WHITE, COLOR_RED); -+ wattr_set(stdscr, d, 0, NULL); -+ wget_wch(stdscr, &f); -+ ]])], -+ [ax_cv_header_ncurses_h_with_ncursesw=yes], -+ [ax_cv_header_ncurses_h_with_ncursesw=no]) -+ ]) -+ AS_IF([test "x$ax_cv_header_ncurses_h_with_ncursesw" = xyes], [ -+ ax_cv_curses_enhanced=yes -+ ax_cv_curses_color=yes -+ ax_cv_curses_obsolete=yes -+ AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions]) -+ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) -+ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) -+ AC_DEFINE([HAVE_NCURSES_H], [1], [Define to 1 if <ncurses.h> is present]) -+ ]) -+ -+ AS_IF([test "x$ax_cv_header_ncursesw_curses_h" = xno && test "x$ax_cv_header_ncursesw_h" = xno && test "x$ax_cv_header_ncurses_h_with_ncursesw" = xno], [ -+ AC_MSG_WARN([could not find a working ncursesw/curses.h, ncursesw.h or ncurses.h]) -+ ]) -+ ]) -+ ]) -+ unset pkg_cv__ax_cv_ncursesw_lib -+ unset pkg_cv__ax_cv_ncursesw_cppflags -+ -+ # Test for Ncurses -+ AS_IF([test "x$CURSES_LIB" = x && test "x$with_ncurses" != xno && test "x$ax_cv_curses_which" = xno], [ -+ _FIND_CURSES_FLAGS([ncurses]) -+ -+ AS_IF([test "x$ax_cv_ncurses" = xno && test "x$with_ncurses" = xyes], [ -+ AC_MSG_ERROR([--with-ncurses specified but could not find Ncurses library]) -+ ]) -+ -+ AS_IF([test "x$ax_cv_ncurses" = xyes], [ -+ ax_cv_curses=yes -+ ax_cv_curses_which=ncurses -+ CURSES_LIB="$pkg_cv__ax_cv_ncurses_lib" -+ CURSES_CPPFLAGS="$pkg_cv__ax_cv_ncurses_cppflags" -+ AC_DEFINE([HAVE_NCURSES], [1], [Define to 1 if the Ncurses library is present]) -+ AC_DEFINE([HAVE_CURSES], [1], [Define to 1 if a SysV or X/Open compatible Curses library is present]) -+ -+ AC_CACHE_CHECK([for working ncurses/curses.h], [ax_cv_header_ncurses_curses_h], [ -+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ -+ @%:@include <ncurses/curses.h> -+ ]], [[ -+ chtype a = A_BOLD; -+ int b = KEY_LEFT; -+ chtype c = COLOR_PAIR(1) & A_COLOR; -+ int g = getattrs(stdscr); -+ int h = getcurx(stdscr) + getmaxx(stdscr); -+ initscr(); -+ init_pair(1, COLOR_WHITE, COLOR_RED); -+ ]])], -+ [ax_cv_header_ncurses_curses_h=yes], -+ [ax_cv_header_ncurses_curses_h=no]) -+ ]) -+ AS_IF([test "x$ax_cv_header_ncurses_curses_h" = xyes], [ -+ ax_cv_curses_color=yes -+ ax_cv_curses_obsolete=yes -+ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) -+ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) -+ AC_DEFINE([HAVE_NCURSES_CURSES_H], [1], [Define to 1 if <ncurses/curses.h> is present]) -+ ]) -+ -+ AC_CACHE_CHECK([for working ncurses.h], [ax_cv_header_ncurses_h], [ -+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ -+ @%:@include <ncurses.h> -+ ]], [[ -+ chtype a = A_BOLD; -+ int b = KEY_LEFT; -+ chtype c = COLOR_PAIR(1) & A_COLOR; -+ int g = getattrs(stdscr); -+ int h = getcurx(stdscr) + getmaxx(stdscr); -+ initscr(); -+ init_pair(1, COLOR_WHITE, COLOR_RED); -+ ]])], -+ [ax_cv_header_ncurses_h=yes], -+ [ax_cv_header_ncurses_h=no]) -+ ]) -+ AS_IF([test "x$ax_cv_header_ncurses_h" = xyes], [ -+ ax_cv_curses_color=yes -+ ax_cv_curses_obsolete=yes -+ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) -+ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) -+ AC_DEFINE([HAVE_NCURSES_H], [1], [Define to 1 if <ncurses.h> is present]) -+ ]) -+ -+ AS_IF([test "x$ax_cv_header_ncurses_curses_h" = xno && test "x$ax_cv_header_ncurses_h" = xno], [ -+ AC_MSG_WARN([could not find a working ncurses/curses.h or ncurses.h]) -+ ]) -+ ]) -+ ]) -+ unset pkg_cv__ax_cv_ncurses_lib -+ unset pkg_cv__ax_cv_ncurses_cppflags -+ -+ # Test for plain Curses (or if CURSES_LIB was set by user) -+ AS_IF([test "x$with_plaincurses" != xno && test "x$ax_cv_curses_which" = xno], [ -+ AS_IF([test "x$CURSES_LIB" != x], [ -+ LIBS="$ax_saved_LIBS $CURSES_LIB" -+ ], [ -+ LIBS="$ax_saved_LIBS -lcurses" -+ ]) -+ -+ AC_CACHE_CHECK([for Curses library], [ax_cv_plaincurses], [ -+ AC_LINK_IFELSE([AC_LANG_CALL([], [initscr])], -+ [ax_cv_plaincurses=yes], [ax_cv_plaincurses=no]) -+ ]) -+ -+ AS_IF([test "x$ax_cv_plaincurses" = xyes], [ -+ ax_cv_curses=yes -+ ax_cv_curses_which=plaincurses -+ AS_IF([test "x$CURSES_LIB" = x], [ -+ CURSES_LIB="-lcurses" -+ ]) -+ AC_DEFINE([HAVE_CURSES], [1], [Define to 1 if a SysV or X/Open compatible Curses library is present]) -+ -+ # Check for base conformance (and header file) -+ -+ AC_CACHE_CHECK([for working curses.h], [ax_cv_header_curses_h], [ -+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ -+ @%:@include <curses.h> -+ ]], [[ -+ chtype a = A_BOLD; -+ int b = KEY_LEFT; -+ initscr(); -+ ]])], -+ [ax_cv_header_curses_h=yes], -+ [ax_cv_header_curses_h=no]) -+ ]) -+ AS_IF([test "x$ax_cv_header_curses_h" = xyes], [ -+ AC_DEFINE([HAVE_CURSES_H], [1], [Define to 1 if <curses.h> is present]) -+ -+ # Check for X/Open Enhanced conformance -+ -+ AC_CACHE_CHECK([for X/Open Enhanced Curses conformance], [ax_cv_plaincurses_enhanced], [ -+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ -+ @%:@define _XOPEN_SOURCE_EXTENDED 1 -+ @%:@include <curses.h> -+ @%:@ifndef _XOPEN_CURSES -+ @%:@error "this Curses library is not enhanced" -+ "this Curses library is not enhanced" -+ @%:@endif -+ ]], [[ -+ chtype a = A_BOLD; -+ int b = KEY_LEFT; -+ chtype c = COLOR_PAIR(1) & A_COLOR; -+ attr_t d = WA_NORMAL; -+ cchar_t e; -+ wint_t f; -+ initscr(); -+ init_pair(1, COLOR_WHITE, COLOR_RED); -+ wattr_set(stdscr, d, 0, NULL); -+ wget_wch(stdscr, &f); -+ ]])], -+ [ax_cv_plaincurses_enhanced=yes], -+ [ax_cv_plaincurses_enhanced=no]) -+ ]) -+ AS_IF([test "x$ax_cv_plaincurses_enhanced" = xyes], [ -+ ax_cv_curses_enhanced=yes -+ ax_cv_curses_color=yes -+ AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions]) -+ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) -+ ]) -+ -+ # Check for color functions -+ -+ AC_CACHE_CHECK([for Curses color functions], [ax_cv_plaincurses_color], [ -+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ -+ @%:@define _XOPEN_SOURCE_EXTENDED 1 -+ @%:@include <curses.h> -+ ]], [[ -+ chtype a = A_BOLD; -+ int b = KEY_LEFT; -+ chtype c = COLOR_PAIR(1) & A_COLOR; -+ initscr(); -+ init_pair(1, COLOR_WHITE, COLOR_RED); -+ ]])], -+ [ax_cv_plaincurses_color=yes], -+ [ax_cv_plaincurses_color=no]) -+ ]) -+ AS_IF([test "x$ax_cv_plaincurses_color" = xyes], [ -+ ax_cv_curses_color=yes -+ AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) -+ ]) -+ -+ # Check for obsolete functions -+ -+ AC_CACHE_CHECK([for obsolete Curses functions], [ax_cv_plaincurses_obsolete], [ -+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[ -+ @%:@include <curses.h> -+ ]], [[ -+ chtype a = A_BOLD; -+ int b = KEY_LEFT; -+ int g = getattrs(stdscr); -+ int h = getcurx(stdscr) + getmaxx(stdscr); -+ initscr(); -+ ]])], -+ [ax_cv_plaincurses_obsolete=yes], -+ [ax_cv_plaincurses_obsolete=no]) -+ ]) -+ AS_IF([test "x$ax_cv_plaincurses_obsolete" = xyes], [ -+ ax_cv_curses_obsolete=yes -+ AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) -+ ]) -+ ]) -+ -+ AS_IF([test "x$ax_cv_header_curses_h" = xno], [ -+ AC_MSG_WARN([could not find a working curses.h]) -+ ]) -+ ]) -+ ]) -+ -+ AS_IF([test "x$ax_cv_curses" != xyes], [ax_cv_curses=no]) -+ AS_IF([test "x$ax_cv_curses_enhanced" != xyes], [ax_cv_curses_enhanced=no]) -+ AS_IF([test "x$ax_cv_curses_color" != xyes], [ax_cv_curses_color=no]) -+ AS_IF([test "x$ax_cv_curses_obsolete" != xyes], [ax_cv_curses_obsolete=no]) -+ -+ LIBS=$ax_saved_LIBS -+ CPPFLAGS=$ax_saved_CPPFLAGS -+ -+ unset ax_saved_LIBS -+ unset ax_saved_CPPFLAGS -+])dnl ---- samtools-1.3/m4/ax_with_htslib.m4 -+++ samtools-1.3/m4/ax_with_htslib.m4 -@@ -0,0 +1,140 @@ -+# =========================================================================== -+# http://www.gnu.org/software/autoconf-archive/ax_with_htslib.html -+# =========================================================================== -+# -+# SYNOPSIS -+# -+# AX_WITH_HTSLIB -+# -+# DESCRIPTION -+# -+# This macro checks whether HTSlib <http://www.htslib.org/> is installed -+# or nearby, and adds a --with-htslib=DIR option to the configure script -+# for specifying the location. It locates either an installation prefix -+# (with 'include' and 'lib' subdirectories) or an HTSlib source tree, as -+# HTSlib is fast-moving and users may wish to use an in-development tree. -+# -+# Different checks occur depending on the --with-htslib argument given: -+# -+# With --with-htslib=DIR, checks whether DIR is a source tree or contains -+# a working installation. -+# By default, searches for a source tree (with a name matching htslib*) -+# within or alongside $srcdir. Produces AC_MSG_ERROR if there are -+# several equally-likely candidates. If there are none, checks for -+# a working default installation. -+# With --with-htslib=system, checks for a working default installation. -+# -+# If a source tree is found or specified, it is added to AC_CONFIG_SUBDIRS -+# (which unfortunately may cause a "you should use literals" warning when -+# autoconf is run). -+# -+# The following output variables are set by this macro: -+# -+# HTSDIR Directory containing HTSlib source tree -+# HTSLIB_CPPFLAGS Preprocessor flags for compiling with HTSlib -+# HTSLIB_LDFLAGS Linker flags for linking with HTSlib -+# -+# The following shell variables may be defined: -+# -+# ax_cv_htslib Set to "yes" if HTSlib was found -+# ax_cv_htslib_which Set to "source", "install", or "none" -+# -+# LICENSE -+# -+# Copyright (C) 2015 Genome Research Ltd -+# -+# Copying and distribution of this file, with or without modification, are -+# permitted in any medium without royalty provided the copyright notice -+# and this notice are preserved. This file is offered as-is, without any -+# warranty. -+ -+#serial 1 -+ -+AC_DEFUN([AX_WITH_HTSLIB], -+[AC_ARG_WITH([htslib], -+ [AS_HELP_STRING([--with-htslib=DIR], -+ [use the HTSlib source tree or installation in DIR]) -+dnl Not indented, to avoid extra whitespace outwith AS_HELP_STRING() -+AS_HELP_STRING([--with-htslib=system], -+ [use only a system HTSlib installation])], -+ [], [with_htslib=search]) -+ -+case $with_htslib in -+yes|search) -+ AC_MSG_CHECKING([location of HTSlib source tree]) -+ case $srcdir in -+ .) srcp= ;; -+ *) srcp=$srcdir/ ;; -+ esac -+ found= -+ for dir in ${srcp}htslib* -- ${srcp}../htslib -- ${srcp}../htslib* -+ do -+ if test "$dir" = "--"; then -+ test -n "$found" && break -+ elif test -f "$dir/hts.c" && test -f "$dir/htslib/hts.h"; then -+ found="${found}1" -+ HTSDIR=$dir -+ fi -+ done -+ if test -z "$found"; then -+ AC_MSG_RESULT([none found]) -+ ax_cv_htslib_which=system -+ elif test "$found" = 1; then -+ AC_MSG_RESULT([$HTSDIR]) -+ ax_cv_htslib_which=source -+ else -+ AC_MSG_RESULT([several directories found]) -+ AC_MSG_ERROR([use --with-htslib=DIR to select which HTSlib to use]) -+ fi -+ ;; -+no) ax_cv_htslib_which=none ;; -+system) ax_cv_htslib_which=system ;; -+*) -+ HTSDIR=$with_htslib -+ if test -f "$HTSDIR/hts.c" && test -f "$HTSDIR/htslib/hts.h"; then -+ ax_cv_htslib_which=source -+ else -+ ax_cv_htslib_which=install -+ fi -+ ;; -+esac -+ -+case $ax_cv_htslib_which in -+source) -+ ax_cv_htslib=yes -+ HTSLIB_CPPFLAGS="-I$HTSDIR" -+ HTSLIB_LDFLAGS="-L$HTSDIR" -+ # We can't use a literal, because $HTSDIR is user-provided and variable -+ AC_CONFIG_SUBDIRS($HTSDIR) -+ ;; -+system) -+ AC_CHECK_HEADER([htslib/sam.h], -+ [AC_CHECK_LIB(hts, hts_version, [ax_cv_htslib=yes], [ax_cv_htslib=no])], -+ [ax_cv_htslib=no], [;]) -+ ax_cv_htslib_which=install -+ HTSDIR= -+ HTSLIB_CPPFLAGS= -+ HTSLIB_LDFLAGS= -+ ;; -+install) -+ ax_saved_CPPFLAGS=$CPPFLAGS -+ ax_saved_LDFLAGS=$LDFLAGS -+ HTSLIB_CPPFLAGS="-I$HTSDIR/include" -+ HTSLIB_LDFLAGS="-L$HTSDIR/lib" -+ CPPFLAGS="$CPPFLAGS $HTSLIB_CPPFLAGS" -+ LDFLAGS="$LDFLAGS $HTSLIB_LDFLAGS" -+ AC_CHECK_HEADER([htslib/sam.h], -+ [AC_CHECK_LIB(hts, hts_version, [ax_cv_htslib=yes], [ax_cv_htslib=no])], -+ [ax_cv_htslib=no], [;]) -+ HTSDIR= -+ CPPFLAGS=$ax_saved_CPPFLAGS -+ LDFLAGS=$ax_saved_LDFLAGS -+ ;; -+none) -+ ax_cv_htslib=no -+ ;; -+esac -+ -+AC_SUBST([HTSDIR]) -+AC_SUBST([HTSLIB_CPPFLAGS]) -+AC_SUBST([HTSLIB_LDFLAGS])]) |